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Discovery of protein modifications using differential tandem mass spectrometry proteomics

UID: 11208

Author(s): Cifani, Paolo*, Li, Zhi, Luo, Danmeng*, Grivainis, Mark, Intlekofer, Andrew M.*, Fenyo, David, Kentsis, Alex* * MSK affiliated

Description
Description from Zenodo:

"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)."
Subject(s)
Protein Processing, Post-Translational
Proteomics
Software
Tandem Mass Spectrometry
Access via Zenodo

Access Restrictions
Free to All
Access Instructions
Creative Commons Attribution 4.0 International
Associated Publications
Cifani P, Li Z, Luo D, Grivainis M, Intlekofer A, Fenyö D, Kentsis A. Discovery of protein modifications using differential tandem mass spectrometry proteomics. Journal of Proteome Research. 2021; 20(4):1835-1848.
Software Used
SAMPEI

open-source algorithm designed for the discovery of functional protein and peptide signaling modifications

X! Tandem

software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.

Dataset Format(s)
PDF, Microsoft Excel, zip
Dataset Size
256.5 MB
Data Catalog Record Updated
2024-05-09