MetaMorpheus

MetaMorpheus identifies peptides and proteoforms from tandem mass spectrometry (MS/MS) data to improve protein inference and post-translational modification (PTM) discovery.

Key Features:

• Multi-Protease Protein Inference: Implements a multi-protease protein inference algorithm that leverages peptides from parallel digestions, maintains peptide-to-protease associations, and computes protease-specific q-values.
• Integrated Analysis: Combines multi-protease search and protein inference to reduce ambiguous identifications and increase the number of identified post-translational modifications.
• Posterior Error Probability Calculation: Computes posterior error probabilities for individual peptide-spectrum matches using a binary decision tree that accounts for limited peak overlap, m/z uncertainty, and noise from coisolated peptides.
• Versatile Search Support: Supports bottom-up, top-down, and nonspecific digestion searches and can be applied to proteogenomic studies.

Scientific Applications:

• Protein Identification and PTM Discovery: Enables precise peptide and proteoform identification and discovery of post-translational modifications from MS/MS data.
• Proteogenomics: Supports integration of proteomic data with genomic information for proteogenomic studies.
• Biological and Disease Research: Facilitates investigation of protein function, regulation, disease mechanisms, and therapeutic targets by improving confidence in peptide-spectrum matches.

Methodology:

Computational methods explicitly include a multi-protease protein inference algorithm that maintains peptide–protease associations and computes protease-specific q-values, and a binary decision tree calculation that computes posterior error probabilities for each peptide-spectrum match; analyses support bottom-up, top-down, and nonspecific digestion searches and proteogenomic datasets.