MS-GF+

MS-GF+ scores tandem mass spectrometry (MS/MS) spectra against peptides derived from protein sequence databases to identify peptides for mass spectrometry-based proteomics.

Key Features:

• Sensitivity and Universality: Achieves high sensitivity, identifying more peptides across diverse spectra types, MS instrument configurations, and experimental protocols.
• Benchmarking Performance: Benchmarked on spectra from different fragmentation methods, multiple enzyme digests, phosphorylated peptides, and peptides with unusual fragmentation propensities such as those produced by alpha-lytic protease.
• Advanced Statistical Approaches: Implements generating functions and derived measures, including spectral energy and spectral probability, and offers alternatives to Delta-scores.
• Error Rate Evaluation: Computes statistical significance via spectral probability to evaluate error rates, improve the sensitivity–specificity tradeoff, address "one-hit-wonders," and reduce reliance on decoy database searches.

Scientific Applications:

• Computational proteomics: Distinguishing correct from false peptide identifications in mass spectrometry-based proteomics studies.
• Phosphoproteomics: Identification and analysis of phosphorylated peptides.
• Novel enzymatic activity analysis: Analysis of peptides generated by novel proteases and experiments that produce unusual fragmentation propensities (e.g., alpha-lytic protease).

Methodology:

Uses generating functions to compute spectral probabilities and spectral energy and assigns statistical significance to peptide-spectrum matches to evaluate error rates and reduce reliance on decoy database searches.