10.5281/zenodo.4313808
https://zenodo.org/records/4313808
oai:zenodo.org:4313808
Paolo Cifani
Paolo Cifani
0000-0002-4403-1277
Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
Zhi Li
Zhi Li
Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
Danmeng Luo
Danmeng Luo
Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
Mark Grivainis
Mark Grivainis
Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
Andrew M. Intlekofer
Andrew M. Intlekofer
Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA.
David Fenyö
David Fenyö
0000-0001-5049-3825
Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
Alex Kentsis
Alex Kentsis
0000-0002-8063-9191
Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
Discovery of protein modifications using differential tandem mass spectrometry proteomics
Zenodo
2020
2020-06-17
10.5281/zenodo.3899479
Creative Commons Attribution 4.0 International
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).