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Discovery of protein modifications using high resolution differential mass spectrometry proteomics

Paolo Cifani; Zhi Li; Danmeng Luo; Mark Grivainis; Andrew M. Intlekofer; David Fenyö; Alex Kentsis


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  <identifier identifierType="DOI">10.5281/zenodo.3899480</identifier>
  <creators>
    <creator>
      <creatorName>Paolo Cifani</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4403-1277</nameIdentifier>
      <affiliation>Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Zhi Li</creatorName>
      <affiliation>Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Danmeng Luo</creatorName>
      <affiliation>Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Mark Grivainis</creatorName>
      <affiliation>Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Andrew M. Intlekofer</creatorName>
      <affiliation>Human Oncology &amp; Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>David Fenyö</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5049-3825</nameIdentifier>
      <affiliation>Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Alex Kentsis</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8063-9191</nameIdentifier>
      <affiliation>Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Discovery of protein modifications using high resolution differential mass spectrometry proteomics</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <dates>
    <date dateType="Issued">2020-06-17</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3899480</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3899479</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This dataset contains processed files generated in the analyses described in &amp;quot;Discovery of protein modifications using high resolution differential mass spectrometry proteomics&amp;quot; by Cifani, Zhi, Luo et al., describing SAMPEI, a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics.&lt;/p&gt;

&lt;p&gt;Using synthetic standards and controlled chemical labeling experiments, we demonstrate high specificity and sensitivity of SAMPEI for the discovery of sub-stoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI is implemented as a Python package, and is available from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).&lt;/p&gt;

&lt;p&gt;The dataset is divided in 3 set of files:&lt;/p&gt;

&lt;p&gt;1. Agnostic_discovery_benchmarking.zip file contains analyses performed to establish relative sensitivity and specificity of agnostic PTM discovery (Figure 2, Figure S3).&lt;/p&gt;

&lt;p&gt;2.&amp;nbsp;Chemoproteomics_of_LPS_stimulated_macrophages.zip file contains&amp;nbsp;RAW264.7&amp;nbsp;cell proteomics identification results from X!tandem and SAMPEI (Figure 3, Figures S4-S7).&lt;/p&gt;

&lt;p&gt;3.&amp;nbsp;Itaconate_adducts_validation.zip file contains analysis to confirm cystein adducts produced by itaconic acid (Figure 5, Figures S8-S12).&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
</resource>
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