changeset 0:b2253cf7db76 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
author recetox
date Fri, 16 May 2025 08:02:01 +0000
parents
children
files ipapy2_MS1_annotation.py ipapy2_MS2_annotation.py ipapy2_clustering.py ipapy2_compute_all_adducts.py ipapy2_compute_bio.py ipapy2_gibbs_sampler.py ipapy2_gibbs_sampler.xml ipapy2_gibbs_sampler_add.py ipapy2_map_isotope_patterns.py macros.xml test-data/MS1_DB.csv test-data/MS1_annotations.csv test-data/MS2_DB.csv test-data/MS2_annotations.csv test-data/MS2_fragmentation_data.csv test-data/MS2_fragmentation_data.tsv test-data/adducts.csv test-data/all_adducts.csv test-data/clean_annotations.csv test-data/clustered_MS1_intensities.csv test-data/compute_bio_db.csv test-data/compute_bio_output.csv test-data/gibbs_sample_add_annotations.csv test-data/gibbs_sample_annotations.csv test-data/mapped_isotope_patterns.csv test-data/mapped_isotope_patterns.parquet test-data/unclustered_MS1_intensities.csv utils.py
diffstat 28 files changed, 2158 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_MS1_annotation.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,73 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, MSArgumentParser
+
+
+def main(
+    input_dataset_database,
+    input_dataset_adduct,
+    ppm,
+    ratiosd,
+    ppmunk,
+    ratiounk,
+    ppmthr,
+    pRTNone,
+    pRTout,
+    output_dataset,
+    ncores,
+):
+    write_func, file_path = output_dataset
+
+    annotations = ipa.MS1annotation(
+        input_dataset_database,
+        input_dataset_adduct,
+        ppm=ppm,
+        ratiosd=ratiosd,
+        ppmunk=ppmunk,
+        ratiounk=ratiounk,
+        ppmthr=ppmthr,
+        pRTNone=pRTNone,
+        pRTout=pRTout,
+        ncores=ncores,
+    )
+    annotations_flat = flattern_annotations(annotations)
+    write_func(annotations_flat, file_path)
+
+
+if __name__ == "__main__":
+    parser = MSArgumentParser("""
+    Annotation of the dataset based on the MS1 information. Prior probabilities
+        are based on mass only, while post probabilities are based on mass, RT,
+        previous knowledge and isotope patterns.
+    """)
+    parser.add_argument(
+        "--input_dataset_database",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "A dataset containing the MS1 data. Ideally obtained from"
+            " map_isotope_patterns"
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_adducts",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing information on all possible adducts.",
+    )
+
+    args = parser.parse_args()
+    main(
+        args.input_dataset_database,
+        args.input_dataset_adducts,
+        args.ppm,
+        args.ratiosd,
+        args.ppmunk,
+        args.ratiounk,
+        args.ppmthr,
+        args.pRTNone,
+        args.pRTout,
+        args.output_dataset,
+        args.ncores,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_MS2_annotation.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,136 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, MSArgumentParser
+
+
+def main(
+    input_dataset_mapped_isotope_patterns,
+    input_dataset_MS2,
+    input_dataset_adducts,
+    input_dataset_MS2_DB,
+    ppm,
+    ratiosd,
+    ppmunk,
+    ratiounk,
+    ppmthr,
+    pRTNone,
+    pRTout,
+    mzdCS,
+    ppmCS,
+    CSunk,
+    evfilt,
+    output_dataset,
+    ncores,
+):
+    annotations = ipa.MSMSannotation(
+        input_dataset_mapped_isotope_patterns,
+        input_dataset_MS2,
+        input_dataset_adducts,
+        input_dataset_MS2_DB,
+        ppm=ppm,
+        ratiosd=ratiosd,
+        ppmunk=ppmunk,
+        ratiounk=ratiounk,
+        ppmthr=ppmthr,
+        pRTNone=pRTNone,
+        pRTout=pRTout,
+        mzdCS=mzdCS,
+        ppmCS=ppmCS,
+        CSunk=CSunk,
+        evfilt=evfilt,
+        ncores=ncores,
+    )
+    annotations_flat = flattern_annotations(annotations)
+    write_func, file_path = output_dataset
+    write_func(annotations_flat, file_path)
+
+
+if __name__ == "__main__":
+    parser = MSArgumentParser(
+        """Annotation of the dataset base on the MS1 and MS2 information. Prior
+    probabilities are based on mass only, while post probabilities are based
+    on mass, RT, previous knowledge and isotope patterns."""
+    )
+    parser.add_argument(
+        "--input_dataset_mapped_isotope_patterns",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "A dataset containing the MS1 data. Ideally obtained from"
+            " map_isotope_patterns"
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_MS2",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing the MS2 fragmentation data",
+    )
+    parser.add_argument(
+        "--input_dataset_adducts",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "A dataset containing the information on all the possible adducts given the"
+            " database. Ideally obtained from compute_all_adducts"
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_MS2_DB",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing the MS2 database",
+    )
+    parser.add_argument(
+        "--mzdCS",
+        type=int,
+        default=0,
+        help="""maximum mz difference allowed when computing cosine similarity
+           scores. If one wants to use this parameter instead of ppmCS, this
+           must be set to 0. Default 0.""",
+    )
+    parser.add_argument(
+        "--ppmCS",
+        type=int,
+        default=10,
+        help="""maximum ppm allowed when computing cosine similarity scores.
+           If one wants to use this parameter instead of mzdCS, this must be
+           set to 0. Default 10.""",
+    )
+    parser.add_argument(
+        "--CSunk",
+        type=float,
+        default=0.7,
+        help="""cosine similarity score associated with the 'unknown' annotation.
+            Default 0.7""",
+    )
+    parser.add_argument(
+        "--evfilt",
+        type=bool,
+        default=False,
+        help="""Default value False. If true, only spectrum acquired with the same
+            collision energy are considered.""",
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset_mapped_isotope_patterns,
+        args.input_dataset_MS2,
+        args.input_dataset_adducts,
+        args.input_dataset_MS2_DB,
+        args.ppm,
+        args.ratiosd,
+        args.ppmunk,
+        args.ratiounk,
+        args.ppmthr,
+        args.pRTNone,
+        args.pRTout,
+        args.mzdCS,
+        args.ppmCS,
+        args.CSunk,
+        args.evfilt,
+        args.output_dataset,
+        args.ncores,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_clustering.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,50 @@
+from ipaPy2 import ipa
+from utils import CustomArgumentParser
+
+
+def main(input_dataset, Cthr, RTwin, Intmode, output_dataset):
+    write_func, file_path = output_dataset
+    clustered_df = ipa.clusterFeatures(
+        input_dataset, Cthr=Cthr, RTwin=RTwin, Intmode=Intmode
+    )
+    write_func(clustered_df, file_path)
+
+
+if __name__ == "__main__":
+    parser = CustomArgumentParser(
+        description=" Clustering MS1 features based on correlation across samples."
+    )
+    parser.add_argument(
+        "--input_dataset",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="The unclustered MS1 intensities file path.",
+    )
+
+    parser.add_argument(
+        "--Cthr",
+        type=float,
+        default=0.8,
+        help="Minimum correlation allowed in each cluster. Default value 0.8.",
+    )
+
+    parser.add_argument(
+        "--RTwin",
+        type=float,
+        default=1,
+        help=(
+            "Maximum difference in RT time between features in the same cluster."
+            " Default value 1."
+        ),
+    )
+
+    parser.add_argument(
+        "--Intmode",
+        type=str,
+        default="max",
+        choices=["max", "ave"],
+        help="intensity mode. Default 'max' or 'ave'.",
+    )
+    args = parser.parse_args()
+    main(args.input_dataset, args.Cthr, args.RTwin, args.Intmode, args.output_dataset)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_compute_all_adducts.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,54 @@
+from ipaPy2 import ipa
+from utils import CustomArgumentParser
+
+
+def main(
+    input_dataset_adducts, input_dataset_database, ionisation, output_dataset, ncores
+):
+    write_func, file_path = output_dataset
+    adducts_df = ipa.compute_all_adducts(
+        input_dataset_adducts, input_dataset_database, ionisation, ncores
+    )
+
+    write_func(adducts_df, file_path)
+
+
+if __name__ == "__main__":
+    parser = CustomArgumentParser(
+        description=" Clustering MS1 features based on correlation across samples."
+    )
+    parser.add_argument(
+        "--input_dataset_adducts",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing information on all possible adducts.",
+    )
+    parser.add_argument(
+        "--input_dataset_database",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="The MS1 database.",
+    )
+    parser.add_argument(
+        "--ionisation",
+        type=int,
+        default=1,
+        choices=[1, -1],
+        help="Default value 1. positive = 1, negative = -1",
+    )
+    parser.add_argument(
+        "--ncores",
+        type=int,
+        default=1,
+        help="Number of cores to use for parallel processing.",
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset_adducts,
+        args.input_dataset_database,
+        args.ionisation,
+        args.output_dataset,
+        args.ncores,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_compute_bio.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,87 @@
+from ipaPy2 import ipa
+from utils import CustomArgumentParser, group_by_peak_id
+
+
+def main(
+    input_dataset_database,
+    input_dataset_annotations,
+    biochemical_mode,
+    connection_list,
+    output_dataset,
+    ncores,
+):
+    """
+    Compute matrix of biochemical connections. Either based on a list of
+    possible connections in the form of a list of formulas or based on the
+    reactions present in the database.
+    """
+
+    if input_dataset_annotations is not None:
+        annotations = group_by_peak_id(input_dataset_annotations)
+    else:
+        annotations = None
+
+    if biochemical_mode == "connections" and connection_list:
+        connections = connection_list.split(",")
+    else:
+        connections = []
+
+    Bio = ipa.Compute_Bio(
+        input_dataset_database,
+        annotations=annotations,
+        mode=biochemical_mode,
+        connections=connections,
+        ncores=ncores,
+    )
+    write_func, file_path = output_dataset
+    write_func(Bio, file_path)
+
+
+if __name__ == "__main__":
+    parser = CustomArgumentParser(
+        description=""" Compute matrix of biochemical connections. Either based on a list of
+    possible connections in the form of a list of formulas or based on the
+    reactions present in the database."""
+    )
+    parser.add_argument(
+        "--input_dataset_database",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "a datset containing the database against which the annotationis performed."
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_annotations",
+        nargs=2,
+        action="load_data",
+        help="a datset containing the annotations of the features.",
+    )
+    parser.add_argument(
+        "--biochemical_mode",
+        type=str,
+        required=True,
+        help="""either 'reactions' (connections are computed based on the reactions
+          present in the database) or 'connections' (connections are computed
+          based on the list of connections provided). Default 'reactions'. """,
+    )
+    parser.add_argument(
+        "--connection_list", type=str, help="list of connections"
+    )
+    parser.add_argument(
+        "--ncores",
+        type=int,
+        default=None,
+        help="number of cores to use for the computation.",
+    )
+    args = parser.parse_args()
+
+    main(
+        args.input_dataset_database,
+        args.input_dataset_annotations,
+        args.biochemical_mode,
+        args.connection_list,
+        args.output_dataset,
+        args.ncores,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_gibbs_sampler.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,133 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, GibbsArgumentParser, group_by_peak_id
+
+
+def main(
+    input_dataset_mapped_isotope_patterns,
+    input_dataset_annotations,
+    integrating_mode,
+    input_dataset_bio,
+    noits,
+    burn,
+    delta_bio,
+    delta_add,
+    all_out,
+    zs,
+    zs_out,
+    output_dataset,
+):
+    annotations_df = input_dataset_annotations
+    annotations_df["post"] = annotations_df["post"].replace("", 0)
+    annotations_df = annotations_df.replace("", None)
+    annotations = group_by_peak_id(annotations_df)
+
+    if not zs:
+        zs = None
+
+    if integrating_mode == "adducts":
+        zs = ipa.Gibbs_sampler_add(
+            input_dataset_mapped_isotope_patterns,
+            annotations,
+            noits=noits,
+            burn=burn,
+            delta_add=delta_add,
+            all_out=all_out,
+            zs=zs,
+        )
+    else:
+        if args.integrating_mode == "biochemical":
+            zs = ipa.Gibbs_sampler_bio(
+                input_dataset_mapped_isotope_patterns,
+                annotations,
+                Bio=input_dataset_bio,
+                noits=noits,
+                burn=burn,
+                delta_bio=delta_bio,
+                all_out=all_out,
+                zs=zs,
+            )
+        else:
+            zs = ipa.Gibbs_sampler_bio_add(
+                input_dataset_mapped_isotope_patterns,
+                annotations,
+                Bio=input_dataset_bio,
+                noits=noits,
+                burn=burn,
+                delta_bio=delta_bio,
+                delta_add=delta_add,
+                all_out=all_out,
+                zs=zs,
+            )
+
+    annotations_flat = flattern_annotations(annotations)
+    write_func, file_path = output_dataset
+    write_func(annotations_flat, file_path)
+
+    if args.all_out:
+        write_func, file_path = zs_out
+        write_func(zs, file_path)
+
+
+if __name__ == "__main__":
+    parser = GibbsArgumentParser(
+        description="""Gibbs sampler considering both biochemical and adducts connections. The
+    function computes the posterior probabilities of the annotations
+    considering the possible biochemical connections reported in Bio and the
+    possible adducts connection.""",
+    )
+    parser.add_argument(
+        "--input_dataset_mapped_isotope_patterns",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="a dataframe containing the measured intensities across several samples.",
+    )
+    parser.add_argument(
+        "--input_dataset_annotations",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="a datset containing the annotations of the features.",
+    )
+    parser.add_argument(
+        "--integrating_mode",
+        type=str,
+        required=True,
+        choices=["adducts", "biochemical", "biochemical_adducts"],
+        help=(
+            "The mode of integration. Options are 'adducts', 'biochemical', or"
+            " 'biochemical_adducts'."
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_bio",
+        nargs=2,
+        action="load_data",
+        type=str,
+        help="""dataframe (2 columns), reporting all the possible connections between
+         compounds. It uses the unique ids from the database. It could be the
+         output of Compute_Bio() or Compute_Bio_Parallel()""",
+    )
+    parser.add_argument(
+        "--delta_bio",
+        type=float,
+        help="""parameter used when computing the conditional priors. The
+               parameter must be positive. The smaller the parameter the more
+               weight the adducts connections have on the posterior
+               probabilities. Default 1.""",
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset_mapped_isotope_patterns,
+        args.input_dataset_annotations,
+        args.integrating_mode,
+        args.input_dataset_bio,
+        args.noits,
+        args.burn,
+        args.delta_bio,
+        args.delta_add,
+        args.all_out,
+        args.zs,
+        args.zs_out,
+        args.output_dataset,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_gibbs_sampler.xml	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,185 @@
+<tool id="ipapy2_gibbs_sampler" name="ipaPy2 gibbs sampler" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>combine multiple information sources in a Gibbs sampler to improve annotation accuracy</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '${__tool_directory__}/ipapy2_gibbs_sampler.py'
+        --input_dataset_mapped_isotope_patterns '${mapped_isotope_patterns}' '${mapped_isotope_patterns.ext}'
+        --input_dataset_annotations '${annotations}' '${annotations.ext}'
+        --integrating_mode '${integrating_mode.integrating_mode}'
+        #if $integrating_mode.integrating_mode == "adducts"
+            --delta_add '${integrating_mode.delta_add}'
+        #elif $integrating_mode.integrating_mode == "biochemical"
+            --input_dataset_bio '${integrating_mode.Bio}' '${integrating_mode.Bio.ext}'
+            --delta_bio '${integrating_mode.delta_bio}'
+        #else
+            --delta_add '${integrating_mode.delta_add}'
+            --input_dataset_bio '${integrating_mode.Bio}' '${integrating_mode.Bio.ext}'
+            --delta_bio '${integrating_mode.delta_bio}'
+        #end if
+        --noits '${noits}'
+        --burn '${burn}'
+        --all_out '${all_out}'
+        #if $zs:
+            --zs '${zs}' '${zs.ext}'
+        #else:
+            --zs '' ''
+        #end if
+        #if $zs_out:
+            --zs_out '${zs_out}' '${zs_out.ext}'
+        #else:
+            --zs_out '' ''
+        #end if
+        --output_dataset '${annotations_out}' '${annotations_out.ext}'
+
+    ]]></command>
+
+    <inputs>
+        <expand macro="gibbs"/>
+        
+        <conditional name="integrating_mode">
+            <param name="integrating_mode" type="select" label="integrating mode" help="select the integrating mode">
+                <option value="adducts">adducts</option>
+                <option value="biochemical">biochemical</option>
+                <option value="both">adducts and biochemical</option>
+            </param>
+            <when value="adducts">
+                <param name="delta_add" type="float" value="1" min="0" label="adducts weight" 
+                        help="parameter used when computing the conditional priors. The parameter must be positive. 
+                        The smaller the parameter the more weight the adducts connections have on the posterior probabilities. Default 1." />
+            </when>
+            <when value="biochemical">
+                <param name="Bio" type="data" format="csv,tsv,tabular,parquet" label="biochemical connections" 
+                        help="dataframe (2 columns), reporting all the possible connections between compounds. It uses the unique ids from the database. 
+                        It could be the output of Compute_Bio() or Compute_Bio_Parallel()." />
+                <param name="delta_bio" type="float" value="1" min="0" label="biochemical weight" 
+                        help="parameter used when computing the conditional priors. The parameter must be positive. 
+                        The smaller the parameter the more weight the biochemical connections have on the posterior probabilities. Default 1." />            
+            </when>
+            <when value="both">
+                <param name="delta_add" type="float" value="1" min="0" label="adducts weight" 
+                        help="parameter used when computing the conditional priors. The parameter must be positive. 
+                        The smaller the parameter the more weight the adducts connections have on the posterior probabilities. Default 1." />
+                <param name="Bio" type="data" format="csv,tsv,tabular,parquet" label="biochemical connections" 
+                        help="dataframe (2 columns), reporting all the possible connections between compounds. It uses the unique ids from the database. 
+                        It could be the output of Compute_Bio() or Compute_Bio_Parallel()." />
+                <param name="delta_bio" type="float" value="1" min="0" label="biochemical weight" 
+                        help="parameter used when computing the conditional priors. The parameter must be positive. 
+                        The smaller the parameter the more weight the biochemical connections have on the posterior probabilities. Default 1." /> 
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} annotations on ${on_string}" name="annotations_out" format_source="mapped_isotope_patterns"/>
+        <data label="${tool.name} zs on ${on_string}" name="zs_out" format="txt">
+            <filter>options['all_out']</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test  expect_num_outputs="2">
+            <param name="mapped_isotope_patterns" value="mapped_isotope_patterns.parquet"/>
+            <param name="annotations" value="clean_annotations.csv"/>
+            <!-- Not the best way to test, but the results are stochastic hence difficult to test-->
+            <output name="annotations_out">
+                <assert_contents>
+                    <has_size value="9185" delta="100" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+.. _ipapy2_gibbs_sampler:
+
+==========================
+ipaPy2 Gibbs Sampler Tool
+==========================
+
+**Tool Description**
+
+This tool implements a Gibbs sampler that integrates multiple sources of information—biochemical connections and adducts connections—to improve the accuracy of metabolite annotation. By iteratively sampling from the posterior distribution, the tool refines annotation probabilities based on both network and chemical relationships.
+
+How it works
+------------
+
+- The Gibbs sampler updates annotation probabilities by considering:
+  - **Adducts connections**: Relationships between features that can be explained by known adduct transformations.
+  - **Biochemical connections**: Relationships between compounds based on known biochemical pathways or reactions.
+- The user can select to use only adducts, only biochemical connections, or both.
+- The influence of each connection type is controlled by the `adducts weight` and `biochemical weight` parameters: smaller values increase the influence of the respective connection type on the posterior probabilities.
+- The process is stochastic, so results may vary between runs.
+
+Inputs
+------
+
+1. **Mapped isotope patterns**  
+   Dataset containing mapped isotope patterns (e.g., output from the ipaPy2 map isotope patterns tool).
+
+2. **Annotations**  
+   Initial annotation table to be refined by the Gibbs sampler.
+
+3. **Integrating mode**  
+   - **adducts**: Use only adducts connections.
+   - **biochemical**: Use only biochemical connections (requires a biochemical connections table).
+   - **both**: Use both adducts and biochemical connections.
+
+4. **Adducts weight (`delta_add`)**  
+   Controls the influence of adducts connections (smaller = more influence).
+
+5. **Biochemical connections**  
+   Table (2 columns) reporting all possible biochemical connections between compounds (required if using biochemical mode).
+
+6. **Biochemical weight (`delta_bio`)**  
+   Controls the influence of biochemical connections (smaller = more influence).
+
+7. **Other parameters**  
+   - **noits**: Number of Gibbs sampler iterations.
+   - **burn**: Number of burn-in iterations.
+   - **all_out**: Output all intermediate results.
+   - **zs**: Optional input for initial state.
+   - **zs_out**: Optional output for sampled states.
+
+Outputs
+-------
+
+- **annotations_out**  
+  Refined annotation table with updated posterior probabilities.
+
+- **zs_out**  
+  (Optional) File containing sampled states from the Gibbs sampler (if `all_out` is enabled).
+
+Example
+-------
+
+Suppose you have mapped isotope patterns and an initial annotation table. You can run the Gibbs sampler as follows:
+
+.. code-block::
+
+    mapped_isotope_patterns.parquet
+    clean_annotations.csv
+
+Choose the integrating mode (e.g., both), set the weights, and run the tool. The output will be a refined annotation table.
+
+Notes
+-----
+
+- The results are stochastic; repeated runs may yield slightly different outputs.
+- For best results, ensure all input files are correctly formatted and contain the required columns.
+- The biochemical connections table should use unique IDs consistent with your annotation table.
+
+References
+----------
+
+- For more details on the Gibbs sampling algorithm and its application in metabolomics, refer to the ipaPy2 documentation or associated publications.
+
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_gibbs_sampler_add.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,76 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, GibbsArgumentParser, group_by_peak_id
+
+
+def main(
+    mapped_isotope_patterns,
+    annotations_df,
+    noits,
+    burn,
+    delta_add,
+    all_out,
+    zs,
+    zs_out,
+    output_dataset,
+):
+    df = mapped_isotope_patterns
+
+    annotations_df = annotations_df
+    annotations_df["post"] = annotations_df["post"].replace("", 0)
+    annotations_df = annotations_df.replace("", None)
+    annotations = group_by_peak_id(annotations_df)
+
+    if not zs:
+        zs = None
+
+    zs = ipa.Gibbs_sampler_add(
+        df,
+        annotations,
+        noits=noits,
+        burn=burn,
+        delta_add=delta_add,
+        all_out=all_out,
+        zs=zs,
+    )
+
+    annotations_flat = flattern_annotations(annotations)
+    write_func, file_path = output_dataset
+    write_func(annotations_flat, file_path)
+
+    if all_out:
+        write_func, file_path = zs_out
+        write_func(zs, file_path)
+
+
+if __name__ == "__main__":
+    parser = GibbsArgumentParser(description="cluster features before IPA pipeline.")
+    parser.add_argument(
+        "--input_dataset_mapped_isotope_patterns",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "A dataset containing the MS1 data. Ideally obtained from"
+            " map_isotope_patterns"
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_annotations",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="a datset containing the annotations of the features.",
+    )
+
+    args = parser.parse_args()
+    main(
+        args.input_dataset_mapped_isotope_patterns,
+        args.input_dataset_annotations,
+        args.noits,
+        args.burn,
+        args.delta_add,
+        args.all_out,
+        args.zs,
+        args.zs_out,
+        args.output_dataset,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_map_isotope_patterns.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,70 @@
+from ipaPy2 import ipa
+from utils import CustomArgumentParser
+
+
+def main(input_dataset, isoDiff, ppm, ionisation, isotope_ratio, output_dataset):
+    clustered_df = input_dataset
+    ipa.map_isotope_patterns(
+        clustered_df,
+        isoDiff=isoDiff,
+        ppm=ppm,
+        ionisation=ionisation,
+        MinIsoRatio=isotope_ratio,
+    )
+    write_func, file_path = output_dataset
+    write_func(clustered_df, file_path)
+
+
+if __name__ == "__main__":
+    parser = CustomArgumentParser(description="mapping isotope patterns in MS1 data.")
+    parser.add_argument(
+        "--input_dataset",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing clustered MS1 intensities.",
+    )
+    parser.add_argument(
+        "--isoDiff",
+        type=float,
+        default=1,
+        help=(
+            "Default value 1. Difference between isotopes of charge 1, does            "
+            "  not need to be exact"
+        ),
+    )
+    parser.add_argument(
+        "--ppm",
+        type=float,
+        default=100,
+        help=(
+            "Default value 100. Maximum ppm value allowed between 2 isotopes.          "
+            "  It is very high on purpose"
+        ),
+    )
+    parser.add_argument(
+        "--ionisation",
+        type=int,
+        default=1,
+        choices=[1, -1],
+        help="Default value 1. positive = 1, negative = -1",
+    )
+    parser.add_argument(
+        "--isotope_ratio",
+        type=float,
+        default=1,
+        help=(
+            "mininum intensity ratio expressed (Default value 1%). Only               "
+            " isotopes with intensity higher than MinIsoRatio% of the main isotope     "
+            "           are considered."
+        ),
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset,
+        args.isoDiff,
+        args.ppm,
+        args.ionisation,
+        args.isotope_ratio,
+        args.output_dataset,
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,71 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.3.0</token>
+    <token name="@PROFILE@">23.0</token>
+
+    <xml name="citations">
+        <citations>
+        <citation type="doi">10.1021/acs.analchem.9b02354</citation>
+        <citation type="doi">10.1093/bioinformatics/btad455</citation>
+        </citations>
+    </xml>
+
+    <xml name="ionisation">
+        <param label="ionisation" name="ionisation" type="select" help="ionisation. positive +1 or negative -1">
+            <option value="1">positive</option>
+            <option value="-1">negative</option>
+        </param>
+    </xml>
+
+    <xml name="ppm">
+        <param name="ppm" type="float" value="100" min="0">
+            <label>ppm between isotopes</label>
+            <help>Maximum ppm value allowed between 2 isotopes. Default value 100.</help>
+        </param>
+    </xml>
+
+    <xml name="ms_unknown">
+        <param name="ppmunk" type="float" optional="true" min="0">
+            <label>ppm for unknown</label>
+            <help>ppm associated to the 'unknown' annotation. If not provided equal to ppm.</help>
+        </param>
+        <param name="ratiounk" type="float" optional="true" value="0.5" min="0">
+            <label>isotope ratio for unknown</label>
+            <help>isotope ratio associated to the 'unknown' annotation.</help>
+        </param>
+    </xml>
+
+    <xml name="ms_options">
+        <param name="ratiosd" type="float" value="0.9" optional="true" min="0">
+            <label>intensity ratio</label>
+            <help>acceptable ratio between predicted intensity and observed intensity of isotopes</help>
+        </param>
+        <param name="ppmthr" type="float" optional="true" min="0">
+            <label>ppm threshold</label>
+            <help>maximum ppm possible for the annotations. if not provided equal to 2*ppm.</help>
+        </param>
+        <param name="pRTNone" type="float" optional="true" value="0.8" min="0">
+            <label>no RT factor</label>
+            <help>multiplicative factor for the RT if no RTrange present in the database.</help>
+        </param>
+        <param name="pRTout" type="float" optional="true" value="0.4" min="0">
+            <label>outside RT factor</label>
+            <help>multiplicative factor for the RT if measured RT is outside the RTrange present in the database.</help>
+        </param>
+    </xml>
+    <xml name="gibbs">
+        <param label="Mapped isotope patterns" name="mapped_isotope_patterns" type="data" format="csv,tsv,tabular,parquet" help="A csv file containing the MS1 data. Ideally obtained from map_isotope_patterns."/>
+        <param label="annotations" name="annotations" type="data" format="csv,tsv,tabular,parquet" help="pandas dataframe containing all the possible annotations for the measured features."/>
+        <param label="gibbs sampler iterations" name="noits" type="integer" value="1000" help="number of iterations if the Gibbs sampler to be run."/>
+        <param label="ignored iterations" name="burn" type="integer" optional="true" value="10" help="number of iterations to be ignored when computing posterior probabilities. If None, is set to 10% of total iterations."/>
+        <param label="output Gibbs parameter" name="all_out" type="boolean" value="false" optional="true" help="logical value. If true the list of assignments found in each iteration is returned by the function. Default False."/>
+        <param label="previous Gibbs sampler" name="zs" type="data" format="txt" optional="true" help="list of assignments computed in a previous run of the Gibbs sampler. Optional, default None."/>
+    </xml>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">ipapy2</requirement>
+            <requirement type="package" version="19.0.0">pyarrow</requirement>
+            <requirement type="package" version="2024.11.0">fastparquet</requirement>
+        </requirements>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MS1_DB.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,54 @@
+id,name,formula,inchi,smiles,RT,adductsPos,adductsNeg,description,pk,MS2,reactions
+C00079,L-Phenylalanine,C9H11NO2,"InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1",,120;160,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,UA005501_1,R00686 R00688 R00689 R00690 R00691 R00692 R00693 R00694;R00695 R00697 R00698 R00699 R01375 R01376 R01795 R03660;R06744 R07211 R08463 R08652 R08690 R09535 R09578 R09579;R10286 R10287 R10495 R10499 R10729 R11068 R11918
+C00082,L-Tyrosine,C9H11NO3,"InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m0/s1",,50;90,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,UA005601_1,R00031 R00728 R00729 R00730 R00731 R00732 R00733 R00734;R00735 R00736 R00737 R00739 R01795 R01815 R02078 R02918;R03539 R04730 R05671 R06626 R06751 R07211 R07212 R08825;R09254 R09521 R09830 R10059 R10246 R10671 R10964 R10968;R11366 R11917 R12150 R12161
+C00114,Choline,C5H14NO,"InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01021 R01022 R01023 R01025 R01026 R01027 R01028 R01029;R01030 R01310 R02381 R02542 R03075 R05739 R05794 R06871;R07377 R07386 R07409 R08212 R08557 R08558 R10285
+C00123,L-Leucine,C6H13NO2,"InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1",,70;110,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01088 R01089 R01090 R01091 R02552 R03657 R08411 R08664;R10944
+C00148,L-Proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1",,35;55,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_specxxxxx_7,R00135 R00671 R01246 R01248 R01249 R01251 R01252 R01253;R01255 R03661 R06746 R09572 R09650 R10507 R10661 R11594;R12056
+C00183,L-Valine,C5H11NO2,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",,40;70,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_specxxxxxx_11,R01212 R01214 R01215 R01434 R01437 R02200 R03665 R04870;R08663 R10031 R10941 R10942
+C00407,L-Isoleucine,C6H13NO2,"InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_spec3xxxxx_2,R02196 R02197 R02199 R02200 R03656 R06726 R09344 R09403;R10027 R10723 R10943 R11078 R11723
+C00431,5-Aminopentanoate,C5H11NO2,"InChI=1S/C5H11NO2/c6-4-2-1-3-5(7)8/h1-4,6H2,(H,7,8)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_spec128577_1,R02273 R02274 R02276 R02825
+C00719,Betaine,C5H11NO2,"InChI=1S/C5H11NO2/c1-6(2,3)4-5(7)8/h4H2,1-3H3",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_spec107xxx_1,R02565 R02566 R02821 R07228 R07244 R08211 R08212 R10061;R10062
+C00763,D-Proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01255 R02825 R02894 R02895 R09496
+C01570,D-Leucine,C6H13NO2,"InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C01799,D-Norvaline,C5H11NO2,"InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C01826,L-Norvaline,C5H11NO2,"InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_specxxxxxx_35,R03732
+C01877,4-Oxoproline,C5H7NO3,"InChI=1S/C5H7NO3/c7-3-1-4(5(8)9)6-2-3/h4,6H,1-2H2,(H,8,9)/t4-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R03290 R03292
+C01879,5-Oxoproline,C5H7NO3,"InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m0/s1",,50;90,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_spec38257_1,R00251 R02743 R03749 R08910 R11861 R11862
+C01933,L-Norleucine,C6H13NO2,"InChI=1S/C6H13NO2/c1-2-3-4-5(7)6(8)9/h5H,2-4,7H2,1H3,(H,8,9)/t5-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_spec59716_1,R03053
+C01957,Secologanate,C16H22O10,"InChI=1S/C16H22O10/c1-2-7-8(3-4-17)9(14(22)23)6-24-15(7)26-16-13(21)12(20)11(19)10(5-18)25-16/h2,4,6-8,10-13,15-16,18-21H,1,3,5H2,(H,22,23)/t7-,8+,10-,11-,12+,13-,15+,16+/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R05833 R05834
+C02237,5-Oxo-D-proline,C5H7NO3,"InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_spec36931_1,R01583
+C02265,D-Phenylalanine,C9H11NO2,"InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R00686 R01374 R01582 R03903
+C02378,6-Aminohexanoate,C6H13NO2,"InChI=1S/C6H13NO2/c7-5-3-1-2-4-6(8)9/h1-5,7H2,(H,8,9)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R00059 R05356 R05507 R10975
+C02486,(3R)-beta-Leucine,C6H13NO2,"InChI=1S/C6H13NO2/c1-4(2)5(7)3-6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01091
+C03263,Coproporphyrinogen III,C36H44N4O8,"InChI=1S/C36H44N4O8/c1-17-21(5-9-33(41)42)29-14-27-19(3)22(6-10-34(43)44)30(39-27)15-28-20(4)24(8-12-36(47)48)32(40-28)16-31-23(7-11-35(45)46)18(2)26(38-31)13-25(17)37-29/h37-40H,5-16H2,1-4H3,(H,41,42)(H,43,44)(H,45,46)(H,47,48)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R03197 R03220 R04178 R06895
+C03290,L-threo-3-Phenylserine,C9H11NO3,"InChI=1S/C9H11NO3/c10-7(9(12)13)8(11)6-4-2-1-3-5-6/h1-5,7-8,11H,10H2,(H,12,13)/t7-,8-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01766
+C03571,2-Amino-2-methylbutanoate,C5H11NO2,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,C5H7NO3,"InChI=1S/C5H7NO3/c7-3-1-4(5(8)9)6-2-3/h2-4,7H,1H2,(H,8,9)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R03291 R03293 R03295 R04443 R04444 R04445
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,C5H7NO3,"InChI=1S/C5H7NO3/c7-3-1-4(5(8)9)6-2-3/h3,7H,1-2H2,(H,8,9)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R02280 R04221 R04446 R04447 R11428
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,C9H11NO3,"InChI=1S/C9H11NO3/c10-8(5-9(12)13)6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R00739
+C04498,p-Coumaroylagmatine,C14H20N4O2,"InChI=1S/C14H20N4O2/c15-14(16)18-10-2-1-9-17-13(20)8-5-11-3-6-12(19)7-4-11/h3-8,19H,1-2,9-10H2,(H,17,20)(H4,15,16,18)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01617
+C05131,(1-Ribosylimidazole)-4-acetate,C10H14N2O6,"InChI=1S/C10H14N2O6/c13-3-6-8(16)9(17)10(18-6)12-2-5(11-4-12)1-7(14)15/h2,4,6,8-10,13,16-17H,1,3H2,(H,14,15)/t6-,8-,9-,10-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R04479
+C05768,Coproporphyrinogen I,C36H44N4O8,"InChI=1S/C36H44N4O8/c1-17-21(5-9-33(41)42)29-14-26-19(3)23(7-11-35(45)46)31(39-26)16-28-20(4)24(8-12-36(47)48)32(40-28)15-27-18(2)22(6-10-34(43)44)30(38-27)13-25(17)37-29/h37-40H,5-16H2,1-4H3,(H,41,42)(H,43,44)(H,45,46)(H,47,48)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R04972 R04973
+C06417,D-Valine,C5H11NO2,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C06418,D-Isoleucine,C6H13NO2,"InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C06420,D-Tyrosine,C9H11NO3,"InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C07457,Amyl nitrite,C5H11NO2,"InChI=1S/C5H11NO2/c1-5(2)3-4-8-6-7/h5H,3-4H2,1-2H3",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C08263,beta-Alaninebetaine,C6H13NO2,"InChI=1S/C6H13NO2/c1-7(2,3)5-4-6(8)9/h4-5H2,1-3H3",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C08307,Hordatine A,C28H38N8O4,"InChI=1S/C28H38N8O4/c29-27(30)35-15-3-1-13-33-23(38)12-6-18-5-11-22-21(17-18)24(25(40-22)19-7-9-20(37)10-8-19)26(39)34-14-2-4-16-36-28(31)32/h5-12,17,24-25,37H,1-4,13-16H2,(H,33,38)(H,34,39)(H4,29,30,35)(H4,31,32,36)/b12-6+/t24-,25+/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C09800,Swertiamarin,C16H22O10,"InChI=1S/C16H22O10/c1-2-7-14(24-6-8-13(21)23-4-3-16(7,8)22)26-15-12(20)11(19)10(18)9(5-17)25-15/h2,6-7,9-12,14-15,17-20,22H,1,3-5H2/t7-,9+,10+,11-,12+,14-,15-,16+/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,VF-NPL-QEHF0132xx_2,
+C11673,Geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,VF-NPL-QEHF00xxxx_74,R05899 R05900
+C15987,4-Methylaminobutyrate,C5H11NO2,"InChI=1S/C5H11NO2/c1-6-4-2-3-5(7)8/h6H,2-4H2,1H3,(H,7,8)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R07515 R10101 R10102
+C16589,2-Oxosuberate,C8H12O5,"InChI=1S/C8H12O5/c9-6(8(12)13)4-2-1-3-5-7(10)11/h1-5H2,(H,10,11)(H,12,13)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R08215 R08328
+C16647,"N,N-Diethylglycine",C6H13NO2,"InChI=1S/C6H13NO2/c1-3-7(4-2)5-6(8)9/h3-5H2,1-2H3,(H,8,9)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R08300
+C16744,Spongothymidine,C10H14N2O6,"InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7+,9-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C16963,Gardoside,C16H22O10,"InChI=1S/C16H22O10/c1-5-8(18)2-6-7(14(22)23)4-24-15(10(5)6)26-16-13(21)12(20)11(19)9(3-17)25-16/h4,6,8-13,15-21H,1-3H2,(H,22,23)/t6-,8+,9-,10-,11-,12+,13-,15+,16+/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C18170,3-Acetamidopropanal,C5H9NO2,"InChI=1S/C5H9NO2/c1-5(8)6-3-2-4-7/h4H,2-3H2,1H3,(H,6,8)",,500;560,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R03899 R09074
+C19579,gamma-Hydroxy-3-pyridinebutanoate,C9H11NO3,"InChI=1S/C9H11NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6,8,11H,3-4H2,(H,12,13)",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R09439 R09440
+C19712,N-Hydroxy-L-phenylalanine,C9H11NO3,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R09579 R09580
+C20807,3-Hydroxy-L-phenylalanine,C9H11NO3,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R10729
+C21092,D-allo-Isoleucine,C6H13NO2,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R11078
+C21096,L-allo-Isoleucine,C6H13NO2,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R11084
+C21308,(S)-beta-Tyrosine,C9H11NO3,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R11366 R11367
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",C14H23NO3,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R11930
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,C10H14N2O6,"InChI=1S/C10H14N2O6/c1-2-6(13)8(10(17)18)12-7(14)4-3-5(11)9(15)16/h1,5-6,8,13H,3-4,11H2,(H,12,14)(H,15,16)(H,17,18)/t5-,6+,8-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
+C22141,L-beta-Ethynylserine,C5H7NO3,,,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MS1_annotations.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,158 @@
+id,name,formula,adduct,m/z,charge,RT range,ppm,isotope pattern score,fragmentation pattern score,prior,post,peak_id
+C00148,L-Proline,C5H10NO2,M+H,116.07060453364,1,35;55,-0.5232473824191379,,,0.3180838666706876,,1
+C00763,D-Proline,C5H10NO2,M+H,116.07060453364,1,,-0.5232473824191379,,,0.3180838666706876,,1
+C18170,3-Acetamidopropanal,C5H10NO2,M+H,116.07060453364,1,500;560,-0.5232473824191379,,,0.3180838666706876,,1
+Unknown,Unknown,,,,,,3.0,,,0.04574839998793704,,1
+C00148,L-Proline,C10H19N2O4,2M+H,231.13393306728,1,35;55,-1.1247473555160623,,,0.3145378636708285,,501
+C00763,D-Proline,C10H19N2O4,2M+H,231.13393306728,1,,-1.1247473555160623,,,0.3145378636708285,,501
+C18170,3-Acetamidopropanal,C10H19N2O4,2M+H,231.13393306728,1,500;560,-1.1247473555160623,,,0.3145378636708285,,501
+Unknown,Unknown,,,,,,3.0,,,0.05638640898751447,,501
+Unknown,Unknown,,,,,,3.0,,,1,1,2
+Unknown,Unknown,,,,,,3.0,,,1,1,2407
+C00183,L-Valine,C5H12NO2,M+H,118.0862545981,1,40;70,-2.171278112469359,,,0.10654352762185176,,3
+C00431,5-Aminopentanoate,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C00719,Betaine,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C01799,D-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C01826,L-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C03571,2-Amino-2-methylbutanoate,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C06417,D-Valine,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C07457,Amyl nitrite,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+C15987,4-Methylaminobutyrate,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,,0.10654352762185176,,3
+Unknown,Unknown,,,,,,3.0,,,0.0411082514033339,,3
+Unknown,Unknown,,,,,,3.0,,,1,1,2015
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-1.2505435832647704,,,0.45629284154229943,,4
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-1.2505435832647704,,,0.45629284154229943,,4
+Unknown,Unknown,,,,,,3.0,,,0.08741431691540112,,4
+C00079,L-Phenylalanine,C18H23N2O4,2M+H,331.16523319619995,1,120;160,-0.9418144439136233,,,0.2401062666341187,,999
+C02265,D-Phenylalanine,C18H23N2O4,2M+H,331.16523319619995,1,,-0.9418144439136233,,,0.2401062666341187,,999
+C03263,Coproporphyrinogen III,C36H46N4O8,M+2H,331.16523319619995,2,,-0.9418144439136233,,,0.2401062666341187,,999
+C05768,Coproporphyrinogen I,C36H46N4O8,M+2H,331.16523319619995,2,,-0.9418144439136233,,,0.2401062666341187,,999
+Unknown,Unknown,,,,,,3.0,,,0.03957493346352525,,999
+Unknown,Unknown,,,,,,3.0,,,1,1,2582
+Unknown,Unknown,,,,,,3.0,,,1,1,2954
+C01957,Secologanate,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386053,4398
+C09800,Swertiamarin,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386053,4398
+C11673,Geniposidic acid,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386053,4398
+C16963,Gardoside,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386053,4398
+C00079,L-Phenylalanine,C9H11NNaO2,M+Na,188.0681965981,1,120;160,-2.1912163112556495,,,0.07890449704227288,0.09672265812976096,4398
+C02265,D-Phenylalanine,C9H11NNaO2,M+Na,188.0681965981,1,,-2.1912163112556495,,,0.07890449704227288,0.07737812650380876,4398
+Unknown,Unknown,,,,,,3.0,,,0.03103831558850615,0.030437893910988,4398
+C00123,L-Leucine,C6H14NO2,M+H,132.10190466256,1,70;110,-1.2116597442118062,,,0.08938513749355873,,5
+C00407,L-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C01570,D-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C01933,L-Norleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C02378,6-Aminohexanoate,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C02486,(3R)-beta-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C06418,D-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C08263,beta-Alaninebetaine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C16647,"N,N-Diethylglycine",C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C21092,D-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C21096,L-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+Unknown,Unknown,,,,,,3.0,,,0.016763487570854132,,5
+Unknown,Unknown,,,,,,3.0,,,1,1,2169
+C00123,L-Leucine,C12H27N2O4,2M+H,263.19653332512,1,70;110,-0.6839950273744673,,,0.08968478708873068,0.10964755446662842,2262
+C00407,L-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C01570,D-Leucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C01933,L-Norleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C02378,6-Aminohexanoate,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C02486,(3R)-beta-Leucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C06418,D-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C08263,beta-Alaninebetaine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C16647,"N,N-Diethylglycine",C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C21092,D-allo-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C21096,L-allo-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+Unknown,Unknown,,,,,,3.0,,,0.01346734202396253,0.013172009800343899,2262
+C01877,4-Oxoproline,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C01879,5-Oxoproline,C5H8NO3,M+H,130.04986908874997,1,50;90,-1.0894955217565612,,,0.10897775351467592,,6
+C02237,5-Oxo-D-proline,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C05131,(1-Ribosylimidazole)-4-acetate,C10H16N2O6,M+2H,130.04986908874997,2,,-1.0894955217565612,,,0.10897775351467592,,6
+C16744,Spongothymidine,C10H16N2O6,M+2H,130.04986908874997,2,,-1.0894955217565612,,,0.10897775351467592,,6
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,C10H16N2O6,M+2H,130.04986908874997,2,,-1.0894955217565612,,,0.10897775351467592,,6
+C22141,L-beta-Ethynylserine,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+Unknown,Unknown,,,,,,3.0,,,0.019200218367916987,,6
+C01877,4-Oxoproline,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C01879,5-Oxoproline,C10H15N2O6,2M+H,259.09246217749995,1,50;90,-0.5572431507691273,,,0.10934932622184204,,33
+C02237,5-Oxo-D-proline,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C05131,(1-Ribosylimidazole)-4-acetate,C10H15N2O6,M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C16744,Spongothymidine,C10H15N2O6,M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,C10H15N2O6,M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C22141,L-beta-Ethynylserine,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+Unknown,Unknown,,,,,,3.0,,,0.01585606400342151,,33
+C00183,L-Valine,C5H12NO2,M+H,118.0862545981,1,40;70,-1.4319880038362247,,,0.10853687713038368,,8
+C00431,5-Aminopentanoate,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C00719,Betaine,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C01799,D-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C01826,L-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C03571,2-Amino-2-methylbutanoate,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C06417,D-Valine,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C07457,Amyl nitrite,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+C15987,4-Methylaminobutyrate,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,,0.10853687713038368,,8
+Unknown,Unknown,,,,,,3.0,,,0.02316810582654676,,8
+Unknown,Unknown,,,,,,3.0,,,1,1,3044
+C08307,Hordatine A,C28H40N8O4,M+2H,276.15807686923,2,,-0.6031662439992381,,,0.8001426388917695,,9
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",C14H23NNaO3,M+Na,276.15701160443,1,,3.2542920594118643,,,0.08245153058258288,,9
+Unknown,Unknown,,,,,,3.0,,,0.11740583052564758,,9
+C08307,Hordatine A,C28H39N8O4,M+H,551.3088777384601,1,,-1.0501163385127417,,,0.8525755147970528,0.8525755147970528,1330
+Unknown,Unknown,,,,,,3.0,,,0.1474244852029472,0.1474244852029472,1330
+C00082,L-Tyrosine,C9H12NO3,M+H,182.08116921767,1,50;90,-1.127066960830867,,,0.12225722517881775,,10
+C03290,L-threo-3-Phenylserine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C06420,D-Tyrosine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C19579,gamma-Hydroxy-3-pyridinebutanoate,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C19712,N-Hydroxy-L-phenylalanine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C20807,3-Hydroxy-L-phenylalanine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C21308,(S)-beta-Tyrosine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+Unknown,Unknown,,,,,,3.0,,,0.021942198569457998,,10
+C00123,L-Leucine,C6H14NO2,M+H,132.10190466256,1,70;110,-1.1934919516598708,,,0.08939961938581567,,19
+C00407,L-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C01570,D-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C01933,L-Norleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C02378,6-Aminohexanoate,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C02486,(3R)-beta-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C06418,D-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C08263,beta-Alaninebetaine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C16647,"N,N-Diethylglycine",C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C21092,D-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C21096,L-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+Unknown,Unknown,,,,,,3.0,,,0.01660418675602744,,19
+C00763,D-Proline,C5H10NO2,M+H,116.07060453364,1,,-0.7084794667090921,,,0.31732884449735516,0.4648341180662727,90
+C00148,L-Proline,C5H10NO2,M+H,116.07060453364,1,35;55,-0.7084794667090921,,,0.31732884449735516,0.23241705903313634,90
+C18170,3-Acetamidopropanal,C5H10NO2,M+H,116.07060453364,1,500;560,-0.7084794667090921,,,0.31732884449735516,0.23241705903313634,90
+Unknown,Unknown,,,,,,3.0,,,0.048013466507934414,0.07033176386745463,90
+C00183,L-Valine,C5H12NO2,M+H,118.0862545981,1,40;70,-1.168621195337573,,,0.10889306818646385,0.13250900714547656,598
+C00431,5-Aminopentanoate,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C00719,Betaine,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C01799,D-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C01826,L-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C03571,2-Amino-2-methylbutanoate,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C06417,D-Valine,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C07457,Amyl nitrite,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+C15987,4-Methylaminobutyrate,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,,0.10889306818646385,0.10600720571638125,598
+Unknown,Unknown,,,,,,3.0,,,0.019962386321825242,0.01943334712347334,598
+C00763,D-Proline,C5H10NO2,M+H,116.07060453364,1,,-0.6585098810914435,,,0.31755854037471093,0.4653271513560653,992
+C00148,L-Proline,C5H10NO2,M+H,116.07060453364,1,35;55,-0.6585098810914435,,,0.31755854037471093,0.23266357567803264,992
+C18170,3-Acetamidopropanal,C5H10NO2,M+H,116.07060453364,1,500;560,-0.6585098810914435,,,0.31755854037471093,0.23266357567803264,992
+Unknown,Unknown,,,,,,3.0,,,0.04732437887586711,0.06934569728786952,992
+Unknown,Unknown,,,,,,3.0,,,1,1,2759
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-0.8260653495714844,,,0.46350041197047365,0.6033199300299021,3460
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-0.8260653495714844,,,0.46350041197047365,0.30165996501495107,3460
+Unknown,Unknown,,,,,,3.0,,,0.07299917605905273,0.09502010495514683,3460
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-0.9440763195286457,,,0.46189826833360753,0.6006082157298959,3512
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-0.9440763195286457,,,0.46189826833360753,0.30030410786494793,3512
+Unknown,Unknown,,,,,,3.0,,,0.07620346333278501,0.09908767640515627,3512
+C00082,L-Tyrosine,C18H23N2O6,2M+H,363.15506243534,1,50;90,-0.7813063051271507,,,0.12262419566264932,0.1487210449495498,3849
+C03290,L-threo-3-Phenylserine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+C06420,D-Tyrosine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+C19579,gamma-Hydroxy-3-pyridinebutanoate,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+C19712,N-Hydroxy-L-phenylalanine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+C20807,3-Hydroxy-L-phenylalanine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+C21308,(S)-beta-Tyrosine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963984,3849
+Unknown,Unknown,,,,,,3.0,,,0.019006434698805603,0.018441103332971248,3849
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-1.104836161281323,,,0.45924063672251225,0.5961224674898229,3897
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-1.104836161281323,,,0.45924063672251225,0.29806123374491145,3897
+Unknown,Unknown,,,,,,3.0,,,0.08151872655497557,0.10581629876526565,3897
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MS2_DB.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,58 @@
+compound_id,id,name,formula,inchi,precursorType,instrument,collision.energy,spectrum
+EMBL-MCF_specxxxxxx_11,EMBL-MCF_spec103039,L-valine,C5H11NO2,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",M+H,Thermo Q-Exactive Plus,35,55.0550575256:5.821211 57.0581207275:0.385600 58.0658950806:0.630274 58.3495445251:0.071247 59.0498695374:0.090730 59.0736999512:0.785509 61.0785980225:0.079884 72.0618743896:0.101367 72.0815124512:100.000000 72.1020126343:0.141023 72.7540664673:0.351120 73.078453064:0.150122 73.084777832:1.597497 77.9532852173:0.072738 81.8233795166:0.070211 89.4410705566:0.064118 101.239570618:0.078913 102.874641418:0.069568 108.20274353:0.069630 110.192855835:0.067897 116.710952759:0.067270 118.012329102:0.098210 118.086357117:18.115100 119.058662415:0.069043 119.089767456:0.289129 121.381546021:0.067230
+EMBL-MCF_specxxxxxx_11,EMBL-MCF_spec353465,L-valine,C5H11NO2,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",M+H,Thermo Q-Exactive Plus,30,49.5028053042:0.000000 49.5031356971:0.000000 49.5034660933:0.000000 55.0516490231:0.000000 55.0520364956:0.000000 55.0524239723:0.000000 55.0551364232:5.709279 55.057419621:0.000000 55.0578071549:0.000000 55.0581946929:0.000000 62.1242926283:0.000000 62.1247571195:0.000000 62.125221616:0.000000 62.1270796539:0.273043 62.128879724:0.000000 62.1293442673:0.000000 62.1298088159:0.000000 68.6293568384:0.000000 68.6298961632:0.000000 68.6304354943:0.000000 68.6336716146:0.819714 68.636343722:0.000000 68.6368831294:0.000000 68.6374225432:0.000000 72.0744414086:0.000000 72.0750218487:0.000000 72.0756022958:0.000000 72.0814071529:100.000000 72.0871348063:0.000000 72.0877154007:0.000000 72.0882960021:0.000000 72.0888766105:0.000000 80.1443393571:0.000000 80.1450199619:0.000000 80.1457005753:0.000000 80.1484231158:0.335739 80.1509981514:0.000000 80.1516788429:0.000000 80.152359543:0.000000 96.6869962311:0.000000 96.687898089:0.000000 96.6887999596:0.000000 96.692407568:0.319198 96.6958653114:0.000000 96.6967672955:0.000000 96.6976692923:0.000000 113.499419269:0.000000 113.500566304:0.000000 113.501713357:0.000000 113.506301742:0.303740 113.510849728:0.000000 113.511996937:0.000000 113.513144163:0.000000 118.056238081:0.000000 118.057454882:0.000000 118.058671703:0.000000 118.065973021:1.629779 118.071627358:0.000000 118.072844404:0.000000 118.074061469:0.000000 118.076495656:0.000000 118.077712777:0.000000 118.078929918:0.000000 118.086233155:4.695500 118.094754455:0.000000 118.095971859:0.000000 118.097189282:0.000000 141.409916709:0.000000 141.411511881:0.000000 141.41310708:0.000000
+EMBL-MCF_specxxxxxx_11,EMBL-MCF_spec27828,L-valine,C5H11NO2,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",M-H,Thermo Q-Exactive Plus,35,55.0173454285:0.819357 58.0282363892:0.155430 59.0124664307:0.288706 60.633266449:0.153079 60.973690033:0.947999 69.9262924194:0.132771 70.0284042358:0.176156 71.0488357544:0.266268 72.0074691772:0.315639 72.0440292358:3.529104 73.0279464722:1.022830 73.2752609253:0.240265 76.9688491821:0.212440 82.6356582642:0.149153 87.0436782837:0.316340 88.0389175415:0.362029 90.0336456299:0.717986 94.9794311523:0.589129 98.0233383179:10.158569 99.0073699951:4.559745 99.9244232178:5.193896 100.039047241:1.673723 100.9246521:0.264670 114.054443359:0.141860 116.033882141:1.352128 116.0704422:100.000000 116.927223206:40.701867 117.0001297:2.245887 117.067260742:1.129880 117.073799133:27.135808 117.92741394:4.083040 118.039916992:5.733336 118.049667358:19.004917 118.074668884:1.418335 127.41884613:0.140517
+EMBL-MCF_specxxxxx_7,EMBL-MCF_spec96902,L-proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1",M+H,Thermo Q-Exactive Plus,35,50.5765228271:0.040013 51.3066940308:0.039949 57.3015365601:0.042916 58.6652603149:0.035802 59.9653396606:0.042015 67.4477233887:0.045719 70.0457839966:0.101931 70.0658874512:100.000000 70.0850067139:0.205387 71.0691986084:0.680943 72.7813644409:0.103985 78.0933685303:0.047067 78.4382324219:0.048423 93.0519866943:0.043284 107.38319397:0.046267 110.270332336:0.039088 115.998878479:0.044442 116.016624451:0.986926 116.027992249:0.055860 116.070838928:48.658605 117.073997498:0.346962 123.482536316:0.042135
+EMBL-MCF_specxxxxx_7,EMBL-MCF_spec353568,L-proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1",M+H,Thermo Q-Exactive Plus,30,49.5028215674:0.000000 49.5031519602:0.000000 49.5034823563:0.000000 54.3425436643:0.000000 54.3429236744:0.000000 54.3433036885:0.000000 54.3448237848:0.099239 54.3463312371:0.000000 54.3467112871:0.000000 54.3470913411:0.000000 55.7668409699:0.000000 55.7672360173:0.000000 55.767631069:0.000000 55.7692113178:0.100512 55.7706660554:0.000000 55.7710611449:0.000000 55.7714562386:0.000000 69.840812971:0.000000 69.8413666391:0.000000 69.8419203138:0.000000 69.8446887858:0.141436 69.8469017737:0.000000 69.8474555142:0.000000 69.8480092613:0.000000 70.0544609359:0.000000 70.0550171465:0.000000 70.0555733637:0.000000 70.0561295876:0.000000 70.056685818:0.000000 70.0572420551:0.000000 70.0577982988:0.000000 70.0583545491:0.000000 70.0589108061:0.000000 70.0594735439:0.000000 70.0600298141:0.000000 70.0661492237:100.000000 70.0716064898:0.000000 70.0721629058:0.000000 70.0727193284:0.000000 70.0732757576:0.000000 81.2673987546:0.000000 81.2680937154:0.000000 81.2687886851:0.000000 81.2715686532:0.099737 81.2740383498:0.000000 81.2747333998:0.000000 81.2754284587:0.000000 116.046563256:0.000000 116.04774912:0.000000 116.048935002:0.000000 116.050120902:0.000000 116.051306821:0.000000 116.052492757:0.000000 116.053678712:0.000000 116.054864685:0.000000 116.056050676:0.000000 116.057280998:0.000000 116.058467026:0.000000 116.070328301:41.389911 116.083377803:0.000000 116.084564231:0.000000 116.085750677:0.000000 116.08693714:0.000000 136.360720074:0.000000 136.36223057:0.000000 136.363741091:0.000000
+EMBL-MCF_specxxxxx_7,EMBL-MCF_spec24658,L-proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1",M-H,Thermo Q-Exactive Plus,35,59.0125083923:0.125338 66.0334091187:1.831800 67.4686431885:0.097145 68.9942626953:0.191050 71.0486068726:1.244641 73.0749969482:0.171682 75.7445220947:0.105140 79.9856109619:0.099816 86.0232925415:1.007817 112.039100647:0.579737 113.08996582:0.109222 113.09765625:0.105680 114.054718018:100.000000 114.932899475:0.766543 115.038848877:0.558991 115.050613403:0.209440 115.058029175:3.018420 115.075042725:4.733047 120.061218262:0.105983
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+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004766,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+Na,Thermo Q Exactive HF,45,50.291872:0.286642 50.314117:0.201290 50.398136:0.249564 50.492357:0.369435 53.170254:0.259153 53.370368:0.245939 53.650726:0.240439 53.698492:0.194736 54.079081:0.176968 54.891412:0.247836 55.169971:0.146144 55.175040:0.207370 55.535200:0.163422 55.871474:0.150468 55.948180:0.208020 56.786975:0.250736 56.789153:0.165745 56.840689:0.233261 56.999692:0.205207 57.023154:0.386090 57.901649:0.306412 59.372319:0.210937 59.482729:0.179738 59.512083:0.292642 60.098428:0.207790 60.224650:0.158187 62.592018:0.241034 63.182763:0.279826 63.968524:0.174817 63.978153:0.242757 65.578897:0.167431 65.862951:0.164734 66.172271:0.206285 66.497148:0.181390 67.417859:0.261016 67.451161:0.250370 68.164352:0.351772 68.695640:0.151692 68.769737:0.332967 69.467014:0.249851 69.472206:0.340743 69.600484:0.232716 69.625522:0.177480 72.286846:0.161405 74.189700:0.211735 74.655021:0.161203 76.644148:0.150363 76.866975:0.260727 76.933510:0.179055 78.165076:0.162678 78.326284:0.169020 79.046650:0.200234 79.634423:0.223137 80.594274:0.272387 80.805078:0.376070 81.212191:0.231139 81.612674:0.216578 82.294102:0.367751 82.787770:0.168332 83.410795:0.219953 84.273941:0.182591 84.341194:0.359709 84.491710:0.238774 85.903089:0.223054 87.044577:0.160708 88.135462:0.284434 88.457742:0.172124 89.071624:0.267222 89.139787:0.161803 89.800416:0.168891 90.385784:0.280926 92.167875:0.182210 93.227458:0.238081 94.778876:0.266937 94.961390:0.356821 95.821838:0.199585 96.513432:0.243565 97.365680:0.193648 98.512326:0.312426 99.319700:0.255776 99.868236:0.215864 101.892797:0.245441 103.047571:0.304010 103.629651:0.189124 107.666334:0.313207 108.385318:0.222987 111.317474:0.313506 114.340229:0.267391 124.156046:0.205840 125.145700:0.403305 129.986981:0.181408 134.647245:0.171597 136.118929:0.263443 136.910011:0.256345 137.254715:0.367531 139.238708:0.265295 139.601901:0.195750 140.482629:0.268871 141.822717:0.240219 145.884523:0.265776 146.194853:0.260012 147.475082:0.273864 149.847691:0.360324 153.053456:0.177009 154.377748:0.256716 160.400893:0.240087 163.433400:0.423656 164.489209:0.277363 164.919767:0.283087 165.450968:0.250227 166.966478:0.224161 169.547393:0.182828 172.255917:0.181271 172.378790:0.255947 173.111548:0.187819 174.004230:0.185994 174.405138:0.210461 175.108515:0.201604 175.392403:0.148499 185.042298:7.317323 187.933658:0.393195 187.999293:0.379400 188.510879:0.250342 188.567583:0.366181 191.068069:4.237766 194.581806:0.215519 199.569560:0.236290 203.052806:24.753241 211.561225:0.389750 213.336333:0.282184 213.586606:0.310044 214.129123:2.672888 214.140771:15.309772 214.152448:7.675977 217.047233:100.000000 218.050476:7.336331 220.546949:0.216157 221.642591:0.343324 227.530992:0.369664 228.407640:0.305072 235.057673:27.939273 240.703285:0.180326 247.030462:0.282121 250.137146:0.173584 252.027688:0.186223 254.994436:0.274720 255.388424:0.185409 256.745875:0.193152 258.998635:0.266829 266.079894:0.388279 267.654632:0.258125 277.315010:0.242886 284.256858:0.259531 285.270722:0.296414 285.379510:0.244385 285.794373:0.289093 286.236298:0.489816 302.569689:0.339617 306.336266:0.171525 307.815762:0.229954 314.349391:0.231322 322.852405:0.178844 337.789918:0.245006 345.687126:0.213045 348.261010:0.372142 351.235962:0.176416 353.311110:0.386310 353.901220:0.232376 354.005342:0.237542 354.245943:0.200864 355.737087:0.225153 360.498677:0.377551 361.602204:0.224303 363.035884:0.179501 367.552376:0.346432 376.102570:0.221369 379.100082:0.435652 381.009394:0.437594 392.316067:0.396484 396.457769:1.023933 397.110811:22.421118 398.114179:0.579765 404.037589:0.200769 410.381374:0.181189 413.533290:0.192424
+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004767,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+Na,Thermo Q Exactive HF,65,50.077123:11.739013 50.739286:7.700284 50.875940:11.843003 51.088842:8.206889 52.382958:11.894099 53.135909:8.466632 53.386498:10.647062 53.542022:9.451332 54.399715:5.694740 54.869749:10.199048 55.055028:16.687354 55.349491:9.515127 55.471935:10.556077 55.519985:6.905906 55.823550:6.855604 57.031343:6.934465 57.033482:8.454007 57.160868:9.304306 57.440152:9.430346 57.452366:8.955852 57.999266:6.231617 58.267700:9.415246 58.646560:8.455486 58.745745:10.927879 59.361780:6.184569 59.751983:8.290914 59.817793:12.250856 60.253236:7.395868 60.258128:9.664340 60.472106:10.284882 60.517404:9.933435 60.519174:10.178908 60.806090:7.549789 60.987380:10.605467 61.881489:14.952185 62.084782:5.977544 62.153867:6.771435 62.330724:8.639680 62.665290:8.881693 63.137181:8.046755 63.481532:10.853617 64.102193:8.451505 64.137291:13.336507 64.560683:9.189229 64.872646:8.171569 65.176177:8.371698 65.180675:9.504529 65.363297:13.282645 65.410963:7.720390 65.647367:9.900097 65.745409:13.128358 66.057422:10.339161 66.207812:16.446935 66.214543:12.645515 66.984020:9.155342 67.146195:14.584399 67.553918:10.572850 67.606431:8.003985 67.895509:6.952498 68.951596:15.118580 69.034002:10.155396 69.768178:8.817668 69.801196:7.525686 70.804343:9.115211 70.806850:7.034606 71.111925:15.536160 72.020948:7.001022 72.825644:9.654823 73.029369:6.529843 74.888325:6.474018 74.933777:10.320279 74.989341:5.891847 75.101044:8.026874 75.387327:13.869311 75.883068:11.797791 75.923973:9.020309 76.953807:13.150080 77.299656:12.470903 77.908134:10.453582 78.074349:8.314687 78.884348:10.399231 79.345431:9.546509 80.438518:8.823068 81.084763:10.599689 81.108573:11.115757 81.179295:7.022586 81.181327:12.939309 81.348416:13.871713 82.220476:6.344572 82.360313:10.153822 82.604557:9.293573 82.696395:5.793922 82.722742:9.032455 82.931957:6.932416 83.128925:7.083101 83.278436:10.388987 83.910490:5.892679 84.424713:7.013939 84.581389:9.395238 85.426314:8.151734 90.886528:13.168281 91.937379:10.048593 92.083720:7.649172 92.314337:11.140691 93.588636:8.231492 93.779709:14.402729 94.735388:11.800587 95.075268:10.143123 95.548796:24.632732 95.919515:11.030388 96.253780:9.655509 96.472653:6.175625 96.518482:11.089504 98.976084:39.974166 100.008134:10.957421 104.492333:6.515993 105.533089:8.134044 106.957604:8.234424 107.456064:14.331576 107.827742:6.992564 108.808078:6.956832 108.871459:14.138412 109.665285:10.580005 110.097308:7.160820 110.261339:6.828943 111.379388:9.605315 111.823085:7.346890 112.587437:14.078870 112.980127:9.448403 113.756928:6.996164 113.776993:14.452535 114.301569:9.474584 115.309952:15.367166 116.603807:9.123549 116.772479:5.807480 118.080707:7.354925 118.255399:6.690636 120.939608:6.862196 123.857761:11.702419 124.825414:11.518107 126.250816:10.678415 127.320116:7.038840 128.589025:8.859551 128.722328:11.112696 128.743328:11.561416 131.223441:10.493044 133.069251:7.750665 133.951934:11.821853 135.311457:8.741656 136.503459:6.006305 137.810130:11.225856 137.891485:13.426054 138.195136:7.764073 138.969588:6.366368 139.175008:6.811476 140.475481:8.804766 141.421536:5.919175 141.659284:7.615612 142.145195:14.537603 144.861097:9.215348 146.720395:9.198667 147.268843:10.764132 147.623900:8.723956 147.891391:7.924883 148.019767:11.555371 149.477405:8.043001 151.715483:14.358210 152.716779:10.425497 153.893940:8.966743 154.832213:13.045119 155.337707:13.375059 155.989739:8.550172 163.675984:10.710801 164.514517:11.521897 164.613493:11.992067 165.086934:14.686391 165.754167:8.935088 168.546477:13.736387 168.615245:8.270692 169.047084:6.474974 169.279834:6.608751 169.408196:8.893119 171.581717:12.261893 175.234333:9.840897 177.823370:10.198081 178.584547:10.173401 178.878130:10.399806 180.768540:11.993213 184.665938:9.046935 185.058855:17.115027 186.674718:7.995379 189.447647:9.053547 201.314155:15.977087 203.520422:12.928873 207.181202:8.987695 217.953897:7.842611 218.640972:6.569061 218.954262:17.051380 219.036902:15.424352 219.275224:6.389159 220.170021:81.141396 220.177812:100.000000 220.191711:72.495210 220.226506:7.201397 221.619628:9.991751 223.224653:11.448137 236.415790:12.120169 246.191274:11.340667 246.809922:7.666341 247.412719:9.638622 253.911207:7.256608 256.115703:7.067352 260.444697:11.739721 265.171347:7.485656 265.627950:11.507197 268.220257:6.502345 271.990845:9.002668 274.123270:6.673062 278.352152:12.077158 282.329124:9.453128 285.568525:9.619689 288.563726:6.729509 291.451054:10.490340 293.413520:8.154911 294.678777:14.678355 295.086587:9.322052 301.896983:8.320727 307.853593:8.760624 311.195445:9.493529 324.998877:7.971823 350.184931:9.054240 352.390618:11.437192 365.502971:8.024946 365.582250:16.554574 367.027823:7.605153 386.885255:10.120403 388.238613:10.721067 399.286137:12.723979 404.153453:9.079737 404.574468:10.855682 406.229457:15.648012 413.700192:7.232840 418.604421:11.329896 420.327904:11.771134
+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004768,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+K,Thermo Q Exactive HF,35,50.348437:0.012559 50.565674:0.012258 50.655566:0.019067 50.899435:0.005046 50.916374:0.012518 51.087534:0.016635 51.194505:0.011723 51.399228:0.004636 51.452796:0.005764 51.478273:0.011573 51.773815:0.012930 51.828544:0.011839 51.850718:0.010508 51.863785:0.011849 52.280336:0.016995 52.471864:0.011753 52.626528:0.018192 53.088866:0.008876 53.931394:0.012598 54.182363:0.011769 54.222033:0.012905 54.278646:0.012201 54.497212:0.005746 54.653926:0.013415 55.055047:0.192452 55.965256:0.010995 56.170393:0.012965 56.424848:0.013317 56.668828:0.012080 56.688419:0.028385 56.965651:0.008907 57.034345:0.016094 57.070688:2.661053 57.145023:0.014071 57.312955:0.011884 57.716649:0.019774 57.836153:0.013111 58.065951:0.005435 58.633978:0.013778 59.049920:0.038257 59.061162:0.151348 59.152096:0.012876 59.795085:0.019209 59.991035:1.072372 60.045188:3.495661 60.237825:0.013965 60.550482:0.012429 60.694087:0.019056 60.734254:0.015887 61.229263:0.019177 62.060906:0.017862 62.875731:0.012536 62.982504:0.097228 63.400924:0.015922 63.895798:0.016468 64.009181:0.012854 64.250710:0.012805 64.274793:0.011675 65.672534:0.017931 65.799567:0.020453 66.212088:0.024493 66.267457:0.020747 66.291782:0.014551 67.055004:0.478872 67.121272:0.014058 67.283382:0.020867 67.287826:0.025838 67.498555:0.005188 67.697323:0.022071 68.244770:0.009442 68.290539:0.016308 68.433156:0.013063 68.618408:0.020934 68.623952:0.014365 69.034238:0.141945 69.070622:0.504334 69.146669:0.020617 69.238657:0.015297 69.877545:0.009309 69.884789:0.012095 70.065940:0.056202 70.288324:0.012315 70.679438:0.021508 70.743279:0.012328 71.049791:0.087610 71.086230:0.364401 72.081500:0.468051 72.152851:0.017554 72.660196:0.013869 72.761324:0.014167 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+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004770,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+K,Thermo Q Exactive HF,65,50.276741:0.255358 50.459141:0.356575 50.685041:0.368993 50.766106:0.220287 51.404994:0.471769 51.549760:0.434605 51.581975:0.283760 51.944100:0.377404 51.985307:0.281515 53.039417:0.196696 53.153152:0.338117 53.178466:0.280809 53.233309:0.118447 53.604153:0.368695 54.062205:0.314036 54.089115:0.243396 54.124538:0.113106 54.255906:0.381666 54.709797:0.114057 54.996336:0.285882 55.018544:0.142792 55.055079:15.903550 55.080078:0.260784 56.050314:1.272417 56.107864:0.339084 56.471537:0.311536 56.965606:29.519084 57.034263:0.134122 57.070700:44.680009 57.746775:0.456824 58.065900:0.564637 58.596710:0.294830 58.707626:0.244022 58.893873:0.438600 59.052419:0.291594 59.061151:0.232915 59.297310:0.486948 59.372904:0.447847 59.479128:0.498587 59.536033:0.312137 59.744575:0.461134 59.792599:0.325119 59.810965:0.307541 59.831890:0.377474 59.991057:34.145702 60.009979:0.348537 60.045214:19.489689 60.259583:0.132196 60.647208:0.425507 61.011397:0.219838 61.210456:0.433814 62.019226:0.169081 62.200892:0.262650 62.222387:0.343558 62.898626:0.337428 63.354894:0.327731 63.540836:0.331808 63.998403:0.153891 64.084594:0.228877 64.619547:0.308951 64.929723:0.447095 65.091502:0.296172 65.883145:0.383198 65.909939:0.324458 67.055039:13.340413 67.102473:0.300202 68.364578:0.405951 68.822696:0.304155 69.034320:3.834076 69.070644:5.117378 69.345580:0.246647 70.065922:1.995227 70.140247:0.448193 70.855210:0.462146 71.050047:0.284667 71.086329:0.876508 71.513481:0.292265 72.081407:0.438528 72.539221:0.219851 72.799267:0.411087 73.047539:1.395743 73.660057:0.315553 74.641182:0.442670 76.076441:0.157823 76.982946:0.344134 77.574027:0.307297 77.696235:0.295970 77.840745:0.115301 78.047265:0.119819 78.295414:0.334981 78.829322:0.326895 79.021928:1.268475 79.054942:7.322220 79.118317:0.275871 79.146697:0.347367 79.253397:0.293428 79.301526:0.228502 80.595769:0.412421 80.948597:0.301716 81.017711:0.164205 81.034179:0.136173 81.070551:10.337726 82.405841:0.278172 83.049712:3.128559 83.086070:0.181267 83.205169:0.339194 83.225340:0.259255 83.457116:0.252076 83.862485:0.350374 84.053089:0.524319 84.081494:0.534419 84.960373:0.397197 85.028970:1.585206 85.040355:0.969726 85.435148:0.331504 86.253400:0.371619 86.794679:0.278410 87.587483:0.323095 88.022188:34.868911 88.076461:0.141876 90.075281:0.115031 90.346459:0.237128 90.493817:0.434106 90.676243:0.235034 91.054812:35.305517 91.057915:7.934511 91.573893:0.392895 93.070473:3.106890 93.426496:0.467686 93.470844:0.345101 94.282037:0.427077 94.608023:0.236928 94.958697:0.448782 95.049698:1.932730 95.086052:5.269640 96.735767:0.338619 96.878035:0.456343 97.040156:0.185691 98.975884:17.664323 98.979290:0.161990 99.031207:0.337493 99.286705:0.418949 100.671787:0.508804 100.676660:0.449723 101.621860:0.105612 102.012850:0.108306 102.575169:0.337093 103.027306:0.320985 103.054696:1.326360 103.679854:0.310306 103.703883:0.303326 104.062650:0.459084 104.239352:0.106660 105.045501:0.127036 105.070329:1.315734 107.049735:0.498335 107.085981:3.834686 109.065251:0.169183 110.044711:0.122008 110.966538:0.303027 111.338481:0.370566 112.039978:0.279761 112.740441:0.400727 113.384646:0.437027 113.751130:0.310185 114.452125:0.335372 115.908700:0.466424 115.993202:0.236828 116.053175:30.727849 116.057484:0.200932 116.986227:14.474533 117.070176:3.511933 117.632200:0.304651 118.815353:0.274342 119.049038:0.363527 119.085851:100.000000 121.065261:0.930724 124.103289:0.118014 125.151956:0.383798 125.757826:0.460405 128.985804:0.191309 129.330463:0.116642 130.109730:0.324299 133.090561:0.386941 134.924463:0.110108 134.996598:3.822936 135.639995:0.283638 138.666513:0.382313 138.907603:0.437033 139.958600:0.405770 142.455688:0.485917 144.587223:0.262181 146.007200:0.223530 146.931419:0.329025 146.996644:0.473221 147.974428:0.432032 148.352327:0.458772 149.010887:0.129092 149.721902:0.438587 151.006638:0.391513 153.007059:0.149685 153.812985:0.395654 155.281877:0.336087 156.571755:0.137121 156.825811:0.398671 158.771318:0.324473 158.939786:0.362168 159.433942:0.135909 161.345801:0.487204 162.991193:0.126685 163.135404:0.320237 164.183511:0.392976 164.690158:0.424252 167.071212:0.119514 168.145148:0.140822 168.855411:0.428176 168.863550:0.368322 169.017212:0.643131 169.256195:0.273221 169.290901:0.507894 170.885416:0.289557 171.375814:0.422638 172.740291:0.338089 175.036203:0.440694 176.406247:0.426842 179.520942:0.391107 179.806659:0.415399 181.000588:0.492177 182.458332:0.350897 183.643183:0.282169 183.878528:0.436233 185.651599:0.511884 186.969417:0.323153 187.027922:0.249803 189.022190:0.149189 189.052400:45.346141 190.055702:0.506076 192.895559:0.470542 194.829910:0.496816 195.032620:1.484533 195.418457:0.327841 197.011521:0.138441 198.754601:0.362625 200.687228:0.292219 202.491967:0.394495 205.017303:0.131164 206.615397:0.123851 206.636102:0.347895 207.033346:1.915223 214.096997:0.242508 214.338714:0.369374 220.153339:1.871714 220.165261:3.131854 220.177701:2.896187 220.931408:0.346184 221.748675:0.341517 222.674827:0.272620 223.027797:1.238634 224.306693:0.597786 225.043582:0.683790 228.162873:0.410163 228.555831:0.353091 230.465034:0.269052 230.803764:0.120857 231.301548:0.440286 231.434123:0.463520 233.186431:0.436834 234.899404:0.258559 235.057824:0.897366 235.900021:0.198647 236.531987:0.335838 239.604297:0.444043 240.841785:0.112790 246.137496:0.123134 247.990561:0.507728 248.642557:0.122545 248.813610:0.386273 251.022927:0.518986 252.950138:0.290585 253.458076:0.443658 254.197571:0.303057 261.927991:0.290871 262.106333:0.316075 265.950936:0.381593 269.033009:1.112565 270.523516:0.265610 272.622472:0.355931 272.896050:0.569295 273.046806:0.133809 274.162227:0.355227 281.322415:0.280197 284.154118:0.204496 284.508672:0.381424 287.043896:1.082642 287.799393:0.348043 293.530290:0.470968 305.280605:0.512617 308.536614:0.119616 313.272753:0.391601 315.944157:0.376624 318.947674:0.254832 327.116737:0.122126 338.306936:0.468363 344.976790:3.271520 349.623226:0.431983 349.895736:0.119697 363.375491:0.505470 366.593597:0.120073 374.008340:0.347449 385.656050:0.423012 394.415562:0.258360 396.221743:0.249522 399.070113:0.536691 412.793880:0.444657 413.750482:0.462484 418.314628:0.260407 435.195625:0.322189 436.034471:0.324944 436.163586:0.524263
+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004771,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+NH4,Thermo Q Exactive HF,35,50.022209:0.005153 50.390025:0.010307 51.006741:0.013698 52.197640:0.010686 52.297595:0.004035 52.651726:0.004315 52.984580:0.015359 52.987535:0.015873 53.242933:0.010814 53.260429:0.012894 53.325777:0.012956 53.348595:0.013010 54.191731:0.005818 55.055112:0.005485 55.487759:0.014505 56.139130:0.005261 56.439405:0.012082 56.811358:0.011564 57.034385:0.014994 57.070690:0.463927 57.100670:0.040052 57.156238:0.004828 57.841677:0.012589 57.862567:0.008491 57.876659:0.014407 57.891099:0.012496 58.065907:0.012038 58.688781:0.005946 58.866487:0.010954 59.061084:0.006487 59.068856:0.013484 59.396251:0.008169 59.464126:0.004540 59.707275:0.014405 60.806277:0.006179 60.819730:0.014340 61.017844:0.013236 61.029205:0.055009 61.155295:0.008487 61.323526:0.007363 61.731487:0.014441 62.019336:0.013577 62.330766:0.004183 62.641562:0.007336 62.690349:0.011418 62.932240:0.004602 62.971066:0.004316 62.982512:0.080665 63.144877:0.011702 63.173385:0.013134 63.230225:0.014170 64.325735:0.005301 64.399789:0.009411 64.501459:0.007327 65.676528:0.004234 66.634179:0.004328 67.054987:0.032647 67.509593:0.010058 69.034244:0.158405 69.070641:0.224909 69.889092:0.007359 70.628716:0.011499 71.013706:0.005294 71.086283:0.226640 71.712029:0.004966 72.488236:0.006307 73.029298:0.006807 73.232867:0.004743 74.289528:0.011878 75.224897:0.004550 75.707833:0.007600 76.076134:0.004841 77.039717:0.033737 77.266788:0.009794 77.697808:0.011902 79.021901:0.034725 79.051137:0.005624 79.054867:0.713759 79.105167:0.015264 79.393745:0.014258 79.559120:0.004594 79.894938:0.014059 80.520341:0.007710 81.002917:0.011329 81.019149:0.123724 81.034179:0.128777 81.070544:0.916652 81.361312:0.013299 81.422477:0.012963 83.049629:0.030306 83.086266:0.169007 83.369455:0.009682 85.029036:1.581629 85.101745:0.017375 86.032329:0.014320 87.044649:0.052664 87.502447:0.005813 87.888259:0.012376 87.923319:0.013542 88.162706:0.011786 89.060328:0.480898 89.881272:0.005623 89.894430:0.012469 90.091742:0.012533 90.508023:0.011096 90.929248:0.012109 91.039532:0.028228 91.054879:0.230298 91.186587:0.006166 91.932448:0.011446 91.967066:0.012963 92.671904:0.004147 93.070416:0.696042 94.026934:0.020037 95.049656:0.025687 95.086040:0.264138 95.302553:0.011196 97.028939:0.311546 97.101603:0.025954 97.480306:0.004333 99.008192:0.023320 99.044643:0.038440 99.677297:0.004746 100.076163:0.046884 101.003588:0.005118 101.375941:0.006166 103.054702:0.081185 103.840991:0.012194 104.347552:0.013421 104.575412:0.015942 104.617912:0.010272 104.760099:0.009181 104.992752:0.441894 105.070313:1.334295 105.676259:0.013891 107.049577:0.207551 107.085880:0.061876 108.108343:0.005781 108.562901:0.004036 108.749092:0.008136 109.028757:0.025250 109.065163:0.005979 109.101588:0.074567 110.046413:0.011891 110.622824:0.008127 111.044782:0.009736 113.059978:0.007224 113.648459:0.014278 114.470357:0.007509 114.913696:0.011781 116.053178:0.074754 116.266733:0.005067 118.087060:0.005312 119.049587:0.046558 119.086337:0.012383 119.628098:0.011054 119.630794:0.013337 120.080995:0.018224 120.416156:0.015319 121.065075:6.497133 121.101528:0.034857 121.260321:0.012999 122.068377:0.479605 122.146376:0.014239 122.668699:0.013777 123.080731:0.047920 123.117035:0.057729 124.158236:0.006061 126.052802:0.661652 126.090872:0.015049 127.039140:0.386497 127.221981:0.006349 129.803212:0.009627 131.049285:0.442781 133.064933:0.614258 133.085819:0.036589 134.580832:0.014038 135.002999:0.082329 135.080473:0.013284 135.117189:0.032848 135.856656:0.007659 137.059614:0.030863 139.075465:0.056869 141.088706:0.004234 143.299501:0.004368 143.553800:0.010542 144.336768:0.015761 144.638533:0.016609 145.049688:0.349804 145.249803:0.015527 146.253646:0.011477 147.044183:0.304861 147.080511:0.016280 148.453191:0.005809 149.023521:0.658300 149.059866:41.997116 150.063158:3.666445 150.250174:0.015184 151.064540:0.004050 151.075559:0.321983 152.989526:0.005193 154.000899:0.012096 154.223053:0.009427 154.947078:0.027095 156.138694:0.015627 156.374250:0.010048 159.044188:2.398061 160.047487:0.123842 160.060572:0.008295 161.059977:0.025974 163.039019:0.005330 163.274157:0.012072 164.920635:0.461101 164.927699:0.008901 164.937275:0.009980 165.054910:0.025238 166.572615:0.015434 166.775268:0.012043 166.916615:0.008224 167.070402:10.407814 167.503450:0.013489 168.073754:0.928916 169.302398:0.004636 172.112391:0.064212 172.143465:0.015383 172.161398:0.007636 172.657370:0.015122 173.131364:0.014122 173.219037:0.006092 174.127752:0.020098 174.515983:0.015981 175.039141:0.758157 176.042575:0.284895 177.054703:22.853309 178.058011:2.346279 179.022363:0.062843 179.061261:0.049309 179.070189:0.569945 180.485662:0.004532 180.894626:0.018401 181.085901:0.040992 181.979498:0.006989 185.099048:0.004432 187.160457:0.012329 187.234548:0.007991 192.564552:0.013458 193.049621:0.470678 194.052948:0.106602 194.924833:0.063218 195.065291:15.646755 196.068635:1.596555 197.081035:0.185211 197.508832:0.016087 204.138076:0.016404 207.098226:0.009205 211.289000:0.005812 212.935366:0.050387 213.075752:0.118430 214.167382:0.216331 214.178642:0.499870 214.187593:0.450921 214.201742:0.067560 214.409656:0.015043 215.091403:0.006763 216.291565:0.014722 219.174746:0.054779 221.171853:0.016303 221.810817:0.014035 221.839079:0.005869 222.899375:0.019856 223.960858:0.006438 227.232766:0.007194 229.895601:0.005117 231.360395:0.004681 240.909208:0.157194 241.153223:0.006476 245.151004:0.018434 246.556854:0.016505 247.092673:0.148676 247.906428:0.044129 248.170592:0.016670 250.178029:0.061182 254.928021:0.186113 256.815458:0.019165 261.074696:0.007663 262.177955:0.552425 266.292422:0.007502 266.575776:0.006438 268.263440:0.291721 270.809448:0.005168 270.938585:0.006288 271.190432:0.006521 272.938338:0.021743 274.176126:0.011762 274.514761:0.006832 274.969869:0.023288 276.193171:0.008758 281.172450:0.020439 286.739103:0.005796 286.894321:0.004785 288.921683:0.019261 290.245394:0.378206 290.881028:0.013767 291.248513:0.006163 292.980872:0.005102 294.990446:0.089010 304.092205:0.011872 305.391328:0.005802 309.005283:0.069956 309.621016:0.010105 310.234937:0.013091 311.044600:0.023038 312.472622:0.006681 312.839280:0.005778 313.973191:0.008224 314.843323:0.008572 315.100292:0.094005 316.901668:0.011747 317.841036:0.106163 318.828882:0.018953 319.836588:1.231555 325.228089:0.018017 327.825290:0.006630 328.832272:0.005098 329.991262:0.007262 331.153401:0.004945 334.843966:0.170654 335.303649:0.818968 335.850605:0.087183 336.839096:1.591119 336.921924:0.005387 337.847030:1.000408 340.918806:0.005749 342.338997:0.008899 345.275614:0.015735 345.420648:0.005223 348.700297:0.014694 349.183433:0.334921 350.947085:0.094555 352.216672:0.005856 354.849519:0.427489 355.011394:0.180822 357.009230:0.027999 358.844115:0.510832 359.217607:0.009194 360.838803:4.023093 361.147138:0.015979 361.841053:0.408061 367.477508:0.005584 369.424854:0.006004 369.836486:0.523268 373.322946:0.017952 374.183577:0.025866 375.180468:0.523084 376.853715:0.058384 378.849350:1.812134 379.851774:0.062083 387.847534:0.176413 390.181427:0.093877 390.226684:0.007245 390.254780:1.081757 390.297857:0.690148 390.336412:0.007223 391.097822:0.007860 391.157842:0.666660 391.193726:2.480531 391.230678:0.233501 391.250842:0.293548 391.300266:0.252835 391.331746:0.152827 392.165943:0.007656 392.195361:0.738046 392.240773:0.108483 392.282992:0.054635 392.311276:0.875601 392.333132:1.127720 392.867022:0.014099 393.115288:0.755684 393.209321:100.000000 393.334690:0.056044 394.117161:0.013418 394.213073:11.163157 394.255401:0.005441 394.304780:0.022087 394.328876:1.041726 407.631410:0.013020
+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004772,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+NH4,Thermo Q Exactive HF,45,50.219187:0.035615 50.403890:0.053475 50.405575:0.050403 50.864766:0.052422 51.353177:0.019236 51.967824:0.040676 52.238972:0.031358 52.660526:0.019986 53.281696:0.072546 53.304135:0.048937 53.307033:0.039956 53.495506:0.042696 54.221948:0.067713 54.355964:0.064455 55.018602:0.075631 55.055032:0.136113 55.139853:0.067291 55.501454:0.101193 57.034298:0.151200 57.070673:1.115161 57.072138:0.028230 57.103128:0.048932 57.409716:0.019854 58.302592:0.077607 58.939505:0.024230 59.464078:0.054385 59.993205:0.076867 60.048520:0.049012 60.244311:0.056869 60.318842:0.061918 60.875071:0.026319 60.981260:0.056665 61.029108:0.058400 61.699373:0.027472 62.019388:0.032783 62.106383:0.067115 62.312551:0.027556 62.982555:0.156381 63.469862:0.040314 63.855475:0.037596 63.862641:0.027372 64.637973:0.047013 64.769096:0.078826 65.135506:0.067607 65.667132:0.024375 66.215372:0.021608 67.054883:0.185828 67.408705:0.025102 67.556513:0.038090 67.972921:0.069961 68.244230:0.025529 68.367924:0.069060 68.954125:0.035206 69.017145:0.040260 69.034262:0.663177 69.070591:1.123556 69.510457:0.026079 69.729143:0.069596 70.033671:0.029271 70.059531:0.024139 70.247607:0.057089 70.831222:0.052335 70.856249:0.075323 71.013632:0.078293 71.086154:0.186476 71.211726:0.064909 71.552987:0.064184 71.722601:0.052455 72.739687:0.045486 72.868811:0.026126 74.736711:0.030851 76.790178:0.023801 78.110214:0.023834 78.183344:0.039147 79.021841:0.106560 79.054892:2.413609 79.388932:0.073536 79.653878:0.075091 80.694217:0.070324 81.019190:0.024026 81.034128:0.364056 81.070556:6.048061 82.073743:0.026693 83.049606:0.023341 83.086193:0.066340 84.421276:0.077317 85.029006:5.270828 85.065395:0.028743 86.853000:0.034834 87.044705:0.094113 89.060418:0.137261 89.412354:0.048108 89.433293:0.029195 89.562452:0.057974 89.802149:0.040385 90.194894:0.026139 90.406444:0.073222 91.039613:0.092034 91.054801:2.167844 91.142539:0.068858 91.338419:0.049196 91.421590:0.032442 91.881936:0.067306 91.977600:0.053607 92.057946:0.068198 92.426162:0.028192 92.653535:0.053297 92.742999:0.048323 93.070450:6.887258 93.281360:0.024288 93.992478:0.029191 95.049705:0.240616 95.086029:0.514656 96.415321:0.042215 96.839114:0.021037 97.028872:0.801920 97.101830:0.090245 97.917935:0.021362 98.671834:0.019865 99.008112:0.082223 99.655526:0.042980 103.054635:1.903927 103.801290:0.020430 103.996295:0.032347 104.343977:0.031571 104.992694:1.239272 105.070382:5.388988 105.073861:0.099530 105.622115:0.024459 105.773499:0.061244 107.049529:0.900833 107.085972:0.159275 108.837515:0.058178 109.065188:0.388001 109.377173:0.026586 110.220297:0.074244 111.091534:0.025271 112.335126:0.026280 113.059977:0.030040 113.197604:0.029809 117.069938:0.040675 117.487307:0.053994 118.666011:0.034027 118.847573:0.066208 118.886169:0.062115 119.049381:0.798458 120.228101:0.024655 120.695142:0.025260 121.065053:52.304084 121.101305:0.151194 122.068360:3.676657 123.080670:0.169854 124.360504:0.061384 124.806147:0.058673 125.756368:0.067075 126.008125:0.027180 126.052568:0.102959 126.195202:0.047269 126.957574:0.030121 127.039212:0.385628 129.012840:0.052388 131.049285:2.563770 132.053064:0.066754 133.064878:0.762054 133.101218:0.031542 137.059428:0.107084 138.768673:0.058174 139.945171:0.022702 140.467429:0.055297 141.394535:0.028068 142.287099:0.058439 142.768166:0.027707 146.406164:0.031457 147.044142:1.050294 148.047359:0.033641 148.176540:0.023232 148.470448:0.078416 149.023394:1.071130 149.059855:100.000000 149.190900:0.029824 150.027231:0.074179 150.063119:9.146777 151.075345:0.166731 152.837221:0.059050 154.333670:0.038879 154.946843:0.027731 157.116503:0.027037 158.632181:0.055419 158.903514:0.024950 159.044139:5.371843 159.629366:0.053529 160.047504:0.091307 160.060252:0.119664 160.445842:0.024868 160.900043:0.058747 161.862200:0.078590 162.045677:0.058737 162.912981:0.022410 163.015852:0.048741 163.951652:0.052117 164.920637:0.804990 166.202922:0.056568 167.013625:0.040948 167.070400:12.302871 168.073638:0.222099 169.368147:0.031102 171.198861:0.053210 171.835498:0.030389 172.111857:0.430027 172.956563:0.029301 173.488753:0.023435 175.015117:0.056671 175.038983:1.191575 176.042110:0.068575 176.428652:0.065192 177.054687:32.046655 178.057985:2.932924 178.195407:0.059130 179.022367:0.090386 179.070211:0.499846 179.248153:0.061305 180.201027:0.075712 183.873449:0.077742 183.964138:0.062472 187.099920:0.071928 193.050677:0.054776 194.267577:0.089211 194.924859:0.434943 195.065315:8.558975 196.068729:0.593563 198.372920:0.071230 203.042643:0.075808 203.634232:0.034727 204.385076:0.031747 207.515010:0.087799 208.770623:0.069123 212.935518:0.174199 214.160356:0.081664 214.165495:0.185104 214.177934:2.338405 214.183632:2.004241 214.940938:0.035942 215.908610:0.090720 216.665941:0.023043 216.793307:0.026610 219.174257:0.036064 219.446441:0.025780 219.512828:0.082543 221.113284:0.027855 221.239530:0.021210 221.401929:0.070327 222.669026:0.035468 222.898513:0.668243 226.410526:0.068115 230.185273:0.050677 230.700597:0.055090 235.581929:0.031249 237.034647:0.030698 240.909276:2.837717 242.483943:0.092441 246.970789:0.042064 250.142477:0.029862 250.513464:0.025500 251.098352:0.034037 252.037987:0.028384 255.454480:0.085278 256.170320:0.058847 257.651588:0.047722 257.825266:0.055062 258.807348:0.027336 260.432902:0.056541 262.178154:0.059748 268.263439:0.540243 269.733806:0.072630 273.351503:0.040682 274.970836:0.027613 278.200437:0.033677 279.074557:0.032834 279.126455:0.024167 279.553382:0.019703 282.309501:0.035016 283.047229:0.062729 288.920733:0.028012 295.920735:0.049880 297.099582:0.074419 304.639964:0.028000 306.932174:0.023567 308.376348:0.084509 309.357506:0.066748 310.850678:0.037587 311.829315:0.033074 312.839009:0.563754 317.840549:0.298019 319.836366:5.109330 320.839019:0.105981 327.825052:0.538164 328.632150:0.036383 328.834217:0.027641 332.400357:0.027939 336.839181:2.318803 337.846846:4.067584 338.844417:0.041476 341.093844:0.024409 344.827663:0.089026 349.183304:0.464497 354.849602:0.128565 360.838794:1.717092 362.298502:0.068820 363.198960:0.031834 364.387730:0.082832 367.842311:0.043720 369.836640:2.286766 375.179949:0.300596 375.586431:0.059739 378.049034:0.031251 378.848916:0.381947 387.847316:0.650265 390.254052:0.454104 391.193947:0.787586 391.229102:0.229624 392.194977:0.094372 392.331189:0.425838 393.209234:97.049725 394.213169:10.997233 401.634864:0.087330 404.450796:0.049664 406.595973:0.031649 407.957759:0.022566
+VF-NPL-QEHF00xxxx_74,VF-NPL-QEHF004773,geniposidic acid,C16H22O10,"InChI=1S/C16H22O10/c17-3-6-1-2-7-8(14(22)23)5-24-15(10(6)7)26-16-13(21)12(20)11(19)9(4-18)25-16/h1,5,7,9-13,15-21H,2-4H2,(H,22,23)/t7-,9-,10-,11-,12+,13-,15+,16+/m1/s1",M+NH4,Thermo Q Exactive HF,65,50.015966:0.082126 50.123059:0.031558 50.134166:0.080586 50.615038:0.085438 51.222691:0.042459 51.411971:0.042638 52.292326:0.080213 52.466225:0.033750 53.039450:3.443839 53.318916:0.111091 53.594838:0.034620 53.680541:0.087208 54.163787:0.042511 55.015012:0.076829 55.018689:2.739466 55.055061:1.623286 56.050355:0.057196 56.450597:0.038184 56.769158:0.087666 56.965578:0.499194 57.034320:0.215740 57.070708:2.077643 57.822880:0.043535 57.890777:0.102156 58.066036:0.292423 58.680137:0.037686 59.186162:0.040456 60.210697:0.082626 60.352594:0.065668 60.833961:0.112892 61.011492:0.185654 61.029197:0.575164 61.420693:0.042440 61.522817:0.091704 61.575661:0.039053 61.637171:0.047610 62.019405:0.040241 62.060928:0.123322 62.208289:0.045824 62.887008:0.072977 62.982425:0.058877 62.989620:0.073699 63.248322:0.072984 63.303196:0.026360 63.705885:0.038366 63.856826:0.031923 64.185771:0.068837 65.425721:0.050233 66.727154:0.082489 67.055021:1.265388 67.133989:0.034391 67.261288:0.073477 68.125099:0.058479 68.250951:0.059789 68.523337:0.038880 68.587340:0.027239 68.693210:0.064564 68.804395:0.080214 69.034274:2.507805 69.070670:1.092955 69.438427:0.088492 70.065719:0.079058 70.274010:0.113878 70.777575:0.051582 71.013530:1.185648 71.049750:0.098955 71.086288:0.084789 71.115556:0.096697 71.452016:0.026702 72.087945:0.104304 72.327517:0.027962 72.535635:0.047931 72.592069:0.050749 72.667125:0.025942 72.739279:0.034885 73.029126:0.145923 73.900244:0.089198 74.086836:0.074097 74.157037:0.029069 74.407339:0.082704 74.601451:0.041165 74.611380:0.052818 74.937692:0.048957 75.139822:0.048198 75.481243:0.102337 76.570640:0.085983 77.039352:0.266250 78.047932:0.039214 78.899346:0.078826 79.022004:0.035870 79.054902:8.092643 80.671531:0.031106 81.034147:3.763689 81.070520:12.997345 81.167899:0.040900 81.424478:0.036521 82.037761:0.096420 82.073987:0.077989 82.509402:0.032126 82.541264:0.060198 83.049554:0.065434 83.579641:0.036697 84.111659:0.084437 84.122547:0.057384 84.241187:0.048509 85.029041:7.332499 85.508622:0.086397 85.658271:0.039010 86.255973:0.066718 87.201803:0.041098 88.532321:0.032037 89.795359:0.099994 90.824329:0.057795 90.963976:0.084398 91.054788:23.177184 92.058150:1.187781 93.070435:29.110100 93.090628:0.115912 93.779095:0.095388 94.073813:1.131137 95.049707:11.378308 95.086150:1.222347 97.028891:1.098560 97.041017:0.073611 97.467940:0.032662 97.895219:0.063778 98.299783:0.067868 98.706553:0.098954 98.779155:0.030834 98.975753:0.147279 100.462481:0.074425 101.489918:0.041007 102.055969:0.068771 102.639334:0.093219 103.029291:0.085701 103.054713:14.486120 104.058056:0.264283 104.871612:0.044572 105.034181:0.046002 105.045194:3.688655 105.070380:8.326169 107.049680:1.863392 107.086218:0.056994 107.248806:0.060478 107.419915:0.031231 107.577171:0.044635 107.762717:0.044758 108.282934:0.064892 108.913658:0.040430 109.028599:0.131442 109.065220:0.518014 109.101082:0.037395 109.367725:0.107060 109.849140:0.043027 109.975232:0.029625 111.998616:0.097490 112.344458:0.083435 114.190178:0.099763 115.054459:0.040397 115.725417:0.038780 115.774204:0.059260 116.030943:0.044225 116.986314:0.101738 117.070265:0.142387 117.973501:0.132836 118.722868:0.083799 118.969767:0.059938 119.049473:2.364206 119.086155:0.117884 119.625205:0.113344 120.081126:0.116759 121.065088:100.000000 122.068426:7.696787 123.939437:0.040113 125.682974:0.058880 128.198223:0.045346 129.447734:0.048467 131.049315:6.514526 131.067732:0.093407 131.238742:0.037909 131.339558:0.103872 132.053087:0.039315 132.065945:0.174990 133.064916:0.450021 133.753356:0.054593 134.612685:0.096151 134.977407:0.106969 134.996675:0.041124 135.645982:0.057259 136.630037:0.072192 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58.358226:0.029422 58.425045:0.019941 59.003246:0.037145 59.003878:0.031861 59.012482:100.000000 59.020767:0.131749 59.461485:0.014682 59.877748:0.031179 59.966088:0.012779 60.015849:2.157602 60.031497:0.029111 60.290783:0.015669 60.845293:0.020087 60.905575:0.033300 61.016714:0.106579 61.987018:13.633483 63.220354:0.019930 63.925737:0.014374 63.961104:14.978412 64.159316:0.015854 64.222226:0.021072 64.343769:0.016032 64.514775:0.015864 64.829263:0.020239 64.854886:0.017866 64.968958:0.041182 65.038327:1.983127 65.668438:0.031575 65.908248:0.016553 65.956913:0.206238 65.997178:0.491789 66.451365:0.022213 67.017583:4.825895 67.606254:0.016123 68.293989:0.030943 68.580268:0.022065 68.996853:9.137858 69.033251:27.831418 69.504372:0.021313 70.036637:0.626035 70.081025:0.015125 70.578732:0.022002 71.012523:20.924826 71.048885:0.107531 71.406019:0.016620 72.015881:0.369856 72.448489:0.018637 72.744103:0.021855 72.991812:2.439169 72.993832:0.022117 73.019328:0.023329 73.028176:0.404100 73.417942:0.018008 74.023429:0.275690 74.251733:0.033901 74.286870:0.016368 74.540137:0.016100 74.613122:0.022744 74.989459:4.165547 75.007413:0.445708 75.489861:0.021723 75.624143:0.025267 75.961028:0.020253 75.988954:0.027689 76.070483:0.015646 76.968748:0.099702 77.469839:0.022126 78.008379:0.034096 78.379895:0.027357 78.957745:2.002686 78.984629:9.119080 79.054070:0.037726 79.383051:0.014804 79.763325:0.015509 79.956058:28.009111 80.025298:0.087347 80.173551:0.026377 80.184583:0.028089 80.434516:0.021756 80.525248:0.020382 80.587815:0.030553 80.955424:0.032307 80.963887:5.508896 80.980369:0.099880 81.033260:1.246223 81.489790:0.030927 81.951855:0.950860 82.118201:0.024352 82.252205:0.023833 82.785900:0.020084 82.959700:0.016702 83.012549:1.146598 83.048939:0.627546 83.053875:0.031226 83.262310:0.023601 83.422024:0.019249 83.823960:0.033850 84.020415:0.097560 84.803317:0.023112 85.028198:6.173408 85.871182:0.023806 85.999962:0.028177 86.023384:0.106213 86.031492:0.029625 86.183441:0.020529 86.969983:0.030540 87.007467:1.496444 87.094406:0.019076 87.353727:0.027082 87.924009:0.211345 88.721809:0.025193 89.023123:2.240798 89.038392:0.023339 89.041546:0.479148 89.883011:0.023248 89.924379:0.245719 89.939888:0.045637 89.943138:0.025088 90.113718:0.017271 90.262605:0.015659 90.851191:0.024394 90.932248:0.330855 91.017701:0.023769 91.020829:1.246174 91.054004:0.382199 91.428081:0.018743 91.726392:0.029681 92.590153:0.031792 92.856370:0.018754 92.884632:0.031710 92.927678:0.022861 93.000070:3.527913 93.017784:0.015239 93.033299:20.470611 93.069673:0.079523 93.174333:0.019019 93.361441:0.018685 93.658544:0.025904 93.971746:0.015038 94.036649:1.136561 94.600534:0.024116 94.979523:19.136463 95.012578:2.500932 95.048948:6.525987 95.452696:0.028508 95.456373:0.028213 95.950992:0.982846 95.974284:0.020624 96.052152:0.051219 96.958826:21.271506 96.975367:0.322772 97.028198:2.209088 97.064518:0.017376 97.930066:0.068999 97.958215:0.030264 98.606577:0.016437 98.763632:0.029036 98.954648:0.404903 99.007460:0.512172 99.398610:0.021384 99.924508:5.778497 99.928054:0.020465 100.756362:0.019912 100.798665:0.032489 100.924619:0.278393 100.932354:2.101996 101.023117:1.052217 101.033232:0.022826 101.922921:0.055989 101.932294:0.018211 102.046561:0.035402 102.050656:0.023385 102.485598:0.028218 103.054165:0.283239 103.918996:1.275414 104.912856:0.016254 104.926819:0.111534 105.033560:0.014942 105.069692:0.355719 105.081729:0.030975 105.427148:0.022716 105.754944:0.031787 106.041161:3.313902 107.012530:0.019580 107.045056:0.037979 107.048986:1.826343 107.085370:0.018100 107.582642:0.024984 107.925225:0.021464 108.020480:0.726080 108.044125:0.017554 108.363179:0.016304 108.995317:0.050023 109.028303:0.313282 109.064459:0.124159 109.078440:0.015548 109.623225:0.015314 109.630415:0.033405 109.666167:0.027654 110.956879:0.053934 110.984476:0.014199 111.007522:1.123038 111.043859:0.117795 112.043060:0.013398 113.023184:1.220350 113.067367:0.019373 113.925102:0.060886 114.347234:0.015713 114.748008:0.017848 114.819013:0.014217 114.947888:0.239311 115.054053:0.040105 115.379538:0.045809 115.919491:5.428841 116.401802:0.015733 116.919698:0.277672 116.927346:2.927619 116.932071:0.046736 117.033313:0.195764 117.069814:0.142141 117.598732:0.023783 117.917842:0.016629 117.927562:0.162613 118.279100:0.024332 118.464427:0.025496 118.726571:0.018598 118.925765:0.018116 119.012958:0.022272 119.049014:3.609988 119.433830:0.021299 119.580912:0.031292 120.052267:0.038198 120.147740:0.018209 121.023742:0.013394 121.028262:2.104942 121.060435:0.041667 121.064655:4.302958 121.682061:0.025351 121.922782:0.018846 122.068097:0.045637 122.363633:0.030110 122.974607:0.315071 123.007549:0.034604 123.043993:1.731978 123.927647:0.029291 123.944897:0.023330 124.047626:0.024026 124.119820:0.015276 124.685263:0.022443 124.770565:0.026503 124.990379:0.147571 124.995971:0.012179 125.303400:0.020437 125.889848:0.012134 126.928741:0.035701 127.111890:0.141861 127.417787:0.031934 127.771004:0.026495 127.819602:0.020994 127.825509:0.065006 128.373341:0.023056 128.538561:0.027347 129.018263:0.028139 129.662207:0.025723 130.041289:0.956084 130.565487:0.044198 130.942691:0.843055 131.049138:0.237121 132.031627:0.013291 132.057002:0.024449 132.137616:0.026015 132.553645:0.020426 132.790064:0.020943 132.922239:0.013811 132.980675:0.017707 133.028690:0.043788 133.064803:0.679731 134.036195:0.839369 134.428454:0.024440 135.044178:0.708360 135.080455:0.134106 136.075901:0.014264 137.023139:0.019505 137.060500:0.031035 139.002539:0.062988 139.039118:0.018140 139.075533:0.051610 141.018280:5.887897 141.803978:0.018726 141.922651:0.026964 142.021792:0.021096 142.348587:0.027192 142.943020:0.152688 143.049267:0.928324 143.928805:0.025196 145.028649:0.130215 145.064927:1.027323 146.035168:0.029510 147.044215:1.677617 147.080947:0.030233 147.861754:0.015649 147.920697:0.016989 147.945481:0.134138 149.008619:2.857589 149.014967:0.024694 149.059848:0.791416 150.007938:0.041892 150.031199:0.019582 150.820655:0.012955 150.896365:0.026032 150.987846:0.208545 151.037825:0.015972 152.162840:0.032110 152.785759:0.019878 152.916563:0.099649 152.967179:0.076813 153.018683:0.031880 153.464212:0.016460 155.987921:0.030018 156.894132:0.048807 157.065067:0.075955 158.036464:0.219900 159.043718:0.045147 159.892562:0.044174 160.891981:0.052404 161.023577:0.339352 161.059761:0.160845 161.294690:0.033072 162.892545:0.262770 163.039792:0.021568 163.075599:0.025167 163.167392:0.016690 164.930622:0.129533 165.054880:0.040522 165.176393:0.030282 165.285965:0.028541 165.357938:0.017590 165.956592:0.013905 166.436374:0.030444 166.660035:0.024727 170.003502:0.087413 170.167409:0.032103 170.388358:0.020914 170.889365:0.054368 171.044461:0.017174 171.886895:0.016402 172.312678:0.042053 173.060906:0.023196 173.117640:0.038584 174.031444:0.030814 174.131365:0.026607 174.991610:0.138596 175.039100:0.053259 176.034641:0.073005 176.271163:0.031507 177.054412:0.036922 177.269537:0.018566 177.451340:0.024767 178.315413:0.035556 179.472173:0.016453 179.881732:0.021836 183.011355:9.359119 184.000884:0.318844 184.015035:0.167251 184.998976:0.031210 185.007204:0.020603 185.060638:0.020132 185.892432:0.020836 187.039224:0.027020 187.052314:0.017331 194.820635:0.018121 196.477210:0.023554 197.027136:3.943346 199.006668:0.040287 199.850342:0.367826 199.876307:0.095043 200.024240:0.039420 200.759485:0.033303 200.850815:0.031970 201.054801:0.015976 202.902266:0.017838 203.658353:0.027901 204.016802:0.106371 205.860341:0.018195 206.996346:0.161833 208.084751:0.021856 208.975727:4.555054 209.976245:0.279944 210.954851:0.111187 210.972890:0.040716 211.024835:0.092602 211.042691:0.494908 212.443494:0.022205 212.774768:0.022316 214.112610:0.021823 216.183153:0.020334 216.501714:0.034185 216.656504:0.022561 218.687330:0.025521 220.019386:0.041574 220.507366:0.030912 220.889907:0.098946 220.904081:0.087737 220.923120:0.110317 220.939031:0.205320 220.953277:0.099630 220.972490:0.137137 221.155925:0.040119 223.027859:2.747732 224.028085:0.070116 225.007523:0.442121 225.058678:0.695722 226.477343:0.029261 226.875449:0.019494 229.180288:0.079931 233.027547:0.049782 235.353177:0.023835 238.762514:0.015450 239.074590:1.814884 242.962166:0.022458 243.102208:0.021575 246.720513:0.013017 250.895942:0.033140 250.942275:0.038878 253.090478:1.386827 253.454830:0.027899 254.093159:0.018537 257.708354:0.023847 260.052536:0.031814 261.016735:0.025666 266.963840:1.650088 267.106282:0.070623 267.964163:0.059238 268.943341:2.635434 268.959482:0.022234 269.155182:0.022939 269.701494:0.015296 269.943882:0.090356 270.185033:0.030366 270.922826:0.722740 272.901542:0.098465 274.881846:0.026220 278.928209:0.020920 279.485894:0.034719 280.906539:0.073036 280.941419:0.023429 282.167065:0.017980 282.886341:0.021902 282.995121:0.664690 283.994613:0.017808 284.094953:0.032234 284.973005:0.038896 286.384848:0.015024 286.983808:0.018930 287.805805:0.032332 287.885997:0.037297 289.054408:0.066883 289.141890:0.017125 291.344982:0.030532 292.005424:0.021400 298.917013:0.109838 300.895693:0.079386 303.625255:0.023614 304.390454:0.022561 309.153116:0.028771 309.820862:0.044423 311.168772:0.026199 312.003854:0.018367 312.170882:0.028238 337.183429:0.016143 338.022350:0.029378 342.868772:0.016829 342.962051:0.064106 345.368151:0.036152 364.343700:0.019476 370.793868:0.027413 372.061941:0.018111 376.553722:0.025230 379.748082:0.031845 381.696889:0.025008 386.356340:0.032556 400.291999:0.025033 407.061422:0.015129 412.917847:0.018043 417.254447:0.022689
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MS2_annotations.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,158 @@
+id,name,formula,adduct,m/z,charge,RT range,ppm,isotope pattern score,fragmentation pattern score,prior,post,peak_id
+C00148,L-Proline,C5H10NO2,M+H,116.07060453364,1,35;55,-0.5232473824191379,,0.9997594969319,0.3180838666706876,,1
+C00763,D-Proline,C5H10NO2,M+H,116.07060453364,1,,-0.5232473824191379,,0.7,0.3180838666706876,,1
+C18170,3-Acetamidopropanal,C5H10NO2,M+H,116.07060453364,1,500;560,-0.5232473824191379,,0.7,0.3180838666706876,,1
+Unknown,Unknown,,,,,,3.0,,0.7,0.04574839998793704,,1
+C00148,L-Proline,C10H19N2O4,2M+H,231.13393306728,1,35;55,-1.1247473555160623,,,0.3145378636708285,,501
+C00763,D-Proline,C10H19N2O4,2M+H,231.13393306728,1,,-1.1247473555160623,,,0.3145378636708285,,501
+C18170,3-Acetamidopropanal,C10H19N2O4,2M+H,231.13393306728,1,500;560,-1.1247473555160623,,,0.3145378636708285,,501
+Unknown,Unknown,,,,,,3.0,,,0.05638640898751447,,501
+Unknown,Unknown,,,,,,3.0,,,1,1,2
+Unknown,Unknown,,,,,,3.0,,,1,1,2407
+C00183,L-Valine,C5H12NO2,M+H,118.0862545981,1,40;70,-2.171278112469359,,0.9993295149795818,0.10654352762185176,,3
+C00431,5-Aminopentanoate,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.8402482064054789,0.10654352762185176,,3
+C00719,Betaine,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.23090277832417302,0.10654352762185176,,3
+C01799,D-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.7,0.10654352762185176,,3
+C01826,L-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.9983086298179682,0.10654352762185176,,3
+C03571,2-Amino-2-methylbutanoate,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.7,0.10654352762185176,,3
+C06417,D-Valine,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.7,0.10654352762185176,,3
+C07457,Amyl nitrite,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.7,0.10654352762185176,,3
+C15987,4-Methylaminobutyrate,C5H12NO2,M+H,118.0862545981,1,,-2.171278112469359,,0.7,0.10654352762185176,,3
+Unknown,Unknown,,,,,,3.0,,0.7,0.0411082514033339,,3
+Unknown,Unknown,,,,,,3.0,,,1,1,2015
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-1.2505435832647704,,0.9992403518152405,0.45629284154229943,,4
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-1.2505435832647704,,0.7,0.45629284154229943,,4
+Unknown,Unknown,,,,,,3.0,,0.7,0.08741431691540112,,4
+C00079,L-Phenylalanine,C18H23N2O4,2M+H,331.16523319619995,1,120;160,-0.9418144439136233,,,0.2401062666341187,,999
+C02265,D-Phenylalanine,C18H23N2O4,2M+H,331.16523319619995,1,,-0.9418144439136233,,,0.2401062666341187,,999
+C03263,Coproporphyrinogen III,C36H46N4O8,M+2H,331.16523319619995,2,,-0.9418144439136233,,,0.2401062666341187,,999
+C05768,Coproporphyrinogen I,C36H46N4O8,M+2H,331.16523319619995,2,,-0.9418144439136233,,,0.2401062666341187,,999
+Unknown,Unknown,,,,,,3.0,,,0.03957493346352525,,999
+Unknown,Unknown,,,,,,3.0,,,1,1,2582
+Unknown,Unknown,,,,,,3.0,,,1,1,2954
+C01957,Secologanate,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386056,4398
+C09800,Swertiamarin,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386056,4398
+C11673,Geniposidic acid,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386056,4398
+C16963,Gardoside,C16H24O10,M+2H,188.06792445238,2,,-0.7441586885047832,,,0.20278817258173704,0.19886533036386056,4398
+C00079,L-Phenylalanine,C9H11NNaO2,M+Na,188.0681965981,1,120;160,-2.1912163112556495,,,0.07890449704227288,0.09672265812976097,4398
+C02265,D-Phenylalanine,C9H11NNaO2,M+Na,188.0681965981,1,,-2.1912163112556495,,,0.07890449704227288,0.07737812650380878,4398
+Unknown,Unknown,,,,,,3.0,,,0.03103831558850615,0.030437893910988004,4398
+C00123,L-Leucine,C6H14NO2,M+H,132.10190466256,1,70;110,-1.2116597442118062,,,0.08938513749355873,,5
+C00407,L-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C01570,D-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C01933,L-Norleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C02378,6-Aminohexanoate,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C02486,(3R)-beta-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C06418,D-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C08263,beta-Alaninebetaine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C16647,"N,N-Diethylglycine",C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C21092,D-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+C21096,L-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.2116597442118062,,,0.08938513749355873,,5
+Unknown,Unknown,,,,,,3.0,,,0.016763487570854132,,5
+Unknown,Unknown,,,,,,3.0,,,1,1,2169
+C00123,L-Leucine,C12H27N2O4,2M+H,263.19653332512,1,70;110,-0.6839950273744673,,,0.08968478708873068,0.10964755446662842,2262
+C00407,L-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C01570,D-Leucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C01933,L-Norleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C02378,6-Aminohexanoate,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C02486,(3R)-beta-Leucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C06418,D-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C08263,beta-Alaninebetaine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C16647,"N,N-Diethylglycine",C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C21092,D-allo-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+C21096,L-allo-Isoleucine,C12H27N2O4,2M+H,263.19653332512,1,,-0.6839950273744673,,,0.08968478708873068,0.08771804357330275,2262
+Unknown,Unknown,,,,,,3.0,,,0.01346734202396253,0.013172009800343897,2262
+C01877,4-Oxoproline,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C01879,5-Oxoproline,C5H8NO3,M+H,130.04986908874997,1,50;90,-1.0894955217565612,,,0.10897775351467592,,6
+C02237,5-Oxo-D-proline,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+C05131,(1-Ribosylimidazole)-4-acetate,C10H16N2O6,M+2H,130.04986908874997,2,,-1.0894955217565612,,,0.10897775351467592,,6
+C16744,Spongothymidine,C10H16N2O6,M+2H,130.04986908874997,2,,-1.0894955217565612,,,0.10897775351467592,,6
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,C10H16N2O6,M+2H,130.04986908874997,2,,-1.0894955217565612,,,0.10897775351467592,,6
+C22141,L-beta-Ethynylserine,C5H8NO3,M+H,130.04986908874997,1,,-1.0894955217565612,,,0.10897775351467592,,6
+Unknown,Unknown,,,,,,3.0,,,0.019200218367916987,,6
+C01877,4-Oxoproline,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C01879,5-Oxoproline,C10H15N2O6,2M+H,259.09246217749995,1,50;90,-0.5572431507691273,,,0.10934932622184204,,33
+C02237,5-Oxo-D-proline,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C05131,(1-Ribosylimidazole)-4-acetate,C10H15N2O6,M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C16744,Spongothymidine,C10H15N2O6,M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,C10H15N2O6,M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+C22141,L-beta-Ethynylserine,C10H15N2O6,2M+H,259.09246217749995,1,,-0.5572431507691273,,,0.10934932622184204,,33
+Unknown,Unknown,,,,,,3.0,,,0.01585606400342151,,33
+C00183,L-Valine,C5H12NO2,M+H,118.0862545981,1,40;70,-1.4319880038362247,,0.22472027286945603,0.10853687713038368,,8
+C00431,5-Aminopentanoate,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.7166018971418139,0.10853687713038368,,8
+C00719,Betaine,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.9998190306618044,0.10853687713038368,,8
+C01799,D-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.7,0.10853687713038368,,8
+C01826,L-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.2683728290855617,0.10853687713038368,,8
+C03571,2-Amino-2-methylbutanoate,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.7,0.10853687713038368,,8
+C06417,D-Valine,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.7,0.10853687713038368,,8
+C07457,Amyl nitrite,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.7,0.10853687713038368,,8
+C15987,4-Methylaminobutyrate,C5H12NO2,M+H,118.0862545981,1,,-1.4319880038362247,,0.7,0.10853687713038368,,8
+Unknown,Unknown,,,,,,3.0,,0.7,0.02316810582654676,,8
+Unknown,Unknown,,,,,,3.0,,,1,1,3044
+C08307,Hordatine A,C28H40N8O4,M+2H,276.15807686923,2,,-0.6031662439992381,,,0.8001426388917695,,9
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",C14H23NNaO3,M+Na,276.15701160443,1,,3.2542920594118643,,,0.08245153058258288,,9
+Unknown,Unknown,,,,,,3.0,,,0.11740583052564758,,9
+C08307,Hordatine A,C28H39N8O4,M+H,551.3088777384601,1,,-1.0501163385127417,,,0.8525755147970528,0.8525755147970528,1330
+Unknown,Unknown,,,,,,3.0,,,0.1474244852029472,0.1474244852029472,1330
+C00082,L-Tyrosine,C9H12NO3,M+H,182.08116921767,1,50;90,-1.127066960830867,,,0.12225722517881775,,10
+C03290,L-threo-3-Phenylserine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C06420,D-Tyrosine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C19579,gamma-Hydroxy-3-pyridinebutanoate,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C19712,N-Hydroxy-L-phenylalanine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C20807,3-Hydroxy-L-phenylalanine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+C21308,(S)-beta-Tyrosine,C9H12NO3,M+H,182.08116921767,1,,-1.127066960830867,,,0.12225722517881775,,10
+Unknown,Unknown,,,,,,3.0,,,0.021942198569457998,,10
+C00123,L-Leucine,C6H14NO2,M+H,132.10190466256,1,70;110,-1.1934919516598708,,,0.08939961938581567,,19
+C00407,L-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C01570,D-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C01933,L-Norleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C02378,6-Aminohexanoate,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C02486,(3R)-beta-Leucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C06418,D-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C08263,beta-Alaninebetaine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C16647,"N,N-Diethylglycine",C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C21092,D-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+C21096,L-allo-Isoleucine,C6H14NO2,M+H,132.10190466256,1,,-1.1934919516598708,,,0.08939961938581567,,19
+Unknown,Unknown,,,,,,3.0,,,0.01660418675602744,,19
+C00763,D-Proline,C5H10NO2,M+H,116.07060453364,1,,-0.7084794667090921,,0.7,0.31732884449735516,0.4834012141941518,90
+C18170,3-Acetamidopropanal,C5H10NO2,M+H,116.07060453364,1,500;560,-0.7084794667090921,,0.7,0.31732884449735516,0.2417006070970759,90
+C00148,L-Proline,C5H10NO2,M+H,116.07060453364,1,35;55,-0.7084794667090921,,0.5843178670387522,0.31732884449735516,0.2017571188584784,90
+Unknown,Unknown,,,,,,3.0,,0.7,0.048013466507934414,0.07314105985029414,90
+C00183,L-Valine,C5H12NO2,M+H,118.0862545981,1,40;70,-1.168621195337573,,0.8378574559502331,0.10889306818646385,0.14423999689377573,598
+C00431,5-Aminopentanoate,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.9997922884476437,0.10889306818646385,0.13769410112039374,598
+C01826,L-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.861580765637193,0.10889306818646385,0.11865923596113684,598
+C00719,Betaine,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.7239471642986,0.10889306818646385,0.09970396371183239,598
+C01799,D-Norvaline,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.7,0.10889306818646385,0.09640589540246598,598
+C03571,2-Amino-2-methylbutanoate,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.7,0.10889306818646385,0.09640589540246598,598
+C06417,D-Valine,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.7,0.10889306818646385,0.09640589540246598,598
+C07457,Amyl nitrite,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.7,0.10889306818646385,0.09640589540246598,598
+C15987,4-Methylaminobutyrate,C5H12NO2,M+H,118.0862545981,1,,-1.168621195337573,,0.7,0.10889306818646385,0.09640589540246598,598
+Unknown,Unknown,,,,,,3.0,,0.7,0.019962386321825242,0.017673225300531382,598
+C00763,D-Proline,C5H10NO2,M+H,116.07060453364,1,,-0.6585098810914435,,0.7,0.31755854037471093,0.532711822955675,992
+C18170,3-Acetamidopropanal,C5H10NO2,M+H,116.07060453364,1,500;560,-0.6585098810914435,,0.7,0.31755854037471093,0.2663559114778375,992
+C00148,L-Proline,C5H10NO2,M+H,116.07060453364,1,35;55,-0.6585098810914435,,0.31942660687310853,0.31755854037471093,0.12154452146279955,992
+Unknown,Unknown,,,,,,3.0,,0.7,0.04732437887586711,0.07938774410368793,992
+Unknown,Unknown,,,,,,3.0,,,1,1,2759
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-0.8260653495714844,,0.7,0.46350041197047365,0.8520902975531525,3460
+Unknown,Unknown,,,,,,3.0,,0.7,0.07299917605905273,0.13420028988724103,3460
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-0.8260653495714844,,0.02252481648783465,0.46350041197047365,0.013709412559606561,3460
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-0.9440763195286457,,0.7,0.46189826833360753,0.8579058992719889,3512
+Unknown,Unknown,,,,,,3.0,,0.7,0.07620346333278501,0.1415363624852028,3512
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-0.9440763195286457,,0.0009101622224469209,0.46189826833360753,0.0005577382428083698,3512
+C00082,L-Tyrosine,C18H23N2O6,2M+H,363.15506243534,1,50;90,-0.7813063051271507,,,0.12262419566264932,0.1487210449495498,3849
+C03290,L-threo-3-Phenylserine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+C06420,D-Tyrosine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+C19579,gamma-Hydroxy-3-pyridinebutanoate,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+C19712,N-Hydroxy-L-phenylalanine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+C20807,3-Hydroxy-L-phenylalanine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+C21308,(S)-beta-Tyrosine,C18H23N2O6,2M+H,363.15506243534,1,,-0.7813063051271507,,,0.12262419566264932,0.11897683595963986,3849
+Unknown,Unknown,,,,,,3.0,,,0.019006434698805603,0.018441103332971248,3849
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,,-1.104836161281323,,0.7,0.45924063672251225,0.8447405025796267,3897
+Unknown,Unknown,,,,,,3.0,,0.7,0.08151872655497557,0.14994790210891099,3897
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.08625459809997,1,120;160,-1.104836161281323,,0.008802979629056072,0.45924063672251225,0.005311595311462173,3897
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MS2_fragmentation_data.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,14 @@
+id,spectrum,ev
+1,51.3066132836457:0.884272376680125 59.9653224110774:0.166663227329473 70.0660655040174:100 70.0850069390593:1.00611899777559 78.0933845254339:0.481097166243338 93.0520161150226:0.029649090172798 110.270322106491:1.0921492738387 115.999010107813:0.989974707817183 116.027792798298:0.251273484648731 116.070742032373:47.3219101599618 117.073847213981:1.49470646616115 123.482225727083:0.380234131070709,35
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MS2_fragmentation_data.tsv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,14 @@
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215.143187153572:9.42437877836737 215.197658905046:1.22506965646728 215.206854195699:0.935252089040873 215.212381309828:1.27447506469765 216.146025253964:1.94871829509553 217.122709973588:2.82644151626009 217.159708569146:1.34449781697203 219.137870800624:4.24791062996558 220.13087659312:0.93389249652413 221.153590848742:1.65750513580378 223.111712712311:2.96112015139161 223.147831273784:1.34201812579944 224.152026171339:1.67922247699858 225.163597906606:4.7516718855187 226.167539853613:0.094882472760319 227.106405172056:3.07598746407454 227.143291098912:2.3501001241357 227.179164175519:4.0083515667083 227.505733855954:0.0326512957079435 228.368664790707:0.416780909205389 229.122508552485:0.0347166722390016 233.13287337508:0.0236027004762381 233.154207131555:7.39711891561718 234.145934028723:0.230518500258709 234.156999394376:0.949505385723783 235.148452948032:0.932207187237675 236.155271880051:2.67998488255742 237.127469385712:0.450533134121631 237.163699606078:2.32783527310192 237.924444457135:1.27146512002802 237.938524073098:0.353539804849902 239.143246674036:0.285333017938545 239.180018419237:0.681074396073314 240.267810770541:3.44176726084169 241.121692950247:4.87355055993669 241.158702280327:3.70290286413885 241.195813626386:7.11705646997989 241.271907018491:0.934292755406609 242.162581185984:1.7700769693132 242.198872081775:0.476083960001657 243.13820688391:0.12378887208942 245.117417843091:0.306093444997643 246.139915898847:0.00964640636584191 249.419721241162:0.337860956150346 251.143132248766:1.79197557289179 251.179159062514:10.7233540763575 252.182530849672:1.86245569819415 253.158428653455:2.05801902501252 255.137254737796:1.01550447153921 255.175012912711:3.48882615136568 256.177816736954:0.758673672763758 256.263633144853:1.34469560165679 257.153282536302:0.882712204472674 259.168897535233:0.0460792216143859 259.205337552569:0.564647296864154 261.031017493396:0.0186510552930597 261.16331635529:1.82077922937701 265.15850337575:0.431476960494877 267.174743309758:0.982423198808772 268.143467397255:0.350443682594747 268.177480861444:0.977417612081246 269.189832543572:42.4262250561634 269.502950985191:0.131943587148066 270.193146347964:9.40146110725397 271.169408509102:2.67852052383876 271.246065956847:1.08749171284156 273.184277161744:0.399676640330587 273.220613069964:0.283877765949673 274.97002641631:0.0289175225153029 276.909786016267:0.900125946582346 279.173697860577:6.30471804012134 280.177931533478:0.684923539980046 282.817991253003:0.0276541807474486 283.168910644151:0.598046041397736 285.204021312885:1.10403140934747 286.187788062307:0.0313416641866809 287.200782658032:0.493574362523094 297.184035118814:27.5798253910538 298.188680872316:5.98948911802382 299.191515189158:0.726664400453241 301.178904401273:0.744859065391576 303.141082627213:0.913833429299177 304.978626498803:0.234843634597634 314.2086119686:1.55701580032134 314.872913729283:1.83311804232856 315.195363338946:9.65326836045561 315.438668636781:0.895363149747874 316.198604507219:2.0438517653717 316.225392232958:0.0858528123626529 316.263124050379:0.60352001092979 317.283893395218:0.161470558595664 323.414992738022:2.19874610356939 327.647774018751:0.944718209920343 331.208683302558:1.60167835390214 332.187347841191:0.200437737894884 332.218868989175:5.54391414002642 332.256889668477:0.541218605014833 332.295891066681:0.830124696156177 332.331289756333:5.79196165763617 333.115262909726:1.18288989721991 333.186033605622:4.74093824894412 333.223861064453:0.430324137659868 333.245103661716:1.32233452040152 333.333959798719:0.574220911532656 334.194553065249:0.586944963562026 334.23560818811:6.5727527554243 334.312377470243:0.382039590606061 334.335824302158:0.48332745855737 335.147747255185:0.0319194199308941 335.167032178466:2.28950301389653 335.188557685502:0.611641363720875 335.21869552541:0.323436300037653 335.23866664578:2.03257037462065 344.810731391444:0.346666792987931	35
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adducts.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,64 @@
+name,calc,Charge,Mult,Mass,Ion_mode,Formula_add,Formula_ded,Multi
+M+H,M+1.007276,1,1,1.007276,positive,H1,FALSE,1
+M+NH4,M+18.033823,1,1,18.033823,positive,N1H4,FALSE,1
+M+Na,M+22.989218,1,1,22.989218,positive,Na1,FALSE,1
+M+K,M+38.963158,1,1,38.963158,positive,K1,FALSE,1
+M+,M-0.00054858,1,1,-0.00054858,positive,FALSE,FALSE,1
+M-H,M-1.007276,-1,1,-1.007276,negative,FALSE,H1,1
+M-2H,M/2-1.007276,-2,1,-1.007276,negative,FALSE,H2,1
+M-3H,M/3-1.007276,-3,1,-1.007276,negative,FALSE,H3,1
+M+FA-H,M+44.998201,-1,1,44.998201,negative,C1O2H2,H1,1
+M+Hac-H,M+59.013851,-1,1,59.013851,negative,C2O2H4,H1,1
+M-,M+0.00054858,-1,1,0.00054858,negative,FALSE,FALSE,1
+M+3H,M/3+1.007276,3,1,1.007276,positive,H3,FALSE,1
+M+2H+Na,M/3+8.334590,3,1,8.33459,positive,H2Na1,FALSE,1
+M+H+2Na,M/3+15.7661904,3,1,15.76619,positive,H1Na2,FALSE,1
+M+3Na,M/3+22.989218,3,1,22.989218,positive,Na3,FALSE,1
+M+2H,M/2+1.007276,2,1,1.007276,positive,H2,FALSE,1
+M+H+NH4,M/2+9.520550,2,1,9.52055,positive,H1N1H4,FALSE,1
+M+H+Na,M/2+11.998247,2,1,11.998247,positive,H1Na1,FALSE,1
+M+H+K,M/2+19.985217,2,1,19.985217,positive,H1K1,FALSE,1
+M+ACN+2H,M/2+21.520550,2,1,21.52055,positive,C2H5N1,FALSE,1
+M+2Na,M/2+22.989218,2,1,22.989218,positive,Na2,FALSE,1
+M+2ACN+2H,M/2+42.033823,2,1,42.033823,positive,C4H8N2,FALSE,1
+M+3ACN+2H,M/2+62.547097,2,1,62.547097,positive,C6H11N3,FALSE,1
+M+CH3OH+H,M+33.033489,1,1,33.033489,positive,C1H5O1,FALSE,1
+M+ACN+H,M+42.033823,1,1,42.033823,positive,C2H4N1,FALSE,1
+M+2Na-H,M+44.971160,1,1,44.97116,positive,Na2,H1,1
+M+IsoProp+H,M+61.06534,1,1,61.06534,positive,C3H9O1,FALSE,1
+M+ACN+Na,M+64.015765,1,1,64.015765,positive,C2H3N1Na1,FALSE,1
+M+2K-H,M+76.919040,1,1,76.91904,positive,K2,H1,1
+M+DMSO+H,M+79.02122,1,1,79.02122,positive,C2H7S1O1,FALSE,1
+M+2ACN+H,M+83.060370,1,1,83.06037,positive,C4H7N2,FALSE,1
+M+IsoProp+Na+H,M+84.05511,1,1,84.05511,positive,C3H9O1Na1,FALSE,1
+2M+H,2M+1.007276,1,2,1.007276,positive,H1,FALSE,2
+2M+NH4,2M+18.033823,1,2,18.033823,positive,N1H4,FALSE,2
+2M+Na,2M+22.989218,1,2,22.989218,positive,Na1,FALSE,2
+2M+3H2O+2H,M+28.02312,1,2,28.02312,positive,H8O6,FALSE,2
+2M+K,2M+38.963158,1,2,38.963158,positive,K1,FALSE,2
+2M+ACN+H,2M+42.033823,1,2,42.033823,positive,C2H4N1,FALSE,2
+2M+ACN+Na,2M+64.015765,1,2,64.015765,positive,C2H3N1Na1,FALSE,2
+M-H2O-H,M-19.01839,-1,1,-19.01839,negative,FALSE,H3O1,1
+M+Na-2H,M+20.974666,-1,1,20.974666,negative,Na1,H2,1
+M+Cl,M+34.969402,-1,1,34.969402,negative,Cl1,FALSE,1
+M+K-2H,M+36.948606,-1,1,36.948606,negative,K1,H2,1
+M+Br,M+78.918885,-1,1,78.918885,negative,Br1,FALSE,1
+M+TFA-H,M+112.985586,-1,1,112.985586,negative,C2F3O2H1,H1,1
+2M-H,2M-1.007276,-1,2,-1.007276,negative,FALSE,H1,2
+2M+FA-H,2M+44.998201,-1,2,44.998201,negative,C1O2H2,H1,2
+2M+Hac-H,2M+59.013851,-1,2,59.013851,negative,C2O2H4,H1,2
+3M-H,3M-1.007276,-1,3,-1.007276,negative,FALSE,H1,3
+M-H2O+H,M-19.01839,1,1,-17.003838,positive,FALSE,H1O1,1
+M-NH3+H,M-16.019273,1,1,-16.019273,positive,H1,N1H3,1
+M+CH2+H,M+15.022926,1,1,15.022926,positive,C1H3,FALSE,1
+M-CH3+H,M-14.016199,1,1,-14.016199,positive,H1,C1H3,1
+M-CH2+H,M-13.008374,1,1,-13.008374,positive,H1,C1H2,1
+M+CHN+H,M+28.018175,1,1,28.018175,positive,C1H2N1,FALSE,1
+M-CHN+H,M-26.003623,1,1,-26.003623,positive,H1,C1H1N1,1
+M-COCH2+H,M-41.003289,-1,1,-41.003289,positive,H1,C2H2O1,1
+M+COCH2+H,M+43.017841,1,1,43.017841,positive,C2H3O1,FALSE,1
+M+CH3+H,M+16.030751,1,1,16.030751,positive,C1H4,FALSE,1
+M+CH3OH+H,M+33.033489,1,1,33.033489,positive,C1H5O1,FALSE,1
+M+CH2O2-H,M+44.998201,-1,1,44.998201,negative,C1H2O2,H1,1
+M+C2H4O2-H,M+59.013851,-1,1,59.013851,negative,C2H4O2,H1,1
+M+CF3CO2H-H,M+112.985586,-1,1,112.985586,negative,C2F3O2H1,H1,1
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_adducts.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,213 @@
+id,name,adduct,formula,charge,m/z,RT,pk,MS2
+C00079,L-Phenylalanine,M+H,C9H12NO2,1,166.08625459809997,120;160,1,UA005501_1
+C00079,L-Phenylalanine,M+Na,C9H11NNaO2,1,188.06819659809997,120;160,1,UA005501_1
+C00079,L-Phenylalanine,M+2H,C9H13NO2,2,83.54676529905,120;160,1,UA005501_1
+C00079,L-Phenylalanine,2M+H,C18H23N2O4,1,331.16523319619995,120;160,1,UA005501_1
+C00082,L-Tyrosine,M+H,C9H12NO3,1,182.08116921766998,50;90,1,UA005601_1
+C00082,L-Tyrosine,M+Na,C9H11NNaO3,1,204.06311121766998,50;90,1,UA005601_1
+C00082,L-Tyrosine,M+2H,C9H13NO3,2,91.544222608835,50;90,1,UA005601_1
+C00082,L-Tyrosine,2M+H,C18H23N2O6,1,363.15506243533997,50;90,1,UA005601_1
+C00114,Choline,M+H,C5H15NO,1,105.11481507522001,,1,
+C00114,Choline,M+Na,C5H14NNaO,1,127.09675707522001,,1,
+C00114,Choline,M+2H,C5H16NO,2,53.06104553761,,1,
+C00114,Choline,2M+H,C10H29N2O2,1,209.22235415044,,1,
+C00123,L-Leucine,M+H,C6H14NO2,1,132.10190466256,70;110,1,
+C00123,L-Leucine,M+Na,C6H13NNaO2,1,154.08384666256,70;110,1,
+C00123,L-Leucine,M+2H,C6H15NO2,2,66.55459033128001,70;110,1,
+C00123,L-Leucine,2M+H,C12H27N2O4,1,263.19653332512,70;110,1,
+C00148,L-Proline,M+H,C5H10NO2,1,116.07060453364001,35;55,1,EMBL-MCF_specxxxxx_7
+C00148,L-Proline,M+Na,C5H9NNaO2,1,138.05254653364,35;55,1,EMBL-MCF_specxxxxx_7
+C00148,L-Proline,M+2H,C5H11NO2,2,58.53894026682,35;55,1,EMBL-MCF_specxxxxx_7
+C00148,L-Proline,2M+H,C10H19N2O4,1,231.13393306728,35;55,1,EMBL-MCF_specxxxxx_7
+C00183,L-Valine,M+H,C5H12NO2,1,118.0862545981,40;70,1,EMBL-MCF_specxxxxxx_11
+C00183,L-Valine,M+Na,C5H11NNaO2,1,140.0681965981,40;70,1,EMBL-MCF_specxxxxxx_11
+C00183,L-Valine,M+2H,C5H13NO2,2,59.546765299049994,40;70,1,EMBL-MCF_specxxxxxx_11
+C00183,L-Valine,2M+H,C10H23N2O4,1,235.16523319619998,40;70,1,EMBL-MCF_specxxxxxx_11
+C00407,L-Isoleucine,M+H,C6H14NO2,1,132.10190466256,,1,EMBL-MCF_spec3xxxxx_2
+C00407,L-Isoleucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,EMBL-MCF_spec3xxxxx_2
+C00407,L-Isoleucine,M+2H,C6H15NO2,2,66.55459033128001,,1,EMBL-MCF_spec3xxxxx_2
+C00407,L-Isoleucine,2M+H,C12H27N2O4,1,263.19653332512,,1,EMBL-MCF_spec3xxxxx_2
+C00431,5-Aminopentanoate,M+H,C5H12NO2,1,118.0862545981,,1,EMBL-MCF_spec128577_1
+C00431,5-Aminopentanoate,M+Na,C5H11NNaO2,1,140.0681965981,,1,EMBL-MCF_spec128577_1
+C00431,5-Aminopentanoate,M+2H,C5H13NO2,2,59.546765299049994,,1,EMBL-MCF_spec128577_1
+C00431,5-Aminopentanoate,2M+H,C10H23N2O4,1,235.16523319619998,,1,EMBL-MCF_spec128577_1
+C00719,Betaine,M+H,C5H12NO2,1,118.0862545981,,1,EMBL-MCF_spec107xxx_1
+C00719,Betaine,M+Na,C5H11NNaO2,1,140.0681965981,,1,EMBL-MCF_spec107xxx_1
+C00719,Betaine,M+2H,C5H13NO2,2,59.546765299049994,,1,EMBL-MCF_spec107xxx_1
+C00719,Betaine,2M+H,C10H23N2O4,1,235.16523319619998,,1,EMBL-MCF_spec107xxx_1
+C00763,D-Proline,M+H,C5H10NO2,1,116.07060453364001,,1,
+C00763,D-Proline,M+Na,C5H9NNaO2,1,138.05254653364,,1,
+C00763,D-Proline,M+2H,C5H11NO2,2,58.53894026682,,1,
+C00763,D-Proline,2M+H,C10H19N2O4,1,231.13393306728,,1,
+C01570,D-Leucine,M+H,C6H14NO2,1,132.10190466256,,1,
+C01570,D-Leucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C01570,D-Leucine,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C01570,D-Leucine,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C01799,D-Norvaline,M+H,C5H12NO2,1,118.0862545981,,1,
+C01799,D-Norvaline,M+Na,C5H11NNaO2,1,140.0681965981,,1,
+C01799,D-Norvaline,M+2H,C5H13NO2,2,59.546765299049994,,1,
+C01799,D-Norvaline,2M+H,C10H23N2O4,1,235.16523319619998,,1,
+C01826,L-Norvaline,M+H,C5H12NO2,1,118.0862545981,,1,EMBL-MCF_specxxxxxx_35
+C01826,L-Norvaline,M+Na,C5H11NNaO2,1,140.0681965981,,1,EMBL-MCF_specxxxxxx_35
+C01826,L-Norvaline,M+2H,C5H13NO2,2,59.546765299049994,,1,EMBL-MCF_specxxxxxx_35
+C01826,L-Norvaline,2M+H,C10H23N2O4,1,235.16523319619998,,1,EMBL-MCF_specxxxxxx_35
+C01877,4-Oxoproline,M+H,C5H8NO3,1,130.04986908874997,,1,
+C01877,4-Oxoproline,M+Na,C5H7NNaO3,1,152.03181108874998,,1,
+C01877,4-Oxoproline,M+2H,C5H9NO3,2,65.528572544375,,1,
+C01877,4-Oxoproline,2M+H,C10H15N2O6,1,259.09246217749995,,1,
+C01879,5-Oxoproline,M+H,C5H8NO3,1,130.04986908874997,50;90,1,EMBL-MCF_spec38257_1
+C01879,5-Oxoproline,M+Na,C5H7NNaO3,1,152.03181108874998,50;90,1,EMBL-MCF_spec38257_1
+C01879,5-Oxoproline,M+2H,C5H9NO3,2,65.528572544375,50;90,1,EMBL-MCF_spec38257_1
+C01879,5-Oxoproline,2M+H,C10H15N2O6,1,259.09246217749995,50;90,1,EMBL-MCF_spec38257_1
+C01933,L-Norleucine,M+H,C6H14NO2,1,132.10190466256,,1,EMBL-MCF_spec59716_1
+C01933,L-Norleucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,EMBL-MCF_spec59716_1
+C01933,L-Norleucine,M+2H,C6H15NO2,2,66.55459033128001,,1,EMBL-MCF_spec59716_1
+C01933,L-Norleucine,2M+H,C12H27N2O4,1,263.19653332512,,1,EMBL-MCF_spec59716_1
+C01957,Secologanate,M+H,C16H23O10,1,375.12857290476,,1,
+C01957,Secologanate,M+Na,C16H22NaO10,1,397.11051490476,,1,
+C01957,Secologanate,M+2H,C16H24O10,2,188.06792445238,,1,
+C01957,Secologanate,2M+H,C32H45O20,1,749.2498698095201,,1,
+C02237,5-Oxo-D-proline,M+H,C5H8NO3,1,130.04986908874997,,1,EMBL-MCF_spec36931_1
+C02237,5-Oxo-D-proline,M+Na,C5H7NNaO3,1,152.03181108874998,,1,EMBL-MCF_spec36931_1
+C02237,5-Oxo-D-proline,M+2H,C5H9NO3,2,65.528572544375,,1,EMBL-MCF_spec36931_1
+C02237,5-Oxo-D-proline,2M+H,C10H15N2O6,1,259.09246217749995,,1,EMBL-MCF_spec36931_1
+C02265,D-Phenylalanine,M+H,C9H12NO2,1,166.08625459809997,,1,
+C02265,D-Phenylalanine,M+Na,C9H11NNaO2,1,188.06819659809997,,1,
+C02265,D-Phenylalanine,M+2H,C9H13NO2,2,83.54676529905,,1,
+C02265,D-Phenylalanine,2M+H,C18H23N2O4,1,331.16523319619995,,1,
+C02378,6-Aminohexanoate,M+H,C6H14NO2,1,132.10190466256,,1,
+C02378,6-Aminohexanoate,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C02378,6-Aminohexanoate,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C02378,6-Aminohexanoate,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C02486,(3R)-beta-Leucine,M+H,C6H14NO2,1,132.10190466256,,1,
+C02486,(3R)-beta-Leucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C02486,(3R)-beta-Leucine,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C02486,(3R)-beta-Leucine,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C03263,Coproporphyrinogen III,M+H,C36H45N4O8,1,661.3231903924,,1,
+C03263,Coproporphyrinogen III,M+Na,C36H44N4NaO8,1,683.3051323924,,1,
+C03263,Coproporphyrinogen III,M+2H,C36H46N4O8,2,331.16523319619995,,1,
+C03263,Coproporphyrinogen III,2M+H,C72H89N8O16,1,1321.6391047847999,,1,
+C03290,L-threo-3-Phenylserine,M+H,C9H12NO3,1,182.08116921766998,,1,
+C03290,L-threo-3-Phenylserine,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C03290,L-threo-3-Phenylserine,M+2H,C9H13NO3,2,91.544222608835,,1,
+C03290,L-threo-3-Phenylserine,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C03571,2-Amino-2-methylbutanoate,M+H,C5H12NO2,1,118.0862545981,,1,
+C03571,2-Amino-2-methylbutanoate,M+Na,C5H11NNaO2,1,140.0681965981,,1,
+C03571,2-Amino-2-methylbutanoate,M+2H,C5H13NO2,2,59.546765299049994,,1,
+C03571,2-Amino-2-methylbutanoate,2M+H,C10H23N2O4,1,235.16523319619998,,1,
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,M+H,C5H8NO3,1,130.04986908874997,,1,
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,M+Na,C5H7NNaO3,1,152.03181108874998,,1,
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,M+2H,C5H9NO3,2,65.528572544375,,1,
+C04281,L-1-Pyrroline-3-hydroxy-5-carboxylate,2M+H,C10H15N2O6,1,259.09246217749995,,1,
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,M+H,C5H8NO3,1,130.04986908874997,,1,
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,M+Na,C5H7NNaO3,1,152.03181108874998,,1,
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,M+2H,C5H9NO3,2,65.528572544375,,1,
+C04282,1-Pyrroline-4-hydroxy-2-carboxylate,2M+H,C10H15N2O6,1,259.09246217749995,,1,
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,M+H,C9H12NO3,1,182.08116921766998,,1,
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,M+2H,C9H13NO3,2,91.544222608835,,1,
+C04368,3-Amino-3-(4-hydroxyphenyl)propanoate,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C04498,p-Coumaroylagmatine,M+H,C14H21N4O2,1,277.16590190146,,1,
+C04498,p-Coumaroylagmatine,M+Na,C14H20N4NaO2,1,299.14784390146,,1,
+C04498,p-Coumaroylagmatine,M+2H,C14H22N4O2,2,139.08658895073,,1,
+C04498,p-Coumaroylagmatine,2M+H,C28H41N8O4,1,553.3245278029201,,1,
+C05131,(1-Ribosylimidazole)-4-acetate,M+H,C10H15N2O6,1,259.09246217749995,,1,
+C05131,(1-Ribosylimidazole)-4-acetate,M+Na,C10H14N2NaO6,1,281.07440417749996,,1,
+C05131,(1-Ribosylimidazole)-4-acetate,M+2H,C10H16N2O6,2,130.04986908874997,,1,
+C05131,(1-Ribosylimidazole)-4-acetate,2M+H,C20H29N4O12,1,517.177648355,,1,
+C05768,Coproporphyrinogen I,M+H,C36H45N4O8,1,661.3231903924,,1,
+C05768,Coproporphyrinogen I,M+Na,C36H44N4NaO8,1,683.3051323924,,1,
+C05768,Coproporphyrinogen I,M+2H,C36H46N4O8,2,331.16523319619995,,1,
+C05768,Coproporphyrinogen I,2M+H,C72H89N8O16,1,1321.6391047847999,,1,
+C06417,D-Valine,M+H,C5H12NO2,1,118.0862545981,,1,
+C06417,D-Valine,M+Na,C5H11NNaO2,1,140.0681965981,,1,
+C06417,D-Valine,M+2H,C5H13NO2,2,59.546765299049994,,1,
+C06417,D-Valine,2M+H,C10H23N2O4,1,235.16523319619998,,1,
+C06418,D-Isoleucine,M+H,C6H14NO2,1,132.10190466256,,1,
+C06418,D-Isoleucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C06418,D-Isoleucine,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C06418,D-Isoleucine,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C06420,D-Tyrosine,M+H,C9H12NO3,1,182.08116921766998,,1,
+C06420,D-Tyrosine,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C06420,D-Tyrosine,M+2H,C9H13NO3,2,91.544222608835,,1,
+C06420,D-Tyrosine,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C07457,Amyl nitrite,M+H,C5H12NO2,1,118.0862545981,,1,
+C07457,Amyl nitrite,M+Na,C5H11NNaO2,1,140.0681965981,,1,
+C07457,Amyl nitrite,M+2H,C5H13NO2,2,59.546765299049994,,1,
+C07457,Amyl nitrite,2M+H,C10H23N2O4,1,235.16523319619998,,1,
+C08263,beta-Alaninebetaine,M+H,C6H14NO2,1,132.10190466256,,1,
+C08263,beta-Alaninebetaine,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C08263,beta-Alaninebetaine,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C08263,beta-Alaninebetaine,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C08307,Hordatine A,M+H,C28H39N8O4,1,551.3088777384601,,1,
+C08307,Hordatine A,M+Na,C28H38N8NaO4,1,573.2908197384601,,1,
+C08307,Hordatine A,M+2H,C28H40N8O4,2,276.15807686923,,1,
+C08307,Hordatine A,2M+H,C56H77N16O8,1,1101.61047947692,,1,
+C09800,Swertiamarin,M+H,C16H23O10,1,375.12857290476,,1,VF-NPL-QEHF0132xx_2
+C09800,Swertiamarin,M+Na,C16H22NaO10,1,397.11051490476,,1,VF-NPL-QEHF0132xx_2
+C09800,Swertiamarin,M+2H,C16H24O10,2,188.06792445238,,1,VF-NPL-QEHF0132xx_2
+C09800,Swertiamarin,2M+H,C32H45O20,1,749.2498698095201,,1,VF-NPL-QEHF0132xx_2
+C11673,Geniposidic acid,M+H,C16H23O10,1,375.12857290476,,1,VF-NPL-QEHF00xxxx_74
+C11673,Geniposidic acid,M+Na,C16H22NaO10,1,397.11051490476,,1,VF-NPL-QEHF00xxxx_74
+C11673,Geniposidic acid,M+2H,C16H24O10,2,188.06792445238,,1,VF-NPL-QEHF00xxxx_74
+C11673,Geniposidic acid,2M+H,C32H45O20,1,749.2498698095201,,1,VF-NPL-QEHF00xxxx_74
+C15987,4-Methylaminobutyrate,M+H,C5H12NO2,1,118.0862545981,,1,
+C15987,4-Methylaminobutyrate,M+Na,C5H11NNaO2,1,140.0681965981,,1,
+C15987,4-Methylaminobutyrate,M+2H,C5H13NO2,2,59.546765299049994,,1,
+C15987,4-Methylaminobutyrate,2M+H,C10H23N2O4,1,235.16523319619998,,1,
+C16589,2-Oxosuberate,M+H,C8H13O5,1,189.07574948461,,1,
+C16589,2-Oxosuberate,M+Na,C8H12NaO5,1,211.05769148461,,1,
+C16589,2-Oxosuberate,M+2H,C8H14O5,2,95.041512742305,,1,
+C16589,2-Oxosuberate,2M+H,C16H25O10,1,377.14422296922,,1,
+C16647,"N,N-Diethylglycine",M+H,C6H14NO2,1,132.10190466256,,1,
+C16647,"N,N-Diethylglycine",M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C16647,"N,N-Diethylglycine",M+2H,C6H15NO2,2,66.55459033128001,,1,
+C16647,"N,N-Diethylglycine",2M+H,C12H27N2O4,1,263.19653332512,,1,
+C16744,Spongothymidine,M+H,C10H15N2O6,1,259.09246217749995,,1,
+C16744,Spongothymidine,M+Na,C10H14N2NaO6,1,281.07440417749996,,1,
+C16744,Spongothymidine,M+2H,C10H16N2O6,2,130.04986908874997,,1,
+C16744,Spongothymidine,2M+H,C20H29N4O12,1,517.177648355,,1,
+C16963,Gardoside,M+H,C16H23O10,1,375.12857290476,,1,
+C16963,Gardoside,M+Na,C16H22NaO10,1,397.11051490476,,1,
+C16963,Gardoside,M+2H,C16H24O10,2,188.06792445238,,1,
+C16963,Gardoside,2M+H,C32H45O20,1,749.2498698095201,,1,
+C18170,3-Acetamidopropanal,M+H,C5H10NO2,1,116.07060453364001,500;560,1,
+C18170,3-Acetamidopropanal,M+Na,C5H9NNaO2,1,138.05254653364,500;560,1,
+C18170,3-Acetamidopropanal,M+2H,C5H11NO2,2,58.53894026682,500;560,1,
+C18170,3-Acetamidopropanal,2M+H,C10H19N2O4,1,231.13393306728,500;560,1,
+C19579,gamma-Hydroxy-3-pyridinebutanoate,M+H,C9H12NO3,1,182.08116921766998,,1,
+C19579,gamma-Hydroxy-3-pyridinebutanoate,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C19579,gamma-Hydroxy-3-pyridinebutanoate,M+2H,C9H13NO3,2,91.544222608835,,1,
+C19579,gamma-Hydroxy-3-pyridinebutanoate,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C19712,N-Hydroxy-L-phenylalanine,M+H,C9H12NO3,1,182.08116921766998,,1,
+C19712,N-Hydroxy-L-phenylalanine,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C19712,N-Hydroxy-L-phenylalanine,M+2H,C9H13NO3,2,91.544222608835,,1,
+C19712,N-Hydroxy-L-phenylalanine,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C20807,3-Hydroxy-L-phenylalanine,M+H,C9H12NO3,1,182.08116921766998,,1,
+C20807,3-Hydroxy-L-phenylalanine,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C20807,3-Hydroxy-L-phenylalanine,M+2H,C9H13NO3,2,91.544222608835,,1,
+C20807,3-Hydroxy-L-phenylalanine,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C21092,D-allo-Isoleucine,M+H,C6H14NO2,1,132.10190466256,,1,
+C21092,D-allo-Isoleucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C21092,D-allo-Isoleucine,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C21092,D-allo-Isoleucine,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C21096,L-allo-Isoleucine,M+H,C6H14NO2,1,132.10190466256,,1,
+C21096,L-allo-Isoleucine,M+Na,C6H13NNaO2,1,154.08384666256,,1,
+C21096,L-allo-Isoleucine,M+2H,C6H15NO2,2,66.55459033128001,,1,
+C21096,L-allo-Isoleucine,2M+H,C12H27N2O4,1,263.19653332512,,1,
+C21308,(S)-beta-Tyrosine,M+H,C9H12NO3,1,182.08116921766998,,1,
+C21308,(S)-beta-Tyrosine,M+Na,C9H11NNaO3,1,204.06311121766998,,1,
+C21308,(S)-beta-Tyrosine,M+2H,C9H13NO3,2,91.544222608835,,1,
+C21308,(S)-beta-Tyrosine,2M+H,C18H23N2O6,1,363.15506243533997,,1,
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",M+H,C14H24NO3,1,254.17506960443,,1,
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",M+Na,C14H23NNaO3,1,276.15701160443,,1,
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",M+2H,C14H25NO3,2,127.59117280221501,,1,
+C21776,"2-({[(4-Methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol",2M+H,C28H47N2O6,1,507.34286320886,,1,
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,M+H,C10H15N2O6,1,259.09246217749995,,1,
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,M+Na,C10H14N2NaO6,1,281.07440417749996,,1,
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,M+2H,C10H16N2O6,2,130.04986908874997,,1,
+C22140,L-gamma-Glutamyl-(3R)-L-beta-ethynylserine,2M+H,C20H29N4O12,1,517.177648355,,1,
+C22141,L-beta-Ethynylserine,M+H,C5H8NO3,1,130.04986908874997,,1,
+C22141,L-beta-Ethynylserine,M+Na,C5H7NNaO3,1,152.03181108874998,,1,
+C22141,L-beta-Ethynylserine,M+2H,C5H9NO3,2,65.528572544375,,1,
+C22141,L-beta-Ethynylserine,2M+H,C10H15N2O6,1,259.09246217749995,,1,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clean_annotations.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,13 @@
+id,name,formula,adduct,m/z,charge,RT range,ppm,isotope pattern score,fragmentation pattern score,prior,post,peak_id
+C00148,L-Proline,C5H10NO2,M+H,116.0706045,1,,-0.522957559042512,0.49693117623427185,0.9997594969319,0.46765490975005014,0.6662337288872859,1
+C00763,D-Proline,C5H10NO2,M+H,116.0706045,1,,-0.522957559042512,0.49693117623427185,0.5,0.46765490975005014,0.333196999344267,1
+Unknown,Unknown,,,,,,5.0,0.006137647531456385,0.5,0.06469018049989968,0.0005692717684471807,1
+C00148,L-Proline,C10H19N2O4,2M+H,231.1339331,1,,-1.1248889183431734,0.4882500598113232,,0.4651697838170355,0.4982045401371164,501
+C00763,D-Proline,C10H19N2O4,2M+H,231.1339331,1,,-1.1248889183431734,0.4882500598113232,,0.4651697838170355,0.4982045401371164,501
+Unknown,Unknown,,,,,,5.0,0.02349988037735366,,0.06966043236592895,0.0035909197257671228,501
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.0862546,1,,-1.2505550232079832,0.49999187630897085,0.9992403518152402,0.46438794712168835,0.666496662619688,4
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.0862546,1,,-1.2505550232079832,0.49999187630897085,0.5,0.46438794712168835,0.33350167525206353,4
+Unknown,Unknown,,,,,,5.0,1.624738205836915e-05,0.5,0.07122410575662326,1.6621282485718676e-06,4
+C00079,L-Phenylalanine,C18H23N2O4,2M+H,331.1652332,1,,-0.9418259186562423,0.4723531124011579,,0.46613787403288154,0.49578398848841876,999
+C02265,D-Phenylalanine,C18H23N2O4,2M+H,331.1652332,1,,-0.9418259186562423,0.4723531124011579,,0.46613787403288154,0.49578398848841876,999
+Unknown,Unknown,,,,,,5.0,0.05529377519768423,,0.06772425193423681,0.008432023023162484,999
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clustered_MS1_intensities.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,49 @@
+ids,rel.ids,mzs,RTs,Int
+1,0,116.0705438,45.77042282,2170016768.0
+88,0,117.0736777,45.78758564,125652040.0
+501,0,231.1336731,46.18394843,25192232.0
+4429,0,232.136923,46.17671467,2635593.5
+2,1,104.1068297,40.8433086,1889171712.0
+106,1,105.110031,40.85338247,106019424.0
+2407,1,106.1108997,40.90054426,5238424.0
+3,2,118.0859982,43.58463793,1415609984.0
+168,2,119.0892369,43.60258524,78531288.0
+2015,2,120.0901826,43.60484775,6344767.5
+4,3,166.0860469,143.3213962,1390904576.0
+78,3,167.0891418,143.2932786,138503872.0
+999,3,331.1649213,143.2538931,14022061.0
+2582,3,168.0925106,143.1810971,4837916.5
+2954,3,168.0898248,143.5532971,4645736.0
+4377,3,332.1685031,143.2804967,2676938.75
+4398,3,188.0677845,143.21329,2658275.25
+5,4,132.1017446,89.38720215,1270735104.0
+146,4,133.1049242,89.37606661,87058072.0
+2169,4,134.1057823,89.54029901,5815301.5
+2262,4,263.1963533,89.4438151,5535454.0
+6,5,130.0497274,65.77235475,1004100672.0
+33,5,259.0923178,65.6674287,337794656.0
+247,5,131.0528786,65.7933134,57219324.0
+356,5,260.0955372,65.66021465,37322208.0
+1968,5,132.0537574,65.76488422,6497118.5
+2849,5,261.0966051,65.6782499,4349269.5
+8,6,118.0860855,53.11058084,880116864.0
+269,6,119.0893396,53.21094659,52531228.0
+3044,6,120.0902492,53.77402655,4017382.5
+9,7,276.1579103,337.0681207,792749696.0
+43,7,276.6590388,337.0572473,263166528.0
+305,7,277.1605616,337.0681214,45549260.0
+1330,7,551.3082988,337.0645472,10376464.0
+2515,7,277.6620576,337.0463591,4970442.5
+10,8,182.080964,67.3676442,752484736.0
+174,8,183.0841719,67.38618111,76511288.0
+3079,8,184.0848847,67.53592151,3977772.75
+19,9,132.101747,82.61404747,710873280.0
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+90,10,116.0705223,63.45684304,40477056.0
+598,11,118.0861166,63.81497405,21994580.0
+992,12,116.0705281,93.01697292,14097951.0
+2759,13,117.0738156,64.05677567,2394117.0
+3460,14,166.0861174,344.7149229,3450380.75
+3512,15,166.0860978,383.7962018,3387522.25
+3849,16,363.1547787,67.76908366,3045993.25
+3897,17,166.0860711,333.6703601,3016967.75
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/compute_bio_db.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,5 @@
+,id,name,formula,inchi,smiles,RT,adductsPos,adductsNeg,description,pk,MS2,reactions
+0,C00148,L-Proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,EMBL-MCF_specxxxxx_7,R00135 R00671 R01246 R01248 R01249 R01251 R01252 R01253;R01255 R03661 R06746 R09572 R09650 R10507 R10661 R11594;R12056
+1,C00763,D-Proline,C5H9NO2,"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R01255 R02825 R02894 R02895 R09496
+2,C00079,L-Phenylalanine,C9H11NO2,"InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,UA005501_1,R00686 R00688 R00689 R00690 R00691 R00692 R00693 R00694;R00695 R00697 R00698 R00699 R01375 R01376 R01795 R03660;R06744 R07211 R08463 R08652 R08690 R09535 R09578 R09579;R10286 R10287 R10495 R10499 R10729 R11068 R11918
+3,C02265,D-Phenylalanine,C9H11NO2,"InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m1/s1",,,M+H;M+Na;M+2H;2M+H,M-H;2M-H;M-2H;3M-H,,1,,R00686 R01374 R01582 R03903
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/compute_bio_output.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,2 @@
+0,1
+C02265,C00079
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gibbs_sample_add_annotations.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,13 @@
+id,name,formula,adduct,m/z,charge,RT range,ppm,isotope pattern score,fragmentation pattern score,prior,post,post Gibbs,chi-square pval,peak_id
+C00148,L-Proline,C5H10NO2,M+H,116.0706045,1,,-0.522957559042512,0.4969311762342718,0.9997594969319,0.4676549097500501,0.6662337288872859,0.701010101010101,0.02133956269536478,1
+C00763,D-Proline,C5H10NO2,M+H,116.0706045,1,,-0.522957559042512,0.4969311762342718,0.5,0.4676549097500501,0.333196999344267,0.298989898989899,0.02133956269536478,1
+Unknown,Unknown,,,,,,5.0,0.0061376475314563,0.5,0.0646901804998996,0.0005692717684471,0.0,0.02133956269536478,1
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.0862546,1,,-1.2505550232079832,0.4999918763089708,0.9992403518152402,0.4643879471216883,0.666496662619688,0.7131313131313132,0.0018568839314650465,4
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.0862546,1,,-1.2505550232079832,0.4999918763089708,0.5,0.4643879471216883,0.3335016752520635,0.2868686868686869,0.0018568839314650465,4
+Unknown,Unknown,,,,,,5.0,1.624738205836915e-05,0.5,0.0712241057566232,1.6621282485718676e-06,0.0,0.0018568839314650465,4
+C00148,L-Proline,C10H19N2O4,2M+H,231.1339331,1,,-1.1248889183431734,0.4882500598113232,,0.4651697838170355,0.4982045401371164,0.6444444444444445,2.9365298688363727e-19,501
+C00763,D-Proline,C10H19N2O4,2M+H,231.1339331,1,,-1.1248889183431734,0.4882500598113232,,0.4651697838170355,0.4982045401371164,0.35454545454545455,2.9365298688363727e-19,501
+Unknown,Unknown,,,,,,5.0,0.0234998803773536,,0.0696604323659289,0.0035909197257671,0.00101010101010101,2.9365298688363727e-19,501
+C00079,L-Phenylalanine,C18H23N2O4,2M+H,331.1652332,1,,-0.9418259186562424,0.4723531124011579,,0.4661378740328815,0.4957839884884187,0.694949494949495,1.3472618909303086e-34,999
+C02265,D-Phenylalanine,C18H23N2O4,2M+H,331.1652332,1,,-0.9418259186562424,0.4723531124011579,,0.4661378740328815,0.4957839884884187,0.30505050505050507,1.3472618909303086e-34,999
+Unknown,Unknown,,,,,,5.0,0.0552937751976842,,0.0677242519342368,0.0084320230231624,0.0,1.3472618909303086e-34,999
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gibbs_sample_annotations.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,13 @@
+id,name,formula,adduct,m/z,charge,RT range,ppm,isotope pattern score,fragmentation pattern score,prior,post,post Gibbs,chi-square pval,peak_id
+C00148,L-Proline,C5H10NO2,M+H,116.0706045,1,,-0.522957559042512,0.4969311762342718,0.9997594969319,0.4676549097500501,0.6662337288872859,0.693939393939394,0.06724474889134864,1
+C00763,D-Proline,C5H10NO2,M+H,116.0706045,1,,-0.522957559042512,0.4969311762342718,0.5,0.4676549097500501,0.333196999344267,0.30606060606060603,0.06724474889134864,1
+Unknown,Unknown,,,,,,5.0,0.0061376475314563,0.5,0.0646901804998996,0.0005692717684471,0.0,0.06724474889134864,1
+C00079,L-Phenylalanine,C9H12NO2,M+H,166.0862546,1,,-1.2505550232079832,0.4999918763089708,0.9992403518152402,0.4643879471216883,0.666496662619688,0.7070707070707071,0.006774150457306132,4
+C02265,D-Phenylalanine,C9H12NO2,M+H,166.0862546,1,,-1.2505550232079832,0.4999918763089708,0.5,0.4643879471216883,0.3335016752520635,0.29292929292929293,0.006774150457306132,4
+Unknown,Unknown,,,,,,5.0,1.624738205836915e-05,0.5,0.0712241057566232,1.6621282485718676e-06,0.0,0.006774150457306132,4
+C00148,L-Proline,C10H19N2O4,2M+H,231.1339331,1,,-1.1248889183431734,0.4882500598113232,,0.4651697838170355,0.4982045401371164,0.5818181818181818,8.354646050993867e-07,501
+C00763,D-Proline,C10H19N2O4,2M+H,231.1339331,1,,-1.1248889183431734,0.4882500598113232,,0.4651697838170355,0.4982045401371164,0.41414141414141414,8.354646050993867e-07,501
+Unknown,Unknown,,,,,,5.0,0.0234998803773536,,0.0696604323659289,0.0035909197257671,0.00404040404040404,8.354646050993867e-07,501
+C00079,L-Phenylalanine,C18H23N2O4,2M+H,331.1652332,1,,-0.9418259186562424,0.4723531124011579,,0.4661378740328815,0.4957839884884187,0.5585858585858586,0.00020832746789075488,999
+C02265,D-Phenylalanine,C18H23N2O4,2M+H,331.1652332,1,,-0.9418259186562424,0.4723531124011579,,0.4661378740328815,0.4957839884884187,0.43737373737373736,0.00020832746789075488,999
+Unknown,Unknown,,,,,,5.0,0.0552937751976842,,0.0677242519342368,0.0084320230231624,0.00404040404040404,0.00020832746789075488,999
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapped_isotope_patterns.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,49 @@
+ids,rel.ids,mzs,RTs,Int,relationship,isotope pattern,charge
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+88,0,117.0736777,45.78758564,125652040.0,bp|isotope,0,1
+501,0,231.1336731,46.18394843,25192232.0,potential bp,1,1
+4429,0,232.136923,46.17671467,2635593.5,potential bp|isotope,1,1
+2,1,104.1068297,40.8433086,1889171712.0,bp,0,1
+106,1,105.110031,40.85338247,106019424.0,bp|isotope,0,1
+2407,1,106.1108997,40.90054426,5238424.0,,,
+3,2,118.0859982,43.58463793,1415609984.0,bp,0,1
+168,2,119.0892369,43.60258524,78531288.0,bp|isotope,0,1
+2015,2,120.0901826,43.60484775,6344767.5,,,
+4,3,166.0860469,143.3213962,1390904576.0,bp,0,1
+78,3,167.0891418,143.2932786,138503872.0,bp|isotope,0,1
+999,3,331.1649213,143.2538931,14022061.0,potential bp,1,1
+2582,3,168.0925106,143.1810971,4837916.5,,,
+2954,3,168.0898248,143.5532971,4645736.0,,,
+4377,3,332.1685031,143.2804967,2676938.75,potential bp|isotope,1,1
+4398,3,188.0677845,143.21329,2658275.25,,,
+5,4,132.1017446,89.38720215,1270735104.0,bp,0,1
+146,4,133.1049242,89.37606661,87058072.0,bp|isotope,0,1
+2169,4,134.1057823,89.54029901,5815301.5,,,
+2262,4,263.1963533,89.4438151,5535454.0,,,
+6,5,130.0497274,65.77235475,1004100672.0,bp,0,1
+33,5,259.0923178,65.6674287,337794656.0,potential bp,1,1
+247,5,131.0528786,65.7933134,57219324.0,bp|isotope,0,1
+356,5,260.0955372,65.66021465,37322208.0,potential bp|isotope,1,1
+1968,5,132.0537574,65.76488422,6497118.5,bp|isotope,0,1
+2849,5,261.0966051,65.6782499,4349269.5,potential bp|isotope,1,1
+8,6,118.0860855,53.11058084,880116864.0,bp,0,1
+269,6,119.0893396,53.21094659,52531228.0,bp|isotope,0,1
+3044,6,120.0902492,53.77402655,4017382.5,,,
+9,7,276.1579103,337.0681207,792749696.0,bp,0,2
+43,7,276.6590388,337.0572473,263166528.0,bp|isotope,0,2
+305,7,277.1605616,337.0681214,45549260.0,bp|isotope,0,2
+1330,7,551.3082988,337.0645472,10376464.0,,,
+2515,7,277.6620576,337.0463591,4970442.5,bp|isotope,0,2
+10,8,182.080964,67.3676442,752484736.0,bp,0,1
+174,8,183.0841719,67.38618111,76511288.0,bp|isotope,0,1
+3079,8,184.0848847,67.53592151,3977772.75,bp|isotope,0,1
+19,9,132.101747,82.61404747,710873280.0,bp,0,1
+362,9,133.1049652,82.606965,49374640.0,bp|isotope,0,1
+90,10,116.0705223,63.45684304,40477056.0,bp,,
+598,11,118.0861166,63.81497405,21994580.0,bp,,
+992,12,116.0705281,93.01697292,14097951.0,bp,,
+2759,13,117.0738156,64.05677567,2394117.0,bp,,
+3460,14,166.0861174,344.7149229,3450380.75,bp,,
+3512,15,166.0860978,383.7962018,3387522.25,bp,,
+3849,16,363.1547787,67.76908366,3045993.25,bp,,
+3897,17,166.0860711,333.6703601,3016967.75,bp,,
Binary file test-data/mapped_isotope_patterns.parquet has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unclustered_MS1_intensities.csv	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,49 @@
+ids,mzs,RTs,sample1,sample2,sample3,sample4,sample5,sample6,sample7,sample8,sample9,sample10
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.py	Fri May 16 08:02:01 2025 +0000
@@ -0,0 +1,297 @@
+import argparse
+from typing import Tuple
+
+import pandas as pd
+
+
+class LoadDataAction(argparse.Action):
+    """
+    Custom argparse action to load data from a file.
+    Supported file formats: CSV, TSV, Tabular and Parquet.
+
+    """
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        """
+        Load data from a file and store it in the namespace.
+        :param namespace: Namespace object
+        :param values: Tuple containing the file path and file extension
+        :param option_string: Option string
+        :return: None
+        """
+
+        file_path, file_extension = values
+        file_extension = file_extension.lower()
+        if file_extension == "csv":
+            df = pd.read_csv(file_path, keep_default_na=False).replace("", None)
+        elif file_extension in ["tsv", "tabular"]:
+            df = pd.read_csv(file_path, sep="\t", keep_default_na=False).replace(
+                "", None
+            )
+        elif file_extension == "parquet":
+            df = pd.read_parquet(file_path).replace("", None)
+        else:
+            raise ValueError(f"Unsupported file format: {file_extension}")
+        setattr(namespace, self.dest, df)
+
+
+class LoadTextAction(argparse.Action):
+    """
+    Custom argparse action to load data from a text file.
+    """
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        """
+        Load data from a text file and store it in the namespace.
+        :param namespace: Namespace object
+        :param values: Tuple containing the file path and file extension
+        :param option_string: Option string
+        :return: None
+        """
+        file_path, _ = values
+        data = []
+        if file_path:
+            with open(file_path, "r") as f:
+                for line in f:
+                    data.append(int(line.strip()))
+        setattr(namespace, self.dest, data)
+
+
+def write_csv(df: pd.DataFrame, file_path: str) -> None:
+    """
+    Write the dataframe to a CSV file.
+
+    Parameters:
+    df (pd.DataFrame): The dataframe to write.
+    file_path (str): The path to the output CSV file.
+    """
+    df.to_csv(file_path, index=False)
+
+
+def write_tsv(df: pd.DataFrame, file_path: str) -> None:
+    """
+    Write the dataframe to a TSV file.
+
+    Parameters:
+    df (pd.DataFrame): The dataframe to write.
+    file_path (str): The path to the output TSV file.
+    """
+    df.to_csv(file_path, sep="\t", index=False)
+
+
+def write_parquet(df: pd.DataFrame, file_path: str) -> None:
+    """
+    Write the dataframe to a Parquet file.
+
+    Parameters:
+    df (pd.DataFrame): The dataframe to write.
+    file_path (str): The path to the output Parquet file.
+    """
+    df.to_parquet(file_path, index=False)
+
+
+def write_text(data: list, file_path: str) -> None:
+    """
+    Write the data to a text file.
+
+    Parameters:
+    data (list): The data to write.
+    file_path (str): The path to the output text file.
+    """
+    if file_path:
+        with open(file_path, "w") as f:
+            for s in data:
+                f.write(str(s) + "\n")
+
+
+class StoreOutputAction(argparse.Action):
+    def __call__(
+        self,
+        parser: argparse.ArgumentParser,
+        namespace: argparse.Namespace,
+        values: Tuple[str, str],
+        option_string: str = None,
+    ) -> None:
+        """
+        Custom argparse action to store the output function and file path based on file extension.
+
+        Parameters:
+        parser (argparse.ArgumentParser): The argument parser instance.
+        namespace (argparse.Namespace): The namespace to hold the parsed values.
+        values (Tuple[str, str]): The file path and file extension.
+        option_string (str): The option string.
+        """
+        file_path, file_extension = values
+        file_extension = file_extension.lower()
+        if file_extension == "csv":
+            write_func = write_csv
+        elif file_extension in ["tsv", "tabular"]:
+            write_func = write_tsv
+        elif file_extension == "parquet":
+            write_func = write_parquet
+        elif file_extension == "txt":
+            write_func = write_text
+        else:
+            raise ValueError(f"Unsupported file format: {file_extension}")
+        setattr(namespace, self.dest, (write_func, file_path))
+
+
+def flattern_annotations(annotations: dict) -> pd.DataFrame:
+    """
+    Flatten the annotations dictionary and convert it to a dataframe.
+
+    Parameters:
+    annotations (dict): The annotations dictionary.
+
+    Returns:
+    pd.DataFrame: The flattened annotations dataframe.
+    """
+    annotations_flat = pd.DataFrame()
+    for peak_id in annotations:
+        annotation = annotations[peak_id]
+        annotation["peak_id"] = peak_id
+        annotations_flat = pd.concat([annotations_flat, annotation])
+    return annotations_flat
+
+
+def group_by_peak_id(df: pd.DataFrame) -> dict:
+    """
+    Convert a pandas dataframe to a dictionary where each key is a unique 'peak_id'
+    and each value is a dataframe subset corresponding to that 'peak_id'.
+
+    Parameters:
+    df (pd.DataFrame): The input dataframe.
+
+    Returns:
+    dict: The dictionary representation of the dataframe.
+    """
+    annotations = {}
+    keys = set(df["peak_id"])
+    for i in keys:
+        annotations[i] = df[df["peak_id"] == i].drop("peak_id", axis=1)
+    return annotations
+
+
+class CustomArgumentParser(argparse.ArgumentParser):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.register("action", "load_data", LoadDataAction)
+        self.register("action", "store_output", StoreOutputAction)
+        self.register("action", "load_text", LoadTextAction)
+        self.add_argument(
+            "--output_dataset",
+            nargs=2,
+            action="store_output",
+            required=True,
+            help="A file path for the output results.",
+        )
+
+
+class MSArgumentParser(CustomArgumentParser):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.add_argument(
+            "--ncores",
+            type=int,
+            default=1,
+            help="The number of cores to use for parallel processing.",
+        )
+        self.add_argument(
+            "--pRTout",
+            type=float,
+            default=0.4,
+            help=(
+                "multiplicative factor for the RT if measured RT is outside the RTrange"
+                " present in the database."
+            ),
+        )
+        self.add_argument(
+            "--pRTNone",
+            type=float,
+            default=0.8,
+            help=(
+                "multiplicative factor for the RT if no RTrange present in the"
+                " database."
+            ),
+        )
+        self.add_argument(
+            "--ppmthr",
+            type=float,
+            help=(
+                "maximum ppm possible for the annotations. if not provided equal to"
+                " 2*ppm."
+            ),
+        )
+        self.add_argument(
+            "--ppm",
+            type=float,
+            required=True,
+            default=100,
+            help="accuracy of the MS instrument used.",
+        )
+        self.add_argument(
+            "--ratiosd",
+            type=float,
+            default=0.9,
+            help=(
+                "acceptable ratio between predicted intensity and observed intensity of"
+                " isotopes."
+            ),
+        )
+        self.add_argument(
+            "--ppmunk",
+            type=float,
+            help=(
+                "pm associated to the 'unknown' annotation. If not provided equal to"
+                " ppm."
+            ),
+        )
+        self.add_argument(
+            "--ratiounk",
+            type=float,
+            default=0.5,
+            help="isotope ratio associated to the 'unknown' annotation.",
+        )
+
+
+class GibbsArgumentParser(CustomArgumentParser):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.add_argument(
+            "--noits",
+            type=int,
+            help="number of iterations if the Gibbs sampler to be run",
+        )
+        self.add_argument(
+            "--burn",
+            type=int,
+            help="""number of iterations to be ignored when computing posterior
+          probabilities. If None, is set to 10% of total iterations""",
+        )
+        self.add_argument(
+            "--delta_add",
+            type=float,
+            default=1,
+            help="""parameter used when computing the conditional priors. The
+                parameter must be positive. The smaller the parameter the more
+                weight the adducts connections have on the posterior
+                probabilities. Default 1.""",
+        )
+        self.add_argument(
+            "--all_out",
+            type=bool,
+            help="Output all the Gibbs sampler results.",
+        )
+        self.add_argument(
+            "--zs_out",
+            nargs=2,
+            action="store_output",
+            help="A file path for the output results of the Gibbs sampler.",
+        )
+        self.add_argument(
+            "--zs",
+            nargs=2,
+            action="load_text",
+            help="""a txt file containing the list of assignments computed in a previous run of the Gibbs sampler.
+            Optional, default None.""",
+        )