A Curated Resource for Phosphosite-specific Signature Analysis.

Area of Science:

• Proteomics and Bioinformatics
• Molecular Signaling and Pathway Analysis

Background:

• Post-translational modifications (PTMs), like phosphorylation, are crucial for orchestrating signaling pathways.
• Current PTM data analysis is gene-centric due to a lack of site-specific databases and tools.
• This limits the detailed understanding of signaling pathway perturbations.

Purpose of the Study:

• To introduce PTMsigDB, a novel database of modification site-specific signatures.
• To develop PTM-Signature Enrichment Analysis (PTM-SEA) for analyzing quantitative mass spectrometry proteomics data.
• To enable site-specific pathway analysis for improved biological insights.

Main Methods:

• Curated PTM signatures from over 2,500 publications into PTMsigDB.
• Adapted single sample Gene Set Enrichment Analysis (ssGSEA) for PTM data.
• Developed PTM-SEA to leverage PTMsigDB for quantitative MS data analysis.

Main Results:

• PTM-SEA demonstrated superior representation of signaling events compared to gene-centric methods using EGF-perturbed cancer cells.
• Analysis of cell-cycle inhibitor-treated cancer cells revealed mechanism-of-action specific signatures of cell cycle kinases.
• Phosphoproteomes of PI3K-inhibited breast cancer cells showed signatures of PI3K inhibitors and downstream targets (AKT, MAPK/ERK).

Conclusions:

• PTMsigDB and PTM-SEA provide a powerful framework for site-specific PTM pathway analysis.
• The approach enhances the understanding of signaling pathway dynamics in various cellular contexts.
• These tools offer improved resolution for analyzing complex proteomics data.