VEMS

VEMS identifies and characterizes post-translational modifications (PTMs) in peptide tandem mass spectrometry (MS/MS) data to enable detailed proteomic analyses.

Key Features:

• Modification-Specific Mass Analysis: Utilizes modification-specific mass increments, neutral losses, and diagnostic fragment ions from peptide mass spectra to identify PTMs.
• Advanced Search Algorithm: Implements a formalized search approach for databases using tandem mass spectra of partially modified (sub-stoichiometrically) peptides to handle the expanded search space from multiple modifications and missed proteolytic cleavages.
• Peptide Scoring Scheme: Incorporates an improved scoring scheme that includes modification-specific ion information from MS/MS spectra to assign PTM type and position on peptides.
• Distinguishing Near-Isobaric Modifications: Differentiates near-isobaric modifications such as lysine trimethylation and acetylation by analyzing diagnostic neutral losses and immonium ions.

Scientific Applications:

• Comprehensive PTM Profiling: Enables analysis of phosphorylation, acetylation, methylation, glycosylation, and other PTMs across large-scale proteomic datasets.
• Large-Scale Proteomics: Facilitates exhaustive searches in large-scale proteomic experiments by accounting for multiple variable modifications and missed cleavages.
• Resolving Modification Isomers: Supports distinguishing near-isobaric modification isomers to improve confidence in PTM assignment and localization.

Methodology:

Searches peptide MS/MS spectra against sequence databases while accounting for up to 16 variable modifications and up to six missed proteolytic cleavage sites.