TopPIC

TopPIC identifies and characterizes proteoforms from top-down mass spectrometry data for proteome-level analysis of proteins and their post-translational modifications.

Key Features:

• Spectral alignment (MS-Align+): MS-Align+ performs spectral alignment to search MS/MS spectra against protein databases and facilitates identification of unexpected post-translational modifications (PTMs).
• Extended generating function for statistics: An extended generating function method computes spectral probabilities and false discovery rates to evaluate the statistical significance of protein–spectrum matches.
• Index-based PTM identification: Index-based algorithms employ two scoring functions—match scores and diagonal scores—to identify peptides/proteins with PTMs and accelerate PTM discovery.
• Benchmarking and performance: Benchmarked against MASCOT, OMSSA, and ProSightPC, TopPIC demonstrated superior performance on complex datasets including Saccharomyces cerevisiae.
• Top-down proteome coverage: Leverages advances in protein separation and mass spectrometry to analyze complex samples and identify hundreds to thousands of proteins (proteoforms).

Scientific Applications:

• Proteoform discovery: Identification and cataloging of proteoforms at the proteome level from top-down MS/MS data.
• PTM analysis: Detection and characterization of unexpected post-translational modifications from MS/MS spectra.
• Biological research: Application to molecular biology, biochemistry, and medical research for interpreting protein dynamics, interactions, and functions.

Methodology:

TopPIC aligns MS/MS spectra to protein databases using MS-Align+, applies index-based algorithms with match scores and diagonal scores to detect PTMs, and computes spectral probabilities and false discovery rates via an extended generating function method.