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Dataset Open Access

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

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).

 

 

Files (191.4 MB)
Name Size
0_Datasets_metadata.xlsx
md5:c8bf8f8291c7de066efdd39048b7837a
12.2 kB Download
1_Agnostic_discovery_benchmarking.zip
md5:5fdf176a6afab7137413cfc623e5c31b
180.6 MB Download
1_Agnostic_discovery_benchmarking_Experimental_design.pdf
md5:93064de493fbc0630d2489ee97e8852b
12.3 kB Download
2_Chemoproteomics_of_LPS_stimulated_macrophages.zip
md5:5d1db01cf212cc7d2d27a493df8b17b0
10.6 MB Download
2_Chemoproteomics_of_LPS_stimulated_macrophages_Experimental_design.pdf
md5:590ed86f29d4e7795bfb33c9a7ef2db0
9.6 kB Download
3_Itaconate_adducts_validation.zip
md5:0c8c1f76c5976d4c9e4caa2034d0c094
213.5 kB Download
3_Itaconate_adducts_validation_Experimental_design.pdf
md5:016223bbea547a35c5727e259f71b8d8
11.4 kB Download
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