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<ProteomeXchangeDataset id="PXD051318" formatVersion="1.4.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.4.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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    <Cv id="MS" fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-Cv/master/psi-ms.obo"/>
    <Cv id="MOD" fullName="PSI-MOD" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo"/>
    <Cv id="UNIMOD" fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"/>
  </CvList>
  <ChangeLog>
    <ChangeLogEntry>Added PubMed Id</ChangeLogEntry>
  </ChangeLog>
  <DatasetSummary announceDate="2024-10-01" hostingRepository="PanoramaPublic" title="A framework for quality control in quantitative proteomics">
    <Description>A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at the protein and peptide levels allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.</Description>
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      <cvParam cvRef="MS" accession="MS:1002854" name="Peer-reviewed dataset"/>
    </ReviewLevel>
    <RepositorySupport>
      <cvParam cvRef="MS" accession="MS:1002856" name="Supported dataset by repository"/>
    </RepositorySupport>
  </DatasetSummary>
  <DatasetIdentifierList>
    <DatasetIdentifier>
      <cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD051318"/>
      <cvParam cvRef="MS" accession="MS:1001921" name="ProteomeXchange accession number version number" value="2"/>
    </DatasetIdentifier>
    <DatasetIdentifier>
      <cvParam cvRef="MS" accession="MS:1002872" name="Panorama Public dataset identifier" value="https://panoramaweb.org/maccoss-sample-qc-system-suitability.url"/>
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  </DatasetIdentifierList>
  <DatasetOriginList>
    <DatasetOrigin>
      <cvParam cvRef="MS" accession="MS:1002868" name="Original data"/>
    </DatasetOrigin>
  </DatasetOriginList>
  <SpeciesList>
    <Species>
      <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Mus musculus"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="10090"/>
    </Species>
    <Species>
      <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Homo sapiens"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="9606"/>
    </Species>
    <Species>
      <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Bos taurus"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="9913"/>
    </Species>
    <Species>
      <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Saccharomyces cerevisiae"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="4932"/>
    </Species>
  </SpeciesList>
  <InstrumentList>
    <Instrument id="instrument_1">
      <cvParam cvRef="MS" accession="MS:1003029" name="Orbitrap Eclipse"/>
    </Instrument>
    <Instrument id="instrument_2">
      <cvParam cvRef="MS" accession="MS:1002732" name="Orbitrap Fusion Lumos"/>
    </Instrument>
    <Instrument id="instrument_3">
      <cvParam cvRef="MS" accession="MS:1002416" name="Orbitrap Fusion"/>
    </Instrument>
  </InstrumentList>
  <ModificationList>
    <cvParam cvRef="UNIMOD" accession="UNIMOD:259" name="Label:13C(6)15N(2)"/>
    <cvParam cvRef="UNIMOD" accession="UNIMOD:267" name="Label:13C(6)15N(4)"/>
  </ModificationList>
  <ContactList>
    <Contact id="lab_head">
      <cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Michael MacCoss"/>
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="maccoss@uw.edu"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="University of Washington"/>
    </Contact>
    <Contact id="dataset_submitter">
      <cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Kristine Tsantilas"/>
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="ktsantil@uw.edu"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="University of Washington"/>
    </Contact>
  </ContactList>
  <PublicationList>
    <Publication id="PMID39248652">
      <cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="39248652"/>
      <cvParam cvRef="MS" accession="MS:1002866" name="Reference" value="Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A Framework for Quality Control in Quantitative Proteomics. J Proteome Res. 2024 Sep 9. doi: 10.1021/acs.jproteome.4c00363. Epub ahead of print. PMID: 39248652."/>
    </Publication>
  </PublicationList>
  <KeywordList>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="quality control"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="proteomics"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="mass spectrometry"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="liquid chromatography"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="sample preparation"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="system suitability"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="quantitative results"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="PRM"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="DIA"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="DDA"/>
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