Dataset Open Access

Discovery of protein modifications using differential tandem mass spectrometry proteomics

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

Recent studies have revealed diverse amino acid, post-translational and non-canonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications from high-resolution tandem peptide mass spectrometry. Termed SAMPEI for Spectral Alignment-based Modified PEptide Identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate specificity and sensitivity of SAMPEI for the discovery of protein modifications in complex cellular extracts. We then apply SAMPEI to mapping chemical protein modifications in differentiating mouse macrophage proteome. SAMPEI revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation which we experimentally validated. SAMPEI’s robust parameterization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules. SAMPEI is implemented as a Python package and is available open-source 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 (256.5 MB)
Name Size
0_Datasets_metadata.xlsx
md5:bf2a5091a802727f142c347db01e2ae7
12.7 kB Download
1_Agnostic_discovery_benchmarking.zip
md5:7328ef504049803cebab6a7efa3e20d2
241.9 MB Download
1_Agnostic_discovery_benchmarking_Experimental_design.pdf
md5:17f489edccde44a70ee81758d7a6ea81
14.5 kB Download
2_Chemoproteomics_of_LPS_stimulated_macrophages.zip
md5:ef4dabbff7737a15455706a2bef676f0
14.3 MB Download
2_Chemoproteomics_of_LPS_stimulated_macrophages_Experimental_design.pdf
md5:897d4afed6da40308b219dc693133de5
10.2 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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