| Previous changeset 17:ab6c14374bc0 (2024-08-15) Next changeset 19:28ffaaa5739f (2025-04-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196 |
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modified:
msconvert.xml msconvert_macros.xml test-data/SciexTest-HPINalone-NE.mzML |
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added:
test-data/small-composite-test-2.mzML test-data/small-composite-test.mzML |
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removed:
msconvert_macros.xml.orig test-data/Rpal_01.mzid test-data/SciexTest-HPINalone-srmAsSpectra.mzXML test-data/SciexTest.mzML test-data/small-analyzer-filter.mzML test-data/small-chargeStatePredictor.mzML test-data/small-deisotope.mzML test-data/small-denoise.mzML test-data/small-index-filter.mzML test-data/small-ms-level-filter.mzML test-data/small-mzWindow.mzML test-data/small-numpressL.mzML test-data/small-numpressLP.mzML test-data/small-numpressLS.mzML test-data/small-numpressP.mzML test-data/small-numpressS.mzML test-data/small-strip-it.mzML test-data/small-threshold.mzML test-data/small-turbocharger.mzML test-data/small-zlib-32.mzXML |
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| diff -r ab6c14374bc0 -r 331a50e8fd2f msconvert.xml --- a/msconvert.xml Thu Aug 15 16:19:28 2024 +0000 +++ b/msconvert.xml Mon Mar 10 07:48:32 2025 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="msconvert" name="msconvert" version="@VERSION@.4"> +<tool id="msconvert" name="msconvert" version="@VERSION@.5" profile="@PROFILE_VERSION@"> <description>Convert and/or filter mass spectrometry files</description> <macros> <import>msconvert_macros.xml</import> @@ -14,7 +14,7 @@ </stdio> <expand macro="msconvertCommand" /> <inputs> - <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" /> + <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" /> <expand macro="msconvertInputParameters" /> </inputs> <expand macro="msconvertOutput" /> |
| b |
| diff -r ab6c14374bc0 -r 331a50e8fd2f msconvert_macros.xml --- a/msconvert_macros.xml Thu Aug 15 16:19:28 2024 +0000 +++ b/msconvert_macros.xml Mon Mar 10 07:48:32 2025 +0000 |
| [ |
| b'@@ -1,6 +1,7 @@\n <macros>\n <token name="@VERSION@">3.0.20287</token>\n <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>\n+ <token name="@PROFILE_VERSION@">24.2</token>\n <xml name="msconvertCommand">\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -61,7 +62,7 @@\n $general_options.acceptZeroLengthSpectra\n $general_options.ignoreUnknownInstrumentError\n \n- #if $general_options.scan_summing.do_scan_summing:\n+ #if $general_options.scan_summing.do_scan_summing == "true":\n --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"\n #end if\n \n@@ -81,7 +82,7 @@\n --stripLocationFromSourceFiles\n \n ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n- #if $data_processing.peak_picking.pick_peaks\n+ #if $data_processing.peak_picking.pick_peaks == "true"\n --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n #end if\n \n@@ -116,11 +117,11 @@\n --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"\n #end for\n \n- #if $data_processing.filter_mz_windows.do_mzwindow_filter\n+ #if $data_processing.filter_mz_windows.do_mzwindow_filter == "true"\n --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"\n #end if\n \n- #if $data_processing.etd_filtering.do_etd_filtering\n+ #if $data_processing.etd_filtering.do_etd_filtering == "true"\n --filter "ETDFilter $data_processing.etd_filtering.remove_precursor\n $data_processing.etd_filtering.remove_charge_reduced\n $data_processing.etd_filtering.remove_neutral_loss\n@@ -128,7 +129,7 @@\n $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"\n #end if\n \n- #if $data_processing.ms2denoise.denoise\n+ #if $data_processing.ms2denoise.denoise == "true"\n --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"\n #end if\n \n@@ -136,7 +137,7 @@\n --filter "MS2Deisotope"\n #end if\n \n- #if $data_processing.demultiplex.demultiplex_on\n+ #if $data_processing.demultiplex.demultiplex_on == "true"\n --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"\n #end if\n \n@@ -165,7 +166,7 @@\n --filter "stripIT"\n #end if\n \n- #if $filtering.filter_ms_levels.do_ms_level_filter\n+ #if $filtering.filter_ms_levels.do_ms_level_filter == "true"\n --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"\n #end if\n \n@@ -206,7 +207,7 @@\n --numpressSlof\n #end if\n \n- #if $settings.gzip_compression\n+ #if $settings.gzip_compression == "true"\n --gzip\n #end if\n \n@@ -253,7 +254,7 @@\n <conditional name="peak_picking">\n <param type="select" name="pick_peaks" label="Apply peak picking?">\n <option value="true">Yes</option>\n- <option value="false">No</option>\n+ <option value="false" selected="true">No</option>\n </'..b'e="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzML" />\n- <param name="strip_it" value="true" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />\n- </test>\n- <test expect_num_outputs="1">\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzML" />\n- <param name="do_ms_level_filter" value="true" />\n- <param name="ms_level_from" value="2" />\n- <param name="ms_level_to" value="2" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />\n- </test>\n- <test expect_num_outputs="1">\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzML" />\n- <param name="polarity" value="positive" />\n- <param name="binary_compression" value="numpressLinearPic" />\n+ <param name="filtering|polarity" value="positive" />\n+ <param name="settings|binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />\n </test>\n <test expect_num_outputs="1">\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n+ <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n- <param name="analyzer" value="IT" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />\n- </test>\n- <test expect_num_outputs="1">\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzML" />\n- <param name="scan_numbers_0|from" value="3" />\n- <param name="scan_numbers_0|to" value="5" />\n- <param name="scan_numbers_1|from" value="11" />\n- <param name="scan_numbers_1|to" value="11" />\n- <param name="scan_numbers_2|from" value="14" />\n- <param name="scan_numbers_2|to" value="16" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" lines_diff="86" ftype="mzml"/> <!-- the scan numbers here produce the same output as the index test above -->\n+ <param name="data_processing|etd_filtering|do_etd_filtering" value="true" />\n+ <param name="data_processing|etd_filtering|remove_precursor" value="true" />\n+ <param name="data_processing|etd_filtering|remove_charge_reduced" value="true" />\n+ <param name="data_processing|etd_filtering|remove_neutral_loss" value="false" />\n+ <param name="data_processing|etd_filtering|blanket_removal" value="false" />\n+ <param name="data_processing|etd_filtering|matching_tolerance" value="50" />\n+ <param name="data_processing|etd_filtering|matching_tolerance_units" value="PPM" />\n+ <param name="settings|binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />\n </test>\n <!--<test>\n <param name="input" value="small.mzML" />\n <param name="output_type" value="mzML" />\n- <param name="binary_compression" value="numpressLinearPic" />\n+ <param name="settings|binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-deisotope-poisson.mzML" />\n </test>-->\n </xml>\n' |
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| diff -r ab6c14374bc0 -r 331a50e8fd2f msconvert_macros.xml.orig --- a/msconvert_macros.xml.orig Thu Aug 15 16:19:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,897 +0,0 @@\n-<macros>\n- <token name="@VERSION@">3.0.19052</token>\n- <token name="@FULL_VERSION@">@VERSION@-089e81090</token>\n- \n- <xml name="msconvertCommand">\n- <command detect_errors="exit_code">\n-<![CDATA[\n- #import re\n- #set $ext = $input.ext\n-\n- ## sanitize display name for use as temp filename\n- #set basename = $re.sub(r\'[^\\w\\.\\-\\+]\',\'_\',$input.element_identifier)\n-\n- #if $ext == \'wiff\':\n- ln -s \'${input.extra_files_path}/wiff\' \'${basename}.wiff\' &&\n- ln -s \'${input.extra_files_path}/wiff_scan\' \'${basename}.wiff.scan\' &&\n- #elif $ext.endswith(\'tar\'):\n- ln -s \'$input\' \'${basename}\' &&\n- tar xf \'${basename}\' &&\n- #set basename = $os.path.splitext($basename)[0]\n- #else\n- ln -s \'$input\' \'${basename}\' &&\n- #end if\n- \n- #if $data_processing.precursor_refinement.use_mzrefinement\n- #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))\n- #set output_refinement_name = os.path.splitext($basename)[0] + \'.mzRefinement.tsv\'\n- ln -s \'$data_processing.precursor_refinement.input_ident\' \'$input_ident_name\' &&\n- #end if\n-\n- uid=`id -u` &&\n- gid=`id -g` &&\n-\n- wine64_anyuser msconvert \'${basename}\'\n- --outdir outputs\n- --${output_type}\n-\n- #if $general_options.combineIonMobilitySpectra:\n- --combineIonMobilitySpectra\n- #end if\n-\n- #if $general_options.simAsSpectra:\n- --simAsSpectra\n- #end if\n-\n- #if $general_options.srmAsSpectra:\n- --srmAsSpectra\n- #end if\n-\n- #if $general_options.acceptZeroLengthSpectra:\n- --acceptZeroLengthSpectra\n- #end if\n-\n- #if $general_options.ignoreUnknownInstrumentError:\n- --ignoreUnknownInstrumentError\n- #end if\n-\n- #if $general_options.scan_summing.do_scan_summing:\n- --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"\n- #end if\n-\n- #if $general_options.multi_run_output.do_multi_run_output:\n- #if len($general_options.multi_run_output.run_index_set) > 0\n- --runIndexSet "\n- #for $index in $general_options.multi_run_output.run_index_set\n- [${index.from},${index.to}]\n- #end for\n- "\n- #end if\n- #else\n- --runIndexSet $general_options.multi_run_output.runIndexSet\n- #end if\n-\n- ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests\n- --stripLocationFromSourceFiles\n-\n- ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n- #if $data_processing.peak_picking.pick_peaks\n- --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n- #end if\n-\n- #if $data_processing.precursor_refinement.use_mzrefinement\n- --filter "mzRefiner $input_ident_name\n- msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n- thresholdScore=$data_processing.precursor_refinement.thresholdScore\n- thresholdValue=$data_processing.precursor_refinement.thresholdValue\n- thresholdStep=$data_processing.precursor_refinement.thresholdStep\n- maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"\n- #end if\n-\n- #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n- --filter "chargeStatePredictor\n- overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n- minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n- maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n- singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n- maxKnownCharge='..b'param name="indices_1|to" value="10" />\n- <param name="indices_2|from" value="13" />\n- <param name="indices_2|to" value="15" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" lines_diff="32" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzml" />\n- <param name="strip_it" value="true" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" lines_diff="100" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzml" />\n- <param name="do_ms_level_filter" value="true" />\n- <param name="ms_level_from" value="2" />\n- <param name="ms_level_to" value="2" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzml" />\n- <param name="polarity" value="positive" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzml" />\n- <param name="analyzer" value="IT" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="license_agreement" value="true" />\n- <param name="output_type" value="mzml" />\n- <param name="scan_numbers_0|from" value="3" />\n- <param name="scan_numbers_0|to" value="5" />\n- <param name="scan_numbers_1|from" value="11" />\n- <param name="scan_numbers_1|to" value="11" />\n- <param name="scan_numbers_2|from" value="14" />\n- <param name="scan_numbers_2|to" value="16" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->\n- </test>\n- <!--<test>\n- <param name="input" value="small.mzML" />\n- <param name="output_type" value="mzml" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-deisotope-poisson.mzML" />\n- </test>-->\n- </xml>\n- <xml name="msconvert_help">\n-**What it does**\n-\n-Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btn323</citation>\n- <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n- year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n- </citations>\n- </xml>\n-\n-</macros>\n' |
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| diff -r ab6c14374bc0 -r 331a50e8fd2f test-data/Rpal_01.mzid --- a/test-data/Rpal_01.mzid Thu Aug 15 16:19:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,78943 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<MzIdentML id="" creationDate="2011-10-31T11:08:11" version="1.1.0" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n- <cvList>\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" uri="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n- <cv id="UNIMOD" fullName="UNIMOD" version="2016-07-01" uri="http://www.unimod.org/obo/unimod.obo"/>\n- <cv id="UO" fullName="Unit Ontology" version="12:10:2011" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n- </cvList>\n- <AnalysisSoftwareList>\n- <AnalysisSoftware id="AS_MyriMatch_2.1.101" name="MyriMatch" version="2.1.101">\n- <SoftwareName><cvParam cvRef="MS" accession="MS:1001585" name="MyriMatch" value=""/></SoftwareName>\n- </AnalysisSoftware>\n- <AnalysisSoftware id="pwiz_3.0.9934" name="ProteoWizard MzIdentML" version="3.0.9934">\n- <ContactRole contact_ref="ORG_PWIZ">\n- <Role><cvParam cvRef="MS" accession="MS:1001267" name="software vendor" value=""/></Role>\n- </ContactRole>\n- <SoftwareName><cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/></SoftwareName>\n- </AnalysisSoftware>\n- </AnalysisSoftwareList>\n- <AuditCollection>\n- <Organization id="ORG_PWIZ" name="ProteoWizard">\n- <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="support@proteowizard.org"/>\n- </Organization>\n- </AuditCollection>\n- <SequenceCollection>\n- <DBSequence id="DBSeq_rev_RPA0498" accession="rev_RPA0498" searchDatabase_ref="SDB"/>\n- <DBSequence id="DBSeq_RPA1332" accession="RPA1332" searchDatabase_ref="SDB"/>\n- <DBSequence id="DBSeq_rev_RPA3341" accession="rev_RPA3341" searchDatabase_ref="SDB"/>\n- <DBSequence 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| diff -r ab6c14374bc0 -r 331a50e8fd2f test-data/SciexTest-HPINalone-NE.mzML --- a/test-data/SciexTest-HPINalone-NE.mzML Thu Aug 15 16:19:28 2024 +0000 +++ b/test-data/SciexTest-HPINalone-NE.mzML Mon Mar 10 07:48:32 2025 +0000 |
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| diff -r ab6c14374bc0 -r 331a50e8fd2f test-data/SciexTest-HPINalone-srmAsSpectra.mzXML --- a/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML Thu Aug 15 16:19:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| diff -r ab6c14374bc0 -r 331a50e8fd2f test-data/small-zlib-32.mzXML --- a/test-data/small-zlib-32.mzXML Thu Aug 15 16:19:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1071 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"\n- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n- xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n- <msRun scanCount="48" startTime="PT0.2961S" endTime="PT29.2342S">\n- <parentFile fileName="file:////small.RAW"\n- fileType="RAWData"\n- fileSha1="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n- <msInstrument msInstrumentID="1">\n- <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n- <msModel category="msModel" value="LTQ FT"/>\n- <msIonisation category="msIonisation" value="electrospray ionization"/>\n- <msMassAnalyzer category="msMassAnalyzer" value="fourier transform ion cyclotron resonance mass spectrometer"/>\n- <msDetector category="msDetector" value="inductive detector"/>\n- <software type="acquisition" name="Xcalibur" version="1.1 Beta 7"/>\n- </msInstrument>\n- <msInstrument msInstrumentID="2">\n- <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n- <msModel category="msModel" value="LTQ FT"/>\n- <msIonisation category="msIonisation" value="electrospray ionization"/>\n- <msMassAnalyzer category="msMassAnalyzer" value="radial ejection linear ion trap"/>\n- <msDetector category="msDetector" value="electron multiplier"/>\n- <software type="acquisition" name="Xcalibur" version="1.1 Beta 7"/>\n- </msInstrument>\n- <dataProcessing>\n- <software type="conversion" name="ProteoWizard software" version="3.0.8981"/>\n- <processingOperation name="Conversion to mzML"/>\n- </dataProcessing>\n- <dataProcessing>\n- <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>\n- <processingOperation name="Conversion to mzML"/>\n- </dataProcessing>\n- <dataProcessing centroided="1">\n- <software type="processing" name="ProteoWizard software" version="3.0.20287"/>\n- <processingOperation name="peak picking"/>\n- <comment>CantWaiT (continuous wavelet transform) peak picker</comment>\n- </dataProcessing>\n- <scan num="1"\n- scanType="Full"\n- centroided="1"\n- msLevel="1"\n- peaksCount="723"\n- polarity="+"\n- retentionTime="PT0.2961S"\n- lowMz="200.00018816645"\n- highMz="2000.009946620377"\n- basePeakMz="810.415283203125"\n- basePeakIntensity="1.471973875e06"\n- totIonCurrent="1.5245068e07"\n- msInstrumentID="1">\n- <peaks compressionType="zlib"\n- compressedLen="5247"\n- precision="32"\n- byteOrder="network"\n- 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