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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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  <dc:creator>Paolo Cifani</dc:creator>
  <dc:creator>Zhi Li</dc:creator>
  <dc:creator>Danmeng Luo</dc:creator>
  <dc:creator>Mark Grivainis</dc:creator>
  <dc:creator>Andrew M. Intlekofer</dc:creator>
  <dc:creator>David Fenyö</dc:creator>
  <dc:creator>Alex Kentsis</dc:creator>
  <dc:date>2020-06-17</dc:date>
  <dc:description>This dataset contains processed files generated in the analyses described in "Discovery of protein modifications using high resolution differential mass spectrometry proteomics" by Cifani, Zhi, Luo et al., describing SAMPEI, a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics.

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).

The dataset is divided in 3 set of files:

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

2. Chemoproteomics_of_LPS_stimulated_macrophages.zip file contains RAW264.7 cell proteomics identification results from X!tandem and SAMPEI (Figure 3, Figures S4-S7).

3. Itaconate_adducts_validation.zip file contains analysis to confirm cystein adducts produced by itaconic acid (Figure 5, Figures S8-S12).

 

 </dc:description>
  <dc:identifier>https://zenodo.org/record/3899480</dc:identifier>
  <dc:identifier>10.5281/zenodo.3899480</dc:identifier>
  <dc:identifier>oai:zenodo.org:3899480</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.3899479</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:title>Discovery of protein modifications using high resolution differential mass spectrometry proteomics</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>
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