<?xml version='1.0' encoding='UTF-8'?>
<ProteomeXchangeDataset id="PXD048072" formatVersion="1.4.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.4.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <CvList>
    <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>
  <DatasetSummary announceDate="2024-01-15" hostingRepository="PanoramaPublic" title="Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation">
    <Description>Protein glycosylation is an essential posttranslational modification in all domains of life. Its impairment in human can result in severe diseases named Congenital Disorders of Glycosylation (CDGs).  Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging targets in proteomics. We established a multiple reaction monitoring (MRM) assay to comprehensively quantify GTs involved in the processes of N-glycosylation, O- and C-mannosylation in the endoplasmic reticulum. High robustness was achieved by using an enriched membrane protein fraction of isotopically labeled HEK 293T cells as an internal protein standard. The analysis of primary skin fibroblasts from eight CDG type I patients with impaired ALG1, ALG2, or ALG11 genes revealed substantial reduction in the levels of corresponding proteins. The abundance of the other GTs, however, remained unchanged on transcript as well as on protein level, indicating that there is no fail-safe mechanism for this essential pathway. The established MRM assay is easily shared with the scientific community via the open source Skyline software environment, including Skyline Batch for automated data analysis. We demonstrate that another research group could easily reproduce all analysis steps even while using different LC-MS hardware.</Description>
    <ReviewLevel>
      <cvParam cvRef="MS" accession="MS:1002855" name="Non 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="PXD048072"/>
      <cvParam cvRef="MS" accession="MS:1001921" name="ProteomeXchange accession number version number" value="1"/>
    </DatasetIdentifier>
    <DatasetIdentifier>
      <cvParam cvRef="MS" accession="MS:1002872" name="Panorama Public dataset identifier" value="https://panoramaweb.org/GTs-MRM.url"/>
    </DatasetIdentifier>
  </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="Homo sapiens"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="9606"/>
    </Species>
  </SpeciesList>
  <InstrumentList>
    <Instrument id="instrument_1">
      <cvParam cvRef="MS" accession="MS:1000931" name="QTRAP 5500"/>
    </Instrument>
    <Instrument id="instrument_2">
      <cvParam cvRef="MS" accession="MS:1001766" name="nanoACQUITY UPLC"/>
    </Instrument>
    <Instrument id="instrument_3">
      <cvParam cvRef="MS" accession="MS:1001510" name="TSQ Vantage"/>
    </Instrument>
  </InstrumentList>
  <ModificationList>
    <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
    <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="Thomas Ruppert"/>
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="t.ruppert@zmbh.uni-heidelberg.de"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Centre for molecular biology, Heidelberg University"/>
    </Contact>
    <Contact id="dataset_submitter">
      <cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Roman Sakson"/>
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="roman.sakson@gmx.net"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Centre for molecular biology, Heidelberg University (ZMBH)"/>
    </Contact>
  </ContactList>
  <PublicationList>
    <Publication id="pubmed_id_pending">
      <cvParam cvRef="MS" accession="MS:1002866" name="Reference" value="Sakson R, Beedgen L, Bernhard P, Alp KM, Lübbehusen N, Röth R, Niesler B, Mayer MP, Thiel C, Ruppert T. Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation. bioRxiv [Internet]. 2020 Jan 1;2020.09.15.291732"/>
    </Publication>
  </PublicationList>
  <KeywordList>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="N-glycosylation"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="glycosylation"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="endoplasmic reticulum"/>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="Congenital disorders of glycosylation"/>
  </KeywordList>
  <FullDatasetLinkList>
    <FullDatasetLink>
      <cvParam cvRef="MS" accession="MS:1002873" name="Panorama Public dataset URI" value="https://panoramaweb.org/GTs-MRM.url"/>
    </FullDatasetLink>
  </FullDatasetLinkList>
</ProteomeXchangeDataset>