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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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    <dct:title>Discovery of protein modifications using high resolution differential mass spectrometry proteomics</dct:title>
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    <dct:description>&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;</dct:description>
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