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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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{
  "description": "<p>This dataset contains processed files generated in the analyses described in &quot;Discovery of protein modifications using high resolution differential mass spectrometry proteomics&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.</p>\n\n<p>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).</p>\n\n<p>The dataset is divided in 3 set of files:</p>\n\n<p>1. Agnostic_discovery_benchmarking.zip file contains analyses performed to establish relative sensitivity and specificity of agnostic PTM discovery (Figure 2, Figure S3).</p>\n\n<p>2.&nbsp;Chemoproteomics_of_LPS_stimulated_macrophages.zip file contains&nbsp;RAW264.7&nbsp;cell proteomics identification results from X!tandem and SAMPEI (Figure 3, Figures S4-S7).</p>\n\n<p>3.&nbsp;Itaconate_adducts_validation.zip file contains analysis to confirm cystein adducts produced by itaconic acid (Figure 5, Figures S8-S12).</p>\n\n<p>&nbsp;</p>\n\n<p>&nbsp;</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA", 
      "@id": "https://orcid.org/0000-0002-4403-1277", 
      "@type": "Person", 
      "name": "Paolo Cifani"
    }, 
    {
      "affiliation": "Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA", 
      "@type": "Person", 
      "name": "Zhi Li"
    }, 
    {
      "affiliation": "Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA", 
      "@type": "Person", 
      "name": "Danmeng Luo"
    }, 
    {
      "affiliation": "Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA", 
      "@type": "Person", 
      "name": "Mark Grivainis"
    }, 
    {
      "affiliation": "Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA.", 
      "@type": "Person", 
      "name": "Andrew M. Intlekofer"
    }, 
    {
      "affiliation": "Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA", 
      "@id": "https://orcid.org/0000-0001-5049-3825", 
      "@type": "Person", 
      "name": "David Feny\u00f6"
    }, 
    {
      "affiliation": "Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA", 
      "@id": "https://orcid.org/0000-0002-8063-9191", 
      "@type": "Person", 
      "name": "Alex Kentsis"
    }
  ], 
  "url": "https://zenodo.org/record/3899480", 
  "datePublished": "2020-06-17", 
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  "identifier": "https://doi.org/10.5281/zenodo.3899480", 
  "@id": "https://doi.org/10.5281/zenodo.3899480", 
  "@type": "Dataset", 
  "name": "Discovery of protein modifications using high resolution differential mass spectrometry proteomics"
}
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