MMS2plot

MMS2plot visualizes and evaluates tandem mass spectrometry (MS/MS) spectra to assist assessment of peptide post-translational modifications (PTMs) and is implemented as an R package.

Key Features:

• Visualization Capabilities: Visualizes multiple MS/MS spectra for modified and non-modified peptides identified within the same raw MS files and produces mirror-style plots for two peptide-spectrum matches (PSMs) and aligned plots for more than two PSMs.
• Batch Processing: Includes a batch mode for processing multiple datasets simultaneously.
• Output Format: Generates vector graphics (PDF) output with recommended widths of 3.35 inches for single-column and 7 inches for double-column publication formats.

Scientific Applications:

• PTM validation in proteomics: Facilitates comparison of fragment ion spectra and retention times between modified and unmodified peptide pairs or groups to aid confirmation and discovery of PTM assignments in shotgun proteomics datasets.

Methodology:

Leverages annotated peptide-spectrum matches from peptide identification algorithms to produce visual representations that highlight similarities and differences in MS/MS fragment ions and retention times in LC-MS/MS datasets.