Orbitrap recognized in `referenceableParamGroupList` but not in `instrumentConfigurationList` ?
This is the file produced by ThermoRawFileParser with default parameters:
<?xml version="1.0" encoding="utf-8"?> <mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" version="1.1.0" id="060623_std_30sec_CarboAmmo_10mM_70-20-10_01" xmlns="http://psi.hupo.org/ms/mzml"> <cvList count="2"> <cv id="MS" fullName="Mass spectrometry ontology" version="4.1.79" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" /> <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" /> </cvList> <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" /> <cvParam cvRef="MS" accession="MS:1000810" value="" name="ion current chromatogram" /> </fileContent> <sourceFileList count="1"> <sourceFile id="RAW1" name="060623_std_30sec_CarboAmmo_10mM_70-20-10_01" location="file:////Users/elliotfontaine/raws/060623_std_30sec_CarboAmmo_10mM_70-20-10_01.raw"> <cvParam cvRef="MS" accession="MS:1000768" value="" name="Thermo nativeID format" /> <cvParam cvRef="MS" accession="MS:1000563" value="" name="Thermo RAW format" /> <cvParam cvRef="MS" accession="MS:1000569" value="2aa446994a290815bb32f4194999d78e62777488" name="SHA-1" /> </sourceFile> </sourceFileList> </fileDescription> <referenceableParamGroupList count="1"> <referenceableParamGroup id="commonInstrumentParams"> <cvParam cvRef="MS" accession="MS:1001742" value="" name="LTQ Orbitrap Velos" /> <cvParam cvRef="MS" accession="MS:1000529" value="SN03173B" name="instrument serial number" /> </referenceableParamGroup> </referenceableParamGroupList> <softwareList count="1"> <software id="ThermoRawFileParser" version="1.4.3"> <cvParam cvRef="MS" accession="MS:1003145" name="ThermoRawFileParser" /> </software> </softwareList> <instrumentConfigurationList count="1"> <instrumentConfiguration id="IC1"> <referenceableParamGroupRef ref="commonInstrumentParams" /> <componentList count="3"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000073" value="" name="electrospray ionization" /> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000079" value="" name="fourier transform ion cyclotron resonance mass spectrometer" /> </analyzer> <detector order="3"> <cvParam cvRef="MS" accession="MS:1000624" value="" name="inductive detector" /> </detector> </componentList> </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="ThermoRawFileParserProcessing"> <processingMethod order="0" softwareRef="ThermoRawFileParser"> <cvParam cvRef="MS" accession="MS:1000544" value="" name="Conversion to mzML" /> </processingMethod> <processingMethod order="1" softwareRef="ThermoRawFileParser"> <cvParam cvRef="MS" accession="MS:1000035" value="" name="peak picking" /> </processingMethod> </dataProcessing> </dataProcessingList> <run id="_060623_std_30sec_CarboAmmo_10mM_70-20-10_01" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2023-06-21T17:30:53.439Z" defaultSourceFileRef="RAW1"> </run> </mzML>
I don't think the analyser is a "fourier transform ion cyclotron resonance mass spectrometer".
This is the one produced by MSConvert for comparison.
<?xml version="1.0" encoding="utf-8"?> <indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd"> <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="060623_std_30sec_CarboAmmo_10mM_70-20-10_01" version="1.1.0"> <cvList count="2"> <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.56" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/> </cvList> <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> </fileContent> <sourceFileList count="1"> <sourceFile id="RAW1" name="060623_std_30sec_CarboAmmo_10mM_70-20-10_01.raw" location="file:///T:\redacted\rawdata\230612_Opti-Timepoints"> <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/> <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/> <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2aa446994a290815bb32f4194999d78e62777488"/> </sourceFile> </sourceFileList> </fileDescription> <referenceableParamGroupList count="1"> <referenceableParamGroup id="CommonInstrumentParams"> <cvParam cvRef="MS" accession="MS:1001742" name="LTQ Orbitrap Velos" value=""/> <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN03173B"/> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> <sample id="_x0031_" name=""> <cvParam cvRef="MS" accession="MS:1000002" name="sample name" value="1"/> </sample> </sampleList> <softwareList count="2"> <software id="Xcalibur" version="2.7.0 SP1"> <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/> </software> <software id="pwiz" version="3.0.22129"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> </softwareList> <instrumentConfigurationList count="2"> <instrumentConfiguration id="IC1"> <referenceableParamGroupRef ref="CommonInstrumentParams"/> <componentList count="3"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/> <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/> </analyzer> <detector order="3"> <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/> </detector> </componentList> <softwareRef ref="Xcalibur"/> </instrumentConfiguration> <instrumentConfiguration id="IC2"> <referenceableParamGroupRef ref="CommonInstrumentParams"/> <componentList count="3"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/> <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/> </analyzer> <detector order="3"> <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/> </detector> </componentList> <softwareRef ref="Xcalibur"/> </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="pwiz_Reader_Thermo_conversion"> <processingMethod order="0" softwareRef="pwiz"> <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> </processingMethod> <processingMethod order="1" softwareRef="pwiz"> <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/> <userParam name="Thermo/Xcalibur peak picking"/> </processingMethod> </dataProcessing> </dataProcessingList> <run id="_x0030_60623_std_30sec_CarboAmmo_10mM_70-20-10_01" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2023-06-21T15:30:53Z" defaultSourceFileRef="RAW1"> </run> </mzML> <indexList count="2"> </indexList> <indexListOffset>522043</indexListOffset> <fileChecksum>822dbcbf725d7759dcd0026dd7d0a6e9061d1d77</fileChecksum> </indexedmzML>