Mercurial > repos > galaxyp > feature_alignment
changeset 0:7ac5166f8bbc draft default tip
"planemo upload for repository https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md commit 75f5dee4cc5cb3dbfac3d1d32d8bceb2a22634d7"
| author | galaxyp |
|---|---|
| date | Fri, 10 Dec 2021 00:30:05 +0000 |
| parents | |
| children | |
| files | feature_alignment.xml macros.xml test-data/feature_alignment_1_openswath_output_cluster_ids.csv test-data/feature_alignment_1_openswath_output_matrix.csv test-data/feature_alignment_2_output_1_ids.csv test-data/feature_alignment_2_output_2_matrix.csv test-data/feature_alignment_3_openswath_input.csv test-data/feature_alignment_3_openswath_output_splinePy_cluster_ids.csv test-data/feature_alignment_3_openswath_output_splineR_cluster_ids.csv test-data/feature_alignment_5_peakview_output_matrix.csv test-data/feature_alignment_openswath_input_1.csv test-data/feature_alignment_peakview_input_2.csv |
| diffstat | 12 files changed, 462 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_alignment.xml Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,292 @@ +<tool id="feature_alignment" name="TRIC" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>integrates information from all available runs via a graph-based alignment strategy</description> + <macros> + <token name="@TOOL_VERSION@">0.11.0</token> + <token name="@GALAXY_VERSION@">0</token> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">msproteomicstools</requirement> + <requirement type="package" version="2.8.6">rpy2</requirement> + </requirements> + <version_command>feature_alignment.py --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + feature_alignment.py + --in #echo '' ''.join([ str($file) for $file in $inputs ]) + --out out.tsv + --out_matrix out_matrix.tsv + --out_ids out_ids.tsv + --file_format '$iformat' + --method '$method_sel.method' + --matrix_output_method '$matrix_output_method' + --realign_method '$realign_method' + #if $max_rt_diff_cond.max_rt_diff_sel == 'opt_max_rt_diff_enabled': + --max_rt_diff '$max_rt_diff_cond.max_rt_diff' + #end if + #if $iso_max_rt_diff_cond.iso_max_rt_diff_sel == 'opt_iso_max_rt_diff_enabled': + --iso_max_rt_diff '$iso_max_rt_diff_cond.iso_max_rt_diff' + #end if + #if $frac_selected_cond.frac_selected_sel == 'opt_frac_selected_enabled': + --frac_selected '$frac_selected_cond.frac_selected' + #end if + #if $fdr_cond.fdr_sel == 'opt_target_fdr': + --target_fdr '$fdr_cond.target_fdr' + #elif $fdr_cond.fdr_sel == 'opt_fdr_cutoff': + --fdr_cutoff '$fdr_cond.fdr_cutoff' + #else: + --target_fdr '0' + #end if + --max_fdr_quality '$max_fdr_quality' + #if $method_sel.method == 'LocalMST' or $method_sel.method == 'LocalMSTAllCluster': + --mst:useRTCorrection '$method_sel.mst_useRTCorrection' + --mst:Stdev_multiplier '$method_sel.mst_Stdev_multiplier' + --mst:useLocalStdev '$method_sel.mst_useLocalStdev' + --mst:useReference '$method_sel.mst_useReference' + #end if + #if $further_params.disable_isotopic_grouping: + --disable_isotopic_grouping + #end if + #if $further_params.dscore_cond.dscore_sel == 'opt_dscore_enabled': + --use_dscore_filter + --dscore_cutoff '$further_params.dscore_cond.dscore_cutoff' + #end if + #if $further_params.nr_high_conf_exp_cond.nr_high_conf_exp_sel == 'opt_nr_high_conf_exp_enabled': + --nr_high_conf_exp '$further_params.nr_high_conf_exp_cond.nr_high_conf_exp' + #end if + #if $further_params.readmethod != 'disabled': + --readmethod '$further_params.readmethod' + #end if + #if $further_params.alignment_score_cond.alignment_score_sel == 'opt_alignment_score_enabled': + --alignment_score '$further_params.alignment_score_cond.alignment_score' + #end if + + #if $iformat == 'openswath': + && cat out.tsv > '$out' + #end if + && cat out_matrix.tsv > '$out_matrix' + && cat out_ids.tsv > '$out_ids' + ]]></command> + <inputs> + <param name="inputs" type="data" multiple="True" format="txt" label="Output files containing all peakgroups from OpenSWATH (using either mProphet or pyProphet) or Peakview." help="(--in)"/> + <param name="iformat" type="select" label="Which input file format is used" help="(--file_format)"> + <option value="openswath" selected="True">OpenSwath</option> + <option value="mprophet">mProphet (mQuest)</option> + <option value="peakview">PeakView</option> + </param> + <conditional name="method_sel"> + <param name="method" type="select" label="Which method to use for the clustering" + help="Note that the MST options will perform a local, MST guided alignment while the other options will use a reference-guided alignment. The global option will also move peaks which are below the selected FDR threshold. (--method)" > + <option value="best_overall" selected="True">best overall</option> + <option value="best_cluster_score">best cluster score</option> + <option value="global_best_cluster_score">global best cluster score</option> + <option value="global_best_overall">global best overall</option> + <option value="LocalMST">LocalMST</option> + <option value="LocalMSTAllCluster">LocalMSTAllCluster</option> + </param> + <when value="best_overall"/> + <when value="best_cluster_score"/> + <when value="global_best_cluster_score"/> + <when value="global_best_overall"/> + <when value="LocalMST"> + <expand macro="mst_params"/> + </when> + <when value="LocalMSTAllCluster"> + <expand macro="mst_params"/> + </when> + </conditional> + <param name="matrix_output_method" type="select" + label="Which columns are written besides Intensity" help="(--matrix_output_method)"> + <option value="none" selected="True">None</option> + <option value="RT">RT</option> + <option value="score">Score</option> + <option value="source">Source</option> + <option value="full">Full</option> + </param> + <param name="realign_method" type="select" label="How to re-align runs in retention time" help="(--realign_method)"> + <option value="diRT" selected="True">Use only deltaiRT (diRT) from the input file</option> + <option value="linear">Perform a linear regression using best peakgroups</option> + <option value="lowess">Use Robust locally weighted regression (lowess smoother)</option> + <option value="splinePy">Use Python native spline from scikits.datasmooth (slow!)</option> + <option value="CVSpline">Splines with cross-validation</option> + <option value="nonCVSpline">Splines without cross-validation</option> + <option value="WeightedNearestNeighbour">WeightedNearestNeighbour</option> + <option value="SmoothLLDMedian">SmoothLLDMedian</option> + <option value="splineR">Perform a spline fit using R</option> + <option value="splineR_external">Perform a spline fit using R (external)</option> + <option value="Earth">Use Multivariate Adaptive Regression Splines using py-earth</option> + <option value="lowess_cython">lowess_cython</option> + </param> + <conditional name="max_rt_diff_cond"> + <param name="max_rt_diff_sel" type="select" label="Enable difference in RT for two aligned features" help="Maximal difference in RT for two aligned features"> + <option value="opt_max_rt_diff_disabled" selected="True">disabled</option> + <option value="opt_max_rt_diff_enabled">set difference in RT</option> + </param> + <when value="opt_max_rt_diff_disabled"/> + <when value="opt_max_rt_diff_enabled"> + <param name="max_rt_diff" type="integer" value="30" label="Difference in RT (in seconds) for two aligned features" help="(--max_rt_diff)"/> + </when> + </conditional> + <conditional name="iso_max_rt_diff_cond"> + <param name="iso_max_rt_diff_sel" type="select" label="Enable difference in RT for two isotopic channels" help="Maximal difference in RT (in seconds) for two isotopic channels in the same run"> + <option value="opt_iso_max_rt_diff_disabled" selected="True">disabled</option> + <option value="opt_iso_max_rt_diff_enabled">set difference in RT</option> + </param> + <when value="opt_iso_max_rt_diff_disabled"/> + <when value="opt_iso_max_rt_diff_enabled"> + <param name="iso_max_rt_diff" type="integer" value="30" label="Difference in RT (in seconds) for two isotopic channels." help="(--iso_max_rt_diff)" /> + </when> + </conditional> + <conditional name="frac_selected_cond"> + <param name="frac_selected_sel" type="select" label="Enable fraction of runs" help="Do not write peakgroup if selected in less than this fraction of runs"> + <option value="opt_frac_selected_disabled" selected="True">disabled</option> + <option value="opt_frac_selected_enabled">set fraction of runs</option> + </param> + <when value="opt_frac_selected_disabled"/> + <when value="opt_frac_selected_enabled"> + <param name="frac_selected" type="float" value="0.0" min="0" max="1" label="Fraction of runs" help="(--frac_selected)"/> + </when> + </conditional> + <conditional name="fdr_cond"> + <param name="fdr_sel" type="select" label="Choose FDR method" help=""> + <option value="opt_fdr_disabled">disabled</option> + <option value="opt_target_fdr" selected="True">Target FDR</option> + <option value="opt_fdr_cutoff">FDR cutoff</option> + </param> + <when value="opt_fdr_disabled"/> + <when value="opt_target_fdr"> + <param name="target_fdr" type="float" value="0.01" label="Target FDR" help="Refers to the desired FDR on assay level. (--target_fdr)"/> + </when> + <when value="opt_fdr_cutoff"> + <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="A fixed m-score cutoff which does not take into account the number of runs (use target_fdr instead). (--fdr_cutoff)" /> + </when> + </conditional> + <param name="max_fdr_quality" type="float" value="0.05" min="0" label="Extension score cutoff" + help="During the extension phase of the algorithm, peakgroups of this quality will still be considered for alignment (in FDR) - it is possible to give a range in the format lower,higher+stepsize,stepsize - e.g. 0,0.31,0.01 (-1 will set it to fdr_cutoff) (--max_fdr_quality)"/> + <section name="further_params" title="Further parameters" expanded="False"> + <param name="disable_isotopic_grouping" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Disable grouping of isotopic variants" + help="Disable grouping of isotopic variants by peptide_group_label, thus disabling matching of isotopic variants of the same peptide across channels. If turned off, each isotopic channel will be matched independently of the other. If enabled, the more certain identification will be used to infer the location of the peak in the other channel. (--disable_isotopic_grouping)"/> + <conditional name="dscore_cond"> + <param name="dscore_sel" type="select" label="Enable the filter by d score (this is mainly for speedup)" help=""> + <option value="opt_dscore_disabled" selected="True">disabled</option> + <option value="opt_dscore_enabled">Use d score filter</option> + </param> + <when value="opt_dscore_disabled"/> + <when value="opt_dscore_enabled"> + <param name="dscore_cutoff" type="float" value="1.96" label="d score cut-off" + help="Quality cutoff to still consider a feature for alignment using the d_score: everything below this d-score is discarded (this is mainly for speedup). (--dscore_cutoff)"/> + </when> + </conditional> + <conditional name="nr_high_conf_exp_cond"> + <param name="nr_high_conf_exp_sel" type="select" label="Enable the filter by d score (this is mainly for speedup)" help=""> + <option value="opt_nr_high_conf_exp_disabled" selected="True">disabled</option> + <option value="opt_nr_high_conf_exp_enabled">Use number of experiments</option> + </param> + <when value="opt_nr_high_conf_exp_disabled"/> + <when value="opt_nr_high_conf_exp_enabled"> + <param name="nr_high_conf_exp" type="integer" value="1" optional="True" label="Number of experiments with high confidence" + help="Number of experiments in which the peptide needs to be identified with high confidence (e.g. above fdr_curoff). (--nr_high_conf_exp)"/> + </when> + </conditional> + <param name="readmethod" type="select" label="Read full or minimal transition groups" optional="True" help="(--readmethod)"> + <option value="disabled" selected="True">disabled</option> + <option value="minimal">minimal</option> + <option value="full">full</option> + </param> + <conditional name="alignment_score_cond"> + <param name="alignment_score_sel" type="select" label="Enable the filter by d score (this is mainly for speedup)" help=""> + <option value="opt_alignment_score_disabled" selected="True">disabled</option> + <option value="opt_alignment_score_enabled">Use number of experiments</option> + </param> + <when value="opt_alignment_score_disabled"/> + <when value="opt_alignment_score_enabled"> + <param name="alignment_score" type="float" value="0.0001" optional="True" label="Alignment score" + help="Minimal score needed for a feature to be considered for alignment between runs (e.g. score needed to be considered an 'anchor point' for pairwise alignment). (--alignment_score)"/> + </when> + </conditional> + </section> + </inputs> + <outputs> + <!-- Matrix containing one peak group per row --> + <data format="tabular" name="out_matrix"/> + <!-- Id file only containing the ids --> + <data format="tabular" name="out_ids"/> + <!-- Output file with filtered peakgroups for quantification --> + <data format="tabular" name="out"> + <filter>iformat == 'openswath'</filter> + </data> + </outputs> + <tests> + <test> + <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="method" value="best_cluster_score" /> + <param name="fdr_sel" value="opt_fdr_disabled" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_matrix" file="feature_alignment_1_openswath_output_matrix.csv" lines_diff="2" ftype="tabular" /> + <output name="out_ids" file="feature_alignment_1_openswath_output_cluster_ids.csv" ftype="tabular" /> + </test> + <test> + <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="method" value="best_overall" /> + <param name="fdr_sel" value="opt_fdr_disabled" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_matrix" file="feature_alignment_2_output_2_matrix.csv" lines_diff="2" ftype="tabular" /> + <output name="out_ids" file="feature_alignment_2_output_1_ids.csv" ftype="tabular" /> + </test> + <test> + <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="realign_method" value="splineR" /> + <param name="method" value="best_cluster_score" /> + <param name="fdr_sel" value="opt_fdr_disabled" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_ids" file="feature_alignment_3_openswath_output_splineR_cluster_ids.csv" ftype="tabular" /> + </test> + <test> + <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" /> + <param name="iformat" value="openswath" /> + <param name="realign_method" value="splinePy" /> + <param name="method" value="best_cluster_score" /> + <param name="fdr_sel" value="opt_fdr_disabled" /> + <param name="max_fdr_quality" value="0.4" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_ids" file="feature_alignment_3_openswath_output_splinePy_cluster_ids.csv" ftype="tabular" /> + </test> + <test> + <param name="inputs" value="feature_alignment_peakview_input_2.csv" ftype="txt" /> + <param name="iformat" value="peakview" /> + <param name="method" value="best_cluster_score" /> + <param name="max_rt_diff_sel" value="opt_max_rt_diff_enabled" /> + <param name="iso_max_rt_diff_sel" value="opt_iso_max_rt_diff_enabled" /> + <param name="frac_selected_sel" value="opt_frac_selected_enabled" /> + <param name="disable_isotopic_grouping" value="True" /> + <param name="nr_high_conf_exp_sel" value="opt_nr_high_conf_exp_enabled" /> + <param name="alignment_score_sel" value="opt_alignment_score_enabled" /> + <param name="max_fdr_quality" value="0.0001" /> + <param name="fdr_sel" value="opt_fdr_cutoff" /> + <param name="fdr_cutoff" value="0.000000001" /> + <param name="matrix_output_method" value="RT" /> + <output name="out_matrix" file="feature_alignment_5_peakview_output_matrix.csv" lines_diff="2" ftype="tabular" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate information from all available runs. The input consists of a set of csv files derived from a targeted proteomics experiment generated by OpenSWATH (using either mProphet or pyProphet) or generated by Peakview. + +There are two basic running modes available. The first one uses a reference-based alignment where a single run is chosen as a reference and all other runs are aligned to it. This is a useful choice for a small number of runs that are chromatographically similar. The second mode generates a guidance tree based on chromatographic similarity of the input runs and uses this tree to align the targeted proteomics runs (the nodes in the tree are runs and the edges are pairwise alignments). Generally this mode is better for a large number of runs or for chromatographically dissimilar samples. + +TRIC is part of msproteomicstools. For additional help please visit the `TRIC documentation <https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md>`_ + +]]> + </help> + <citations> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,10 @@ +<?xml version="1.0" ?> +<macros> + <xml name="mst_params"> + <param name="mst_useRTCorrection" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use aligned peakgroup RT to continue threading" help="Use aligned peakgroup RT to continue threading in MST algorithm. It is highly recommend to set this to 'True'"/> + <param name="mst_Stdev_multiplier" type="float" value="-1.0" label="Standard deviation multiplier" + help="Turn on adaptive RT tolerances: How many standard deviations the peakgroup can deviate in RT during the alignment (if less than max_rt_diff, then max_rt_diff is used). It is recommended to set this to a value between 2.0 and 4.0."/> + <param name="mst_useLocalStdev" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use local standard deviation" help="Use standard deviation of local region of the chromatogram. This is experimental and may not work."/> + <param name="mst_useReference" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use a reference-based tree for alignment" help=""/> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_1_openswath_output_cluster_ids.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,15 @@ +f_10695898602322980677 +f_1127496644798128693 +f_13169006090966118307 +f_13533807518639064717 +f_14033255530503723792 +f_15970037542975291475 +f_17032480123683661142 +f_17124686349881931625 +f_17231814870828860734 +f_17254733915653094913 +f_1946229642962775443 +f_6146381832908670245 +f_7259477005084093710 +f_7695999890006491586 +f_7995570933545899074
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_1_openswath_output_matrix.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,2 @@ +Peptide Protein Intensity_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_0_0 RT_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_0_0 Intensity_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_1_0 RT_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_1_0 Intensity_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_2_0 RT_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_2_0 Intensity_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_3_0 RT_dataset_04182c5f-3bb8-4de3-99d9-50c0de9c87fe.dat_3_0 RT_mean RT_std pg_pvalue +17365_TLDTAAEKIVETATR/3_run0 Spyo_Exp3652_DDB_SeqID_324814 120.0 24.5656409693 50.0 18.2354661146 100.0 38.7373461565 130.0 36.7481804498 29.57165842255 8.501202368326412 1.3988719619301746e-10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_2_output_1_ids.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,4 @@ +f_10695898602322980677 +f_14033255530503723792 +f_7259477005084093710 +f_7995570933545899074
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_2_output_2_matrix.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,2 @@ +Peptide Protein Intensity_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_0_0 RT_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_0_0 Intensity_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_1_0 RT_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_1_0 Intensity_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_2_0 RT_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_2_0 Intensity_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_3_0 RT_dataset_149f3c1b-64bd-46ee-ac39-cc3dd54f302d.dat_3_0 RT_mean RT_std pg_pvalue +17365_TLDTAAEKIVETATR/3_run0 Spyo_Exp3652_DDB_SeqID_324814 120.0 24.5656409693 130.0 88.9418431607 100.0 38.7373461565 130.0 36.7481804498 47.248252684075 24.675612494332714 1.201290380110036e-09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_3_openswath_input.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,33 @@ +transition_group_record decoy transition_group_id run_id filename RT id Sequence FullPeptideName ProteinName assay_rt delta_rt leftWidth norm_RT peak_apices_sum rightWidth aggr_Peak_Area peak_group_rank d_score m_score iRT_of_assay comment Charge aggr_Peak_Apex aggr_Fragment_Annotation sn_ratio Intensity +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4157.2848086113 f_14033255530503723792 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-06 61.1 cluster TRUE 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4236.7508741707 f_13169006090966118307 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 104.0317065287 4199.740234375 64.1108995811 8628 4261.1899414063 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 2 -3.1954820554 0.0005 61.1 cluster FALSE 2 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 1 250 +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4396.94273305 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+strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4149.633676731 f_1127496644798128693 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 -199.2590928254 3933.4499511719 55.2860439144 381 3957.3500976563 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 3 -1.8881030993 0.325723046 61.1 NA 2 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 1 120 +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4857.7861318076 f_7695999890006491586 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 270.9862086544 4438.6899414063 68.9583866448 3605 4486.4799804688 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 4 -1.8914462466 0.3350264606 61.1 NA 2 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 1 130 +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4545.5372693098 f_7995570933545899074 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 38.7373461565 4199.7202148438 62.2205422539 997 4250.9301757813 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 2 0.440521846 0.3 61.1 cluster TRUE 2 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 1 100 +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4697.2778585929 f_13533807518639064717 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 110.4779354397 4261.169921875 64.3018309281 5641 4315.7900390625 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 1 -1.4000010917 0.15 61.1 cluster FALSE 2 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 1 80 +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4400.5531316006 f_15970037542975291475 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 -186.2467915526 3988.0700683594 55.6934570662 512 4011.9599609375 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 3 -1.6324942375 0.3278895544 61.1 NA 2 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 1 20 +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4761.797222448 f_10695898602322980677 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 36.7481804498 4134.8701171875 62.1581880861 1624 4186.080078125 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 2 2.8268775648 0.1 61.1 cluster TRUE 2 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 1 130 +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4842.7563496649 f_6146381832908670245 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 117.7073076667 4213.3901367188 64.4992677521 13028 4264.58984375 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 -1.2538849522 0.1 61.1 cluster FALSE 2 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 60 +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 5002.5892306441 f_17231814870828860734 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 277.5401886459 4384.080078125 69.1211247371 6969 4425.0400390625 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 4 -2.1006079776 0.3411849331 61.1 NA 2 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 1 40 +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4550.661382069 f_17124686349881931625 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 -174.3876599292 3943.6899414063 56.0528131928 610 3960.7600097656 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 3 -1.1356280226 0.3069359946 61.1 NA 2 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 1 20 +pg1 FALSE trgr1 0 split_hroest_K120808_combined.featureXML 100 1 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg1 FALSE trgr1 1 split_hroest_K120808_combined.featureXML 200 2 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg1 FALSE trgr1 2 split_hroest_K120808_combined.featureXML 300 3 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg1 FALSE trgr1 3 split_hroest_K120808_combined.featureXML 400 4 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 0 split_hroest_K120808_combined.featureXML 5000 5 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 1 split_hroest_K120808_combined.featureXML 5200 6 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 2 split_hroest_K120808_combined.featureXML 5400 7 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg2 FALSE trgr2 3 split_hroest_K120808_combined.featureXML 5600 8 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 0 split_hroest_K120808_combined.featureXML 2000 9 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 1 split_hroest_K120808_combined.featureXML 2100 10 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 2 split_hroest_K120808_combined.featureXML 2300 11 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg3 FALSE trgr3 3 split_hroest_K120808_combined.featureXML 2500 12 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 0 split_hroest_K120808_combined.featureXML 2100 9 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 1 split_hroest_K120808_combined.featureXML 2200 10 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 2 split_hroest_K120808_combined.featureXML 2400 11 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 +pg4 FALSE trgr4 3 split_hroest_K120808_combined.featureXML 2600 12 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-011 61.1 forAlignment 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_3_openswath_output_splinePy_cluster_ids.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,31 @@ +1 +10 +10 +11 +11 +12 +12 +2 +3 +4 +5 +6 +7 +8 +9 +9 +f_10695898602322980677 +f_1127496644798128693 +f_13169006090966118307 +f_13533807518639064717 +f_14033255530503723792 +f_15970037542975291475 +f_17032480123683661142 +f_17124686349881931625 +f_17231814870828860734 +f_17254733915653094913 +f_1946229642962775443 +f_6146381832908670245 +f_7259477005084093710 +f_7695999890006491586 +f_7995570933545899074
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_3_openswath_output_splineR_cluster_ids.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,31 @@ +1 +10 +10 +11 +11 +12 +12 +2 +3 +4 +5 +6 +7 +8 +9 +9 +f_10695898602322980677 +f_1127496644798128693 +f_13169006090966118307 +f_13533807518639064717 +f_14033255530503723792 +f_15970037542975291475 +f_17032480123683661142 +f_17124686349881931625 +f_17231814870828860734 +f_17254733915653094913 +f_1946229642962775443 +f_6146381832908670245 +f_7259477005084093710 +f_7695999890006491586 +f_7995570933545899074
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_5_peakview_output_matrix.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,3 @@ +Peptide Protein Intensity_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_002_SW.wiff (sample 1)_0 RT_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_002_SW.wiff (sample 1)_0 Intensity_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_003_SW.wiff (sample 1)_0 RT_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_003_SW.wiff (sample 1)_0 Intensity_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_004_SW.wiff (sample 1)_0 RT_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_004_SW.wiff (sample 1)_0 Intensity_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_005_SW.wiff (sample 1)_0 RT_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_005_SW.wiff (sample 1)_0 Intensity_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_006_SW.wiff (sample 1)_0 RT_dataset_6b0147ab-64bc-4532-8b71-f590fada827e.dat_ywu_L121218_006_SW.wiff (sample 1)_0 RT_mean RT_std pg_pvalue +LIGNMALLPLR+2 Actin-related protein 2/3 complex subunit 3 musculus 2900.0 80.41 3700.0 80.3267592431513 2300.0 80.2970686001864 2300.0 80.385140821583 3200.0 80.3699472702056 80.35778318702526 0.04067369369496349 1.0 +LIGNMALLPLR+3 Actin-related protein 2/3 complex subunit 3 musculus 150.0 80.33 97.0 80.3372300313998 140.0 80.3072715711995 120.0 80.3546761207408 98.0 80.2433156865484 80.3144986819777 0.03870524941407648 1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_openswath_input_1.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,17 @@ +transition_group_record decoy transition_group_id run_id filename RT id Sequence FullPeptideName ProteinName assay_rt delta_rt leftWidth norm_RT peak_apices_sum rightWidth aggr_Peak_Area peak_group_rank d_score m_score iRT_of_assay comment Charge aggr_Peak_Apex aggr_Fragment_Annotation sn_ratio Intensity Comment: The following columns are for mProphet Tr iRT_empirical iRT_predicted protein transition_group_pepseq +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4157.2848086113 f_14033255530503723792 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 24.5656409693 4134.8798828125 61.8076522795 3884 4172.4301757813 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 4.6430186544 2.70626830372887e-06 61.1 cluster TRUE 2 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 5502.000000;5889.000000;2222.000000;2512.000000;1460.000000;1020.000000 1 120 4157.2848086113 4157.2848086113 4147.2848086113 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4236.7508741707 f_13169006090966118307 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 104.0317065287 4199.740234375 64.1108995811 8628 4261.1899414063 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 2 -3.1954820554 0.0005 61.1 cluster FALSE 2 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 791.000000;18367.000000;540.000000;22477.000000;750.000000;560.000000 1 250 4236.7508741707 4236.7508741707 4226.7508741707 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4396.94273305 f_17032480123683661142 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 264.223565408 4377.25 68.7539061792 5567 4431.8701171875 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 4 -3.3249147171 0.3220580725 61.1 NA 2 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 280.000000;1351.000000;280.000000;920.000000;31052.000000;860.000000 1 150 4396.94273305 4396.94273305 4386.94273305 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R02/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 0 split_hroest_K120808_combined.featureXML 4103.0075035304 f_17254733915653094913 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4132.719167642 -29.7116641116 4083.669921875 60.2344769173 460 4110.9799804688 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 3 -1.1571588178 0.2855822027 61.1 NA 2 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 30.000000;380.000000;230.000000;970.000000;490.000000;90.000000 1 180 4103.0075035304 4103.0075035304 4093.0075035304 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4237.834612717 f_7259477005084093710 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 88.9418431607 4220.2099609375 63.6912797891 5950 4257.759765625 100.000000;11940.000000;90.000000;14746.000000;310.000000;100.000000 1 -1.2978089457 0.005 61.1 cluster FALSE but FDR below 1% 2 100.000000;11940.000000;90.000000;14746.000000;310.000000;100.000000 100.000000;11940.000000;90.000000;14746.000000;310.000000;100.000000 1 130 4237.834612717 4237.834612717 4227.834612717 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4167.1282356709 f_1946229642962775443 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 18.2354661146 4128.0400390625 61.629163735 967 4196.3198242188 2368.000000;3613.000000;1050.000000;1430.000000;750.000000;440.000000 2 1.2528426368 0.0590706643 61.1 cluster TRUE 2 2368.000000;3613.000000;1050.000000;1430.000000;750.000000;440.000000 2368.000000;3613.000000;1050.000000;1430.000000;750.000000;440.000000 1 50 4167.1282356709 4167.1282356709 4157.1282356709 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 4204.9589978683 f_546336782280825114 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 56.0662283119 4199.7299804688 62.7324789567 180 4216.7998046875 390.000000;180.000000;30.000000;160.000000;130.000000;70.000000 4 -1.9709294327 0.3276775879 61.1 NA 2 390.000000;180.000000;30.000000;160.000000;130.000000;70.000000 390.000000;180.000000;30.000000;160.000000;130.000000;70.000000 1 220 4204.9589978683 4204.9589978683 4194.9589978683 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl1_R03/split_hroest_K120808_all_peakgroups_for_pedros.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 1 split_hroest_K120808_combined.featureXML 3949.633676731 f_1127496644798128693 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4148.8927695564 -199.2590928254 3933.4499511719 55.2860439144 381 3957.3500976563 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 3 -1.8881030993 0.325723046 61.1 NA 2 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 220.000000;240.000000;40.000000;180.000000;1062.000000;20.000000 1 120 3949.633676731 3949.633676731 3939.633676731 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4457.7861318076 f_7695999890006491586 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 270.9862086544 4438.6899414063 68.9583866448 3605 4486.4799804688 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 4 -1.8914462466 0.3350264606 61.1 NA 2 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 130.000000;1110.000000;150.000000;430.000000;19792.000000;780.000000 1 130 4457.7861318076 4457.7861318076 4447.7861318076 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4225.5372693098 f_7995570933545899074 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 38.7373461565 4199.7202148438 62.2205422539 997 4250.9301757813 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 2 0.440521846 0.3 61.1 cluster TRUE 2 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 1983.000000;3069.000000;1130.000000;1100.000000;710.000000;410.000000 1 100 4225.5372693098 4225.5372693098 4215.5372693098 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4297.2778585929 f_13533807518639064717 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 110.4779354397 4261.169921875 64.3018309281 5641 4315.7900390625 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 1 -1.4000010917 0.15 61.1 cluster FALSE 2 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 620.000000;10240.000000;320.000000;14723.000000;780.000000;310.000000 1 80 4297.2778585929 4297.2778585929 4287.2778585929 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R02/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 2 split_hroest_K120808_combined.featureXML 4000.5531316006 f_15970037542975291475 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4186.7999231532 -186.2467915526 3988.0700683594 55.6934570662 512 4011.9599609375 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 3 -1.6324942375 0.3278895544 61.1 NA 2 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 420.000000;420.000000;60.000000;290.000000;1273.000000;20.000000 1 20 4000.5531316006 4000.5531316006 3990.5531316006 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4161.797222448 f_10695898602322980677 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 36.7481804498 4134.8701171875 62.1581880861 1624 4186.080078125 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 2 2.8268775648 0.1 61.1 cluster TRUE 2 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 3522.000000;4438.000000;1680.000000;1940.000000;1291.000000;690.000000 1 130 4161.797222448 4161.797222448 4151.797222448 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4242.7563496649 f_6146381832908670245 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 117.7073076667 4213.3901367188 64.4992677521 13028 4264.58984375 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 -1.2538849522 0.1 61.1 cluster FALSE 2 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 540.000000;21788.000000;450.000000;30697.000000;870.000000;240.000000 1 60 4242.7563496649 4242.7563496649 4232.7563496649 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 4402.5892306441 f_17231814870828860734 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 277.5401886459 4384.080078125 69.1211247371 6969 4425.0400390625 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 4 -2.1006079776 0.3411849331 61.1 NA 2 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 160.000000;1521.000000;320.000000;550.000000;35766.000000;520.000000 1 40 4402.5892306441 4402.5892306441 4392.5892306441 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR +strep_align/Strep0_Repl2_R03/split_hroest_K120808_all_peakgroups_forpedro.xls:17365_TLDTAAEKIVETATR/3_run0 0 0 FALSE 17365_TLDTAAEKIVETATR/3_run0 3 split_hroest_K120808_combined.featureXML 3950.661382069 f_17124686349881931625 TLDTAAEKIVETATR TLDTAAEKIVETATR Spyo_Exp3652_DDB_SeqID_324814 4125.0490419982 -174.3876599292 3943.6899414063 56.0528131928 610 3960.7600097656 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 3 -1.1356280226 0.3069359946 61.1 NA 2 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 360.000000;410.000000;30.000000;320.000000;1331.000000;40.000000 1 20 3950.661382069 3950.661382069 3940.661382069 Spyo_Exp3652_DDB_SeqID_324814 TLDTAAEKIVETATR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/feature_alignment_peakview_input_2.csv Fri Dec 10 00:30:05 2021 +0000 @@ -0,0 +1,22 @@ +"Time" "peakGroup" "Sample" "Pep.Index" "Protein" "Decoy" "Peptide" "Confidence" "Precursor.MZ" "Precursor.Charge" "Peak.RT" "Transition.Areas" "Average.Peak" "Median.RT" "MaxPeak.RT" "MaxPeak.Intensity" "Score" "AbsoluteMzError" "MedianMzError" "RtConsistency" "ExpectedRt" "ChroWidthConsistency" "IntensityPattern" "YIons" "MatchProbability" "SignalToNoise" "HLIntensityCorrelation" "Xcorr2DPeaks" "Num.Prerranked.groups" "Num.Evaluated.groups" "Preranking" "RT" "ExpectedRT" "RTHeight" "ExpectedRTHeight" "RT50Width" "RTNoise" "NumRTPeaksAboveSN" "MZ" "ExpectedMZ" "MZHeight" "MZ50Width" "Charge" "ExpectedCharge" "Mono" "Used" "YIonMZ" "ExpectedYIons" "X" "aligned_rt" "aligned_rt_diff" +"11:23:15" 1 "ywu_L121218_002_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.9226304650383 "611.4239_y5:null_null_null,498.3398_y4:2033.1569058655_151.076127468725_8.85330715163171,713.4014_b7:1365.37315120079_70_5.18589778942739,600.3174_b6:1359.22114090841_123.833655084656_6.17151478387135,529.2803_b5:null_null_null,682.461_y6:null_null_null," "80.05:10,80.19:176,80.22:351.9,80.45:176,80.62:3" 80.33 80.27 150 1.9e+08 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.73 0.53 0.13 1 1 1 "80.3875450179245_80.2681172911531_80.3242628231043_80.3408775664709_80.3491145712847_80.2517647442096" 79.9226304650383 "93.2277914764818_151.076127468725_70_123.833655084656_66.6648179751019_81" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.138196816636594_0.256866657170733_0.350689583333335_0.232522379159306_0.318119040562934_0.387719615516488" "4.95061404883585_8.85330715163171_5.18589778942739_6.17151478387135_5.99752823804411_4.55081763169696" "1_1_1_1_2_1" "611.422011040799_498.348530307152_713.409665210068_600.319850643079_529.289683045948_682.44857252014" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "13.6666666666667_13.3333333333333_13.3333333333333_20.3333333333333_13.3333333333333_20.3333333333333" "0.0160945543258322_0.0488412904473989_0.0358163514524676_0.0173936213901698_0.00974217047485126_0.00661567511519934" "1_1_1_1_2_1" "1_1_1_1_1_1" "False_True_True_True_True_False" "True_True_True_True_True_True" "0_288.213417469409_385.259600476745_498.348530307152_0_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.33 0 +"11:45:05" 1 "ywu_L121218_002_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9217331132498 "984.5659_y9:63172.9695350965_2913.21957472496_32.6363403871121,682.461_y6:27701.8619944977_1377.43938585543_8.62548016272112,813.5015_y7:6817.05357691055_561.21992990478_20.6417114060844,927.5444_y8:6259.08450213339_255.668467680939_22.7189417125541,826.4855_b8:null_null_null,713.4014_b7:2489.71458466376_294.551253757974_41.7198927051708," "80.01:450.6,80.2:2935.3,80.46:5870.5,80.55:2935.3,80.69:470.2" 80.41 80.38 2900 8.5e+11 0.054 0.074 0.03 0.089 0.14 0.02 0.0099 0.035 1 0.5 0.23 18 3 1 "80.3847265781083_80.3635034220867_80.4302157655778_80.3627289651931_80.4304769279579_80.4789452144931" 79.9217331132498 "2913.21957472496_1377.43938585543_561.21992990478_255.668467680939_430.552794744168_294.551253757974" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.328344360247897_0.331599877802205_0.197121681696942_0.482989703137633_0.482827452321217_0.158959141540507" "32.6363403871121_8.62548016272112_20.6417114060844_22.7189417125541_30.1972793139185_41.7198927051708" "3_1_2_4_2_5" "984.540922640428_682.467753766226_813.511891732749_927.557670439387_826.501929646604_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "168.333333333333_131_61.3333333333333_30.6666666666667_13.6666666666667_N/A" "0.0076031054517216_0.0457597515854786_0.0374294178778882_0.029309592705431_0.0324639638558892_N/A" "0_1_1_1_1_0" "1_1_1_1_1_1" "Unknown_True_True_True_False_Unknown" "True_True_True_True_True_True" "175.14154928442_288.17524862357_385.259246937153_498.347439687727_611.424923681304_682.467753766226_813.511891732749_927.557670439387_984.540922640428_1097.64646750353_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.41 0 +"11:45:05" 2 "ywu_L121218_002_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9217331132498 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:26415.0318094871_1505.72434561968_31.2090056959494,713.4014_b7:null_null_null," "78.92:92.8,79.11:814.4,79.2:1628.7,79.41:814.4,79.6:165.3" 79.23 79.24 1500 210000 0.5 0.5 0.75 0.089 0.5 0.75 0.79 0.52 0.005 0.5 0.75 18 3 2 "79.2280349897488_N/A_N/A_79.2267074012329_79.2366567324793_N/A" 79.9217331132498 "9165.04035107153_N/A_N/A_1142.347612787_1505.72434561968_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.289693645651596_N/A_N/A_0.272703094160448_0.300779618806786_N/A" "30.595322958426_N/A_N/A_21.6487619093028_31.2090056959494_N/A" "1_N/A_N/A_1_1_N/A" "984.583643522916_682.439745778068_813.462829826501_927.560190138688_826.487700788133_713.332836640461" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "1026_17_17.0000000002328_139_169_20.3333333333333" "0.0528225874248847_0.00915705196894123_0.00419014783278726_0.061628638481011_0.0583090823893144_0.0152053454114593" "1_2_0_1_0_5" "1_1_1_1_1_1" "False_True_Unknown_False_Unknown_False" "True_False_False_True_True_False" "175.11498948848_288.172165486245_0_0_0_682.419638638861_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.23 0 +"11:45:05" 3 "ywu_L121218_002_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9217331132498 "984.5659_y9:1616.42988483826_131.233156543058_21.2872124526729,682.461_y6:1300.21980511359_95.9807853822131_6.67305574172559,813.5015_y7:840.098846386696_132.276870446228_20.5933104277774,927.5444_y8:373.882902853722_72.6421801600245_18.8812537139364,826.4855_b8:675.788180660378_163.110710100234_24.663600700104,713.4014_b7:null_null_null," "75.71:392.1,75.74:463,75.88:925.9,75.92:463,76.05:289.6" 75.83 75.77 160 45000 0.5 0.5 0.079 0.52 0.47 0.37 0.55 0.19 0.64 0.5 0.36 18 3 3 "75.8303010940226_75.9070595744131_75.9403833333333_75.7686_75.7686_75.8341911820244" 79.9217331132498 "131.233156543058_95.9807853822131_132.276870446228_72.6421801600245_163.110710100234_383.871236201916" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.214956620442308_0.228138567048632_0.0911129845835745_0.0797467732449491_0.0691309903446609_0.468465832653436" "21.2872124526729_6.67305574172559_20.5933104277774_18.8812537139364_24.663600700104_43.7497137357593" "7_3_8_15_6_4" "984.560648952255_N/A_813.483650376649_N/A_N/A_713.391815610818" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "34_N/A_16.6666666666667_N/A_N/A_30.3333333332557" "0.00557728288197268_N/A_0.0327104558474502_N/A_N/A_0.00377009978888054" "0_0_1_0_0_3" "1_1_1_1_1_1" "Unknown_Unknown_True_Unknown_Unknown_False" "True_True_True_True_True_True" "0_288.222821731842_0_498.274877624178_611.370451935052_0_813.483650376649_0_984.560648952255_1097.57090085832_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.83 0 +"12:21:59" 1 "ywu_L121218_003_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.4599885783973 "611.4239_y5:695.955480627102_81.5958365448391_3.92152729414383,498.3398_y4:2243.25091199125_97.2531292215032_4.25943739856399,713.4014_b7:534.424645320621_50.6392833808782_5.91082136540284,600.3174_b6:801.413919946023_87.4041774769889_5.92348122073576,529.2803_b5:798.734694509919_60_6.99582870957075,682.461_y6:null_null_null," "79.53:40,79.61:203.9,79.76:407.8,79.85:203.9,79.99:20.2" 79.75 79.71 97 3.3e+09 0.5 0.5 0.05 0.13 0.05 0.05 0.05 0.075 0.83 0.5 0.05 1 1 1 "79.7691692602483_79.7130270329789_79.7873518870944_79.7355352702599_79.7529370487846_N/A" 79.4599885783973 "81.5958365448391_97.2531292215032_50.6392833808782_87.4041774769889_60_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.107360617963792_0.280681766658262_0.204320329342025_0.180310757496116_0.340557962256085_N/A" "3.92152729414383_4.25943739856399_5.91082136540284_5.92348122073576_6.99582870957075_N/A" "1_1_1_1_3_N/A" "611.418595146455_498.342011099309_N/A_N/A_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "13.3333333333333_20_N/A_N/A_N/A_N/A" "0.0261766851290304_0.0237477931120793_N/A_N/A_N/A_N/A" "1_1_0_0_0_0" "1_1_1_1_1_1" "True_True_Unknown_Unknown_Unknown_Unknown" "True_True_True_True_True_False" "175.112053679092_0_385.264683849443_498.342011099309_611.418595146455_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3372300313998 -0.587230031399798 +"12:46:07" 1 "ywu_L121218_003_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.4590914543314 "984.5659_y9:62342.0136655603_3725.01197116701_35.7878492666171,682.461_y6:31194.2841276724_1510.20616405492_8.31637249686309,813.5015_y7:17403.6864015132_679.389066434029_16.3739140748602,927.5444_y8:5519.99473730796_375.366186119185_20.4467322079474,826.4855_b8:9659.95632589417_647.450474018238_32.0915835709068,713.4014_b7:null_null_null," "79.26:234.4,79.59:3631,79.78:7262,79.84:3631,80.01:378" 79.74 79.76 3700 1e+14 0.04 0.12 0.064 0.054 0.17 0.059 0.015 0.02 0.005 0.5 0.079 19 3 1 "79.7644577758905_79.736637618253_79.6580663228811_79.7277414786923_79.7445548837875_79.7672655310848" 79.4590914543314 "3725.01197116701_1510.20616405492_679.389066434029_375.366186119185_647.450474018238_454.98845996843" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.252816287122201_0.322681716367526_0.533268176929752_0.250343589188574_0.202465161099397_0.115193810826725" "35.7878492666171_8.31637249686309_16.3739140748602_20.4467322079474_32.0915835709068_51.1608860889051" "3_1_1_2_2_6" "984.536780957495_682.463636500082_813.507963873021_927.559458911263_826.478931662218_713.40785184937" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "92_193.666666666667_68.3333333333333_40.6666666666667_34.3333333330229_17" "0.0276704712633773_0.0404383442378276_0.0640770868197933_0.0118932230194559_0.00286275658686463_0.0188505919459203" "1_1_1_1_0_2" "1_1_1_1_1_1" "True_True_True_True_Unknown_False" "True_True_True_True_True_True" "175.136478361909_288.219494139316_385.261722178417_498.341615915194_611.425582744104_682.463636500082_813.507963873021_927.559458911263_984.536780957495_1097.66028200887_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3267592431513 -0.586759243151263 +"12:46:07" 2 "ywu_L121218_003_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.4590914543314 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:29093.9585385698_1776.12676050086_32.0297652471469,713.4014_b7:null_null_null," "78.46:130.6,78.65:944.6,78.8:1889.2,78.92:944.6,79.15:95.5" 78.75 78.76 1800 1200000 0.34 0.36 0.75 0.079 0.5 0.75 0.29 0.57 0.005 0.5 0.75 19 3 2 "78.7516732973404_N/A_N/A_78.7550152573598_78.7610379920924_N/A" 79.4590914543314 "10741.5857445992_N/A_N/A_1246.10699307787_1776.12676050086_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.221542651828784_N/A_N/A_0.201619487133527_0.27424393414789_N/A" "34.7194778603106_N/A_N/A_21.0092462057853_32.0297652471469_N/A" "1_N/A_N/A_1_1_N/A" "984.580681795204_682.412940381784_N/A_927.554781758257_826.486868259013_713.454301638241" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "1048.66666666667_54.6666666666667_N/A_130.666666666667_165_16.9999999997672" "0.0571396809709768_0.0146609016740058_N/A_0.0544077444664026_0.0564364522343794_0.00384563761019763" "1_1_0_1_0_0" "1_1_1_1_1_1" "False_True_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.115723500999_288.140261041746_385.20544320406_498.307462939696_0_682.412940381784_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.2581620805884 -0.508162080588434 +"12:46:07" 3 "ywu_L121218_003_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.4590914543314 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:691.792131017952_86.7456409023798_20.2324044441414,826.4855_b8:null_null_null,713.4014_b7:null_null_null," "75.42:65.3,75.44:61.8,75.48:123.6,75.62:61.8,75.65:25.3" 75.55 75.55 87 700 0.5 0.5 0.75 0.52 0.5 0.75 0.79 0.94 0.14 0.5 0.75 19 3 3 "75.515728211372_N/A_N/A_75.5542535029337_75.5291360931461_75.5490535702549" 79.4590914543314 "159.55142461883_N/A_N/A_86.7456409023798_153.566740036464_589.545536155857" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.233981881483984_N/A_N/A_0.181763038584251_0.203343671103326_0.211959115150307" "33.3173351222639_N/A_N/A_20.2324044441414_29.8936920366768_45.1053314143605" "6_N/A_N/A_13_10_3" "984.562623822968_682.449936903196_N/A_927.555999078148_826.472048592545_713.397062064111" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "17_13.3333333333333_N/A_17_20.6666666666667_47.6666666666667" "0.0193737662615376_0.00860394757592076_N/A_0.0341759906041261_0.0121736639329129_0.011965251708034" "2_1_0_1_2_4" "1_1_1_1_1_1" "False_False_Unknown_True_False_False" "True_False_False_True_True_True" "0_0_385.261526700595_498.339646411046_0_0_0_927.555999078148_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.868341077206 -0.318341077205986 +"13:22:36" 1 "ywu_L121218_004_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.5941352903303 "611.4239_y5:981.529311549473_85.6745843821705_4.28290555684228,498.3398_y4:2929.44226409681_136.365977283862_8.34150108955811,713.4014_b7:946.500696399436_102.958269334049_5.14035968205949,600.3174_b6:985.500645026059_69.5706747125369_6.26787860726159,529.2803_b5:1228.13210503255_78.8876311302884_6.32066783717301,682.461_y6:null_null_null," "79.59:20,79.65:248.2,79.82:496.4,79.95:248.2,80.05:27.9" 79.82 79.78 140 2.1e+09 0.5 0.5 0.05 0.075 0.05 0.05 0.13 0.075 0.88 0.5 0.05 1 1 1 "79.8672435017827_79.7753312858912_79.822602587473_79.7341166556411_79.8169180816553_N/A" 79.5941352903303 "85.6745843821705_136.365977283862_102.958269334049_69.5706747125369_78.8876311302884_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.2207251287725_0.462644753675093_0.0981768021016762_0.283719440970074_0.300852034803768_N/A" "4.28290555684228_8.34150108955811_5.14035968205949_6.26787860726159_6.32066783717301_N/A" "1_1_1_1_2_N/A" "N/A_498.345883997847_N/A_600.31381437701_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "N/A_17_N/A_13.666666666657_N/A_N/A" "N/A_0.0128009741875417_N/A_0.0171189848325639_N/A_N/A" "0_1_0_1_0_0" "1_1_1_1_1_1" "Unknown_True_Unknown_True_Unknown_Unknown" "True_True_True_True_True_False" "0_0_385.25028700361_498.345883997847_0_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3072715711995 -0.487271571199457 +"13:44:11" 1 "ywu_L121218_004_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.5932466525774 "984.5659_y9:59350.8897150608_2346.981786619_37.9850649135046,682.461_y6:25402.5280414736_1045.80405098809_9.24410350622813,813.5015_y7:null_null_null,927.5444_y8:6720.00225295179_341.829994810099_22.500243015707,826.4855_b8:7962.23771878778_351.679036694103_27.9535393342726,713.4014_b7:3370.9048792541_310.987177223065_50.5129761020436," "79.38:462.8,79.65:2471.1,79.89:4942.3,79.99:2471.1,80.12:587.3" 79.81 79.87 2300 2.2e+12 0.02 0.035 0.054 0.035 0.064 0.059 0.054 0.045 0.96 0.5 0.079 19 3 1 "79.8655754146358_79.8125854686426_N/A_79.8072962597494_79.8068814119591_79.8342454526662" 79.5932466525774 "2346.981786619_1045.80405098809_N/A_341.829994810099_351.679036694103_310.987177223065" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.460607016991432_0.372185583367596_N/A_0.337054687245228_0.284042639751561_0.198687224187736" "37.9850649135046_9.24410350622813_N/A_22.500243015707_27.9535393342726_50.5129761020436" "3_1_N/A_3_2_8" "984.54412171768_682.459661149262_813.505010674639_927.541877166025_826.479639562907_713.399278756883" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "66.6666666666667_129.333333333333_47.3333333333333_34_58_48.3333333334886" "0.0203211645107331_0.0457507127225654_0.0172405581129169_0.0236701516765834_0.0110095043589808_0.00377008711996041" "0_1_1_1_0_0" "1_1_1_1_1_1" "Unknown_True_True_True_Unknown_Unknown" "True_True_False_True_True_True" "175.094242661756_0_385.257400075649_498.346535478075_0_682.459661149262_813.505010674639_927.541877166025_984.54412171768_1097.64207812938_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.2970686001864 -0.487068600186447 +"13:44:11" 2 "ywu_L121218_004_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.5932466525774 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:26988.3571806801_1242.06579174239_28.1463102270691,713.4014_b7:null_null_null," "78.4:80,78.61:671.2,78.69:1342.4,78.99:671.2,79.15:132.9" 78.75 78.77 1200 240000 0.5 0.5 0.75 0.1 0.5 0.75 0.55 0.56 0.005 0.5 0.75 19 3 2 "78.7709618895227_N/A_N/A_78.7362705149892_78.7665756385286_N/A" 79.5932466525774 "8200.54297293411_N/A_N/A_1046.46993273883_1242.06579174239_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.364551540637535_N/A_N/A_0.311138762997999_0.387639946441894_N/A" "34.0759603040267_N/A_N/A_22.6269080936769_28.1463102270691_N/A" "1_N/A_N/A_1_1_N/A" "984.579576585091_682.416911372046_N/A_927.55151614531_826.486656597102_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "788.333333333333_30.6666666666279_N/A_99.3333333333333_133_N/A" "0.0549850992857728_0.0110619424380047_N/A_0.0522652403715256_0.0330430027009925_N/A" "1_1_0_1_0_0" "1_1_1_1_1_1" "False_True_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.118294298464_288.171120788381_0_498.261175365341_0_682.416911372046_0_927.487720887883_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.2236940972108 -0.473694097210839 +"13:44:11" 3 "ywu_L121218_004_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.5932466525774 "984.5659_y9:null_null_null,682.461_y6:487.622841645393_67.838204803993_10.1878758557517,813.5015_y7:1251.42638959628_83.99640834848_15.2696454208248,927.5444_y8:802.530857351084_94.9514553355621_23.3873732406492,826.4855_b8:2116.82682057388_93.8999939045934_24.9992358409247,713.4014_b7:8400.96587037062_361.441398078293_42.7967568687811," "75.54:366.2,75.63:549,75.71:1098,75.88:549,75.88:382.6" 75.72 75.73 360 110000 0.5 0.5 0.064 0.5 0.33 0.49 0.39 0.38 0.41 0.5 0.23 19 3 3 "75.7413648403638_75.7125397592966_75.7797150693882_75.7102065610464_75.6818057434095_75.7257400175026" 79.5932466525774 "95.4169912035431_67.838204803993_83.99640834848_94.9514553355621_93.8999939045934_361.441398078293" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.111815963110161_0.103571761493953_0.298491938261336_0.128106561858687_0.375088371585207_0.508762750205463" "24.1539043280043_10.1878758557517_15.2696454208248_23.3873732406492_24.9992358409247_42.7967568687811" "8_10_10_15_14_4" "984.534676918139_N/A_N/A_927.547362333476_N/A_713.421618928001" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "20_N/A_N/A_13.6666666666279_N/A_17.3333333333721" "0.0169492559898572_N/A_N/A_0.0113711962044363_N/A_0.00735180586298156" "2_0_0_0_0_0" "1_1_1_1_1_1" "False_Unknown_Unknown_Unknown_Unknown_Unknown" "True_True_True_True_True_True" "0_288.211043636487_385.264512219043_498.252009977079_611.364062894888_0_0_927.547362333476_984.521573915163_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.9045088180345 -0.184508818034487 +"14:20:24" 1 "ywu_L121218_005_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.9022825324857 "611.4239_y5:null_null_null,498.3398_y4:1957.59662571505_71_3.61550816886865,713.4014_b7:1218.25696633481_121.84400798392_3.58936646398049,600.3174_b6:1226.6347800692_96.5584103096044_5.23123217996062,529.2803_b5:null_null_null,682.461_y6:null_null_null," "79.88:,80.06:144.7,80.22:289.4,80.25:144.7,80.39:" 80.16 80.16 120 1300000 0.53 0.53 0.13 0.13 1.1 0.13 0.13 0.13 0.8 0.53 0.13 2 2 1 "80.1896334837763_80.1190874613199_80.1636833333333_80.1791221816136_N/A_N/A" 79.9022825324857 "88.5903776759515_71_121.84400798392_96.5584103096044_N/A_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.141058315271366_0.538021041320476_0.0891532295453175_0.186385159239165_N/A_N/A" "4.799543168614_3.61550816886865_3.58936646398049_5.23123217996062_N/A_N/A" "1_1_1_1_N/A_N/A" "611.423457785713_498.341442700864_713.417449795644_N/A_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "20.3333333333333_13.6666666666667_13.3333333333333_N/A_N/A_N/A" "0.0212835904377471_0.00615193294339633_0.00754028676976759_N/A_N/A_N/A" "1_0_1_0_0_0" "1_1_1_1_1_1" "False_Unknown_True_Unknown_Unknown_Unknown" "True_True_True_True_False_False" "175.113007915228_288.210964140498_385.257060097493_498.341442700864_0_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3546761207408 -0.194676120740766 +"14:20:24" 2 "ywu_L121218_005_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.9022825324857 "611.4239_y5:237.139918345548_50_5.81089025078037,498.3398_y4:null_null_null,713.4014_b7:null_null_null,600.3174_b6:null_null_null,529.2803_b5:604.822733679008_50_5.84875423484373,682.461_y6:null_null_null," "76.9:10,76.95:55,76.99:110,77.1:55,77.16:10" 77.02 77.07 50 18000 0.5 0.5 0.5 0.25 0.5 0.5 0.13 0.78 0.3 0.5 0.5 2 2 2 "77.0718166666667_N/A_N/A_N/A_76.9653454548867_N/A" 79.9022825324857 "50_N/A_N/A_N/A_50_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.0748460510710487_N/A_N/A_N/A_0.227524141302524_N/A" "5.81089025078037_N/A_N/A_N/A_5.84875423484373_N/A" "2_N/A_N/A_N/A_3_N/A" "611.399733556906_N/A_N/A_N/A_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "13.6666666667443_N/A_N/A_N/A_N/A_N/A" "0.003407076373378_N/A_N/A_N/A_N/A_N/A" "0_0_0_0_0_0" "1_1_1_1_1_1" "Unknown_Unknown_Unknown_Unknown_Unknown_Unknown" "True_False_False_False_True_False" "175.11612482527_288.20391954051_0_0_611.399733556906_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 76.9363785388898 0.0836214611102264 +"14:41:58" 1 "ywu_L121218_005_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9013811937706 "984.5659_y9:54504.2487947933_2346.89844194463_28.2652353191458,682.461_y6:23900.2853571278_1136.37611113786_8.83212333560757,813.5015_y7:16462.999754284_479.947501717744_15.7459166107246,927.5444_y8:2808.87298979646_211.166251296316_21.7672255119924,826.4855_b8:12843.7825090803_344.456091861769_26.8421456405486,713.4014_b7:6386.29443529435_346.966277724737_39.1336618238081," "79.81:586.1,80.02:2708.8,80.15:5417.6,80.39:2708.8,80.55:544.3" 80.19 80.21 2300 3.4e+12 0.015 0.03 0.02 0.054 0.3 0.045 0.015 0.025 1 0.5 0.25 17 3 1 "80.2055254761197_80.1678005775601_80.1236157452456_80.1298752652172_80.3453169673917_80.2766031443511" 79.9013811937706 "2346.89844194463_1136.37611113786_479.947501717744_211.166251296316_344.456091861769_346.966277724737" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.386429353702596_0.345192643361528_0.638635527453815_0.289176323871828_1.0089259828532_0.421858940854634" "28.2652353191458_8.83212333560757_15.7459166107246_21.7672255119924_26.8421456405486_39.1336618238081" "3_1_1_3_2_5" "984.561188358471_682.459757169908_813.502558690091_927.545028427178_826.481568312005_713.414426592075" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "154_128_58_27.6666666666667_31.3333333330229_17.6666666666667" "0.0567411016096457_0.0406922873836493_0.0486266667712698_0.0595571596061291_0.00596002034103549_0.017680927771039" "1_1_1_1_0_1" "1_1_1_1_1_1" "True_True_True_True_Unknown_True" "True_True_True_True_True_True" "175.146381438637_288.169958659576_385.25952207415_498.340892378339_0_682.459757169908_813.502558690091_927.545028427178_984.561188358471_1097.65594185049_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.385140821583 -0.195140821582996 +"14:41:58" 2 "ywu_L121218_005_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9013811937706 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:1971.74513686026_188.967749435471_24.6808895619121,826.4855_b8:276.294621487137_80.423408961467_24.892510709682,713.4014_b7:828.629806500073_96.465899249044_30.5272604380943," "84.13:309.4,84.13:308.2,84.19:616.4,84.29:308.2,84.36:185" 84.21 84.17 190 280000 0.5 0.5 0.45 0.59 0.28 0.4 0.15 0.63 0.025 0.5 0.41 17 3 3 "84.1093848762754_N/A_N/A_84.1697364072487_84.2425333333333_84.2597481405261" 79.9013811937706 "93.4177538816948_N/A_N/A_188.967749435471_80.423408961467_96.465899249044" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.0965222044969778_N/A_N/A_0.189356602081119_0.0572815629052883_0.184135559569626" "16.8237649871685_N/A_N/A_24.6808895619121_24.892510709682_30.5272604380943" "7_N/A_N/A_6_17_11" "984.577840105363_N/A_N/A_927.4892316412_N/A_713.382206763948" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "20.3333333333333_N/A_N/A_51.3333333333333_N/A_24.6666666665114" "0.0217094817319321_N/A_N/A_0.0460492398619863_N/A_0.00221415268822511" "1_0_0_1_0_0" "1_1_1_1_1_1" "False_Unknown_Unknown_True_Unknown_Unknown" "True_False_False_True_True_True" "175.081038268756_0_385.269250122434_0_611.408819829957_682.385422670494_0_927.4892316412_984.520203718785_1097.62631108442_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 84.5889756066712 -0.378975606671162 +"14:41:58" 3 "ywu_L121218_005_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.9013811937706 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:27214.5880128003_1619.62210021012_27.0185402209066,713.4014_b7:null_null_null," "78.75:96.1,79.03:857,79.09:1714,79.24:857,79.6:91.8" 79.12 79.13 1600 170000 0.5 0.5 0.75 0.094 0.5 0.75 0.98 0.47 0.005 0.5 0.75 17 3 2 "79.1125003656006_N/A_N/A_79.1000430920699_79.1308137268277_N/A" 79.9013811937706 "8724.7220556348_N/A_N/A_1098.94642173841_1619.62210021012_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.30529645043265_N/A_N/A_0.28974172985771_0.207437748411635_N/A" "28.9149839908288_N/A_N/A_22.3764494040067_27.0185402209066_N/A" "1_N/A_N/A_1_1_N/A" "984.579444474793_682.4129949412_N/A_927.559248908603_826.490960645532_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "845.666666666667_20.3333333333333_N/A_95.6666666666667_145.666666666667_N/A" "0.0592007849844549_0.0323979559369718_N/A_0.0589224094388783_0.0501346478230289_N/A" "1_5_0_1_0_0" "1_1_1_1_1_1" "False_False_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.111045764841_0_0_498.312993927756_0_0_0_0_984.509911839606_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.2713192717295 -0.151319271729491 +"15:17:17" 1 "ywu_L121218_006_SW.wiff (sample 1)" 27886 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+3" 1 404.2495 3 79.3525458229509 "611.4239_y5:1351.40506787869_90_5.66958929140032,498.3398_y4:2028.06882500123_97.6219697496854_4.57339987647979,713.4014_b7:1104.08944174806_88.7463292320892_5.71095956606776,600.3174_b6:1145.43396175162_91_5.95762734469545,529.2803_b5:376.288704810932_72.4676647082672_5.95080784466231,682.461_y6:null_null_null," "79.42:5.6,79.54:224.1,79.59:448.2,79.76:224.1,79.88:12.9" 79.62 79.54 98 2.2e+11 0.05 0.05 0.05 0.075 0.05 0.05 0.13 0.075 0.83 0.5 0.05 1 1 1 "79.6701410827928_79.5354174144454_79.6240287429621_79.6483166666667_79.5910666666667_N/A" 79.3525458229509 "90_97.6219697496854_88.7463292320892_91_72.4676647082672_N/A" "3000_1433.09997558594_1160.90002441406_1060.09997558594_918.900024414063_702.700012207031" "0.243758544421155_0.528428748833363_0.252555047733111_0.0799652972863214_0.076932157665965_N/A" "5.66958929140032_4.57339987647979_5.71095956606776_5.95762734469545_5.95080784466231_N/A" "1_1_1_1_2_N/A" "611.418113158727_N/A_713.400590977468_600.322472828647_N/A_N/A" "611.423889160156_498.33984375_713.401428222656_600.3173828125_529.2802734375_682.460998535156" "20.3333333333333_N/A_13.3333333333333_13.3333333333333_N/A_N/A" "0.00468367310111262_N/A_0.0414710329371246_0.0432300631625822_N/A_N/A" "0_0_1_1_0_0" "1_1_1_1_1_1" "Unknown_Unknown_True_True_Unknown_Unknown" "True_True_True_True_True_False" "0_0_385.256450887155_0_611.418113158727_0_0_0_0_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.2433156865484 -0.623315686548437 +"15:39:10" 1 "ywu_L121218_006_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.3516493884757 "984.5659_y9:57015.9032730408_3179.28802151898_34.5062572331775,682.461_y6:26547.8533866248_1531.53349058906_10.1540308260467,813.5015_y7:null_null_null,927.5444_y8:4710.14571196128_311.046685958132_23.7671628541292,826.4855_b8:5623.87054918893_485.363560547921_29.2921895090756,713.4014_b7:4968.18006465682_402.277941635504_47.7510039603103," "79.38:446.9,79.61:3202.7,79.78:6405.4,79.84:3202.7,79.95:516.6" 79.74 79.75 3200 2e+11 0.04 0.099 0.054 0.074 0.079 0.05 0.03 0.05 0.96 0.5 0.11 19 3 1 "79.7538373722019_79.7293599802324_N/A_79.671285566448_79.7388333575673_79.7769170027905" 79.3516493884757 "3179.28802151898_1531.53349058906_N/A_311.046685958132_485.363560547921_402.277941635504" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.335977407753276_0.227270600175473_N/A_0.26323496889087_0.127107804290631_0.225343354901668" "34.5062572331775_10.1540308260467_N/A_23.7671628541292_29.2921895090756_47.7510039603103" "3_1_N/A_3_3_5" "984.534684514473_682.462535513611_813.512211224397_927.558700957285_826.491007832543_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "69.3333333333333_151.666666666667_51.3333333333333_33.6666666666667_34.3333333333333_N/A" "0.0232913063407523_0.0484521503117321_0.0528403844602963_0.0372070591787406_0.011611557602123_N/A" "1_1_1_0_0_0" "1_1_1_1_1_1" "True_True_True_Unknown_Unknown_Unknown" "True_True_False_True_True_True" "0_0_385.259700124044_498.343092902756_611.425227124944_682.462535513611_813.512211224397_927.558700957285_984.534684514473_1097.63287202846_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 80.3699472702056 -0.629947270205562 +"15:39:10" 2 "ywu_L121218_006_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.3516493884757 "984.5659_y9:null_null_null,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:30225.8937522149_1578.76916894474_27.7677453844382,713.4014_b7:null_null_null," "78.23:84.3,78.5:837.8,78.75:1675.6,78.86:837.8,79.26:109.4" 78.72 78.71 1600 680000 0.5 0.5 0.75 0.079 0.5 0.75 0.29 0.49 0.005 0.5 0.75 19 3 3 "78.6972657502929_N/A_N/A_78.7246723666666_78.710089674726_N/A" 79.3516493884757 "8552.38452203284_N/A_N/A_1156.23139827393_1578.76916894474_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.345281234297929_N/A_N/A_0.212948211561695_0.364075487293974_N/A" "33.5613071852383_N/A_N/A_20.3437924072273_27.7677453844382_N/A" "1_N/A_N/A_1_1_N/A" "984.581835479902_682.422470048131_N/A_927.559966067391_826.490992297568_N/A" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "808.333333333333_30.6666666666667_N/A_104.666666666667_136_N/A" "0.0564204975522671_0.0107670058432632_N/A_0.0539109831117912_0.0382135553466014_N/A" "1_1_0_1_0_0" "1_1_1_1_1_1" "False_False_Unknown_False_Unknown_Unknown" "True_False_False_True_True_False" "175.121945199736_288.155893868708_385.191182750177_498.315041890289_0_682.398807140688_0_927.46721133992_0_1097.5832007727_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 79.3075423860607 -0.587542386060747 +"15:39:10" 3 "ywu_L121218_006_SW.wiff (sample 1)" 27884 "Actin-related protein 2/3 complex subunit 3 musculus " "False" "LIGNMALLPLR+2" 1 605.8707 2 79.3516493884757 "984.5659_y9:2983.34258884189_204.233382842502_26.6140968851804,682.461_y6:null_null_null,813.5015_y7:null_null_null,927.5444_y8:null_null_null,826.4855_b8:1097.63001565599_96.1437667326109_29.0428178025378,713.4014_b7:null_null_null," "75.28:166.9,75.37:223.8,75.51:447.6,75.59:223.8,75.71:128.1" 75.48 75.5 200 300 0.5 0.5 0.75 0.5 0.5 0.75 0.79 0.76 0.41 0.5 0.75 19 3 2 "75.4965974403081_75.4808681471833_N/A_N/A_75.4739254353535_N/A" 79.3516493884757 "204.233382842502_113.737738289296_N/A_N/A_96.1437667326109_N/A" "10000_5313_2413_952.200012207031_587.799987792969_492.100006103516" "0.236583966499282_0.236357229187504_N/A_N/A_0.207585875881321_N/A" "26.6140968851804_9.84331227136362_N/A_N/A_29.0428178025378_N/A" "6_4_N/A_N/A_17_N/A" "984.55870899699_682.485838605534_N/A_927.482983309254_N/A_713.391664896205" "984.56591796875_682.460998535156_813.501525878906_927.54443359375_826.485534667969_713.401428222656" "13.6666666666667_13.3333333333721_N/A_13.6666666666279_N/A_40.9999999995343" "0.0268199630233994_0.00491664653850421_N/A_0.0188067448916627_N/A_0.00436698871874341" "1_2_0_2_0_2" "1_1_1_1_1_1" "True_False_Unknown_False_Unknown_False" "True_True_False_False_True_False" "0_288.107964759873_385.172450640585_0_0_0_0_0_984.55870899699_0_0" "175.118952332091_288.203016420091_385.255780348091_498.339844436091_611.423908524091_682.461022372091_813.501508180091_927.544435716091_984.565899484091_1097.64996357209_1210.73402766009" NA 75.7407228994736 -0.26072289947362