MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non-Modified Peptides

Area of Science:

• Proteomics
• Bioinformatics
• Mass Spectrometry

Background:

• Many protein post-translational modifications (PTMs) are undetected in mass spectrometry (MS) data due to low fragment ion abundance.
• Evaluating PTM assignments requires comparing modified and unmodified peptide spectra and retention times.

Purpose of the Study:

• To introduce MMS2plot, an R package designed for visualizing peptide-spectrum matches (PSMs).
• To facilitate the evaluation and discovery of PTMs in large-scale proteomics datasets.

Main Methods:

• Developed MMS2plot as an R package for visualizing PSMs.
• Implemented batch processing capabilities for efficient analysis.
• Ensured output generation in vector graphics format for publication quality.

Main Results:

• MMS2plot enables the visualization of PSMs for multiple peptides.
• The package facilitates comparison of fragment ion spectra and retention times.
• Generated output images are suitable for evaluation and publication.

Conclusions:

• MMS2plot is a valuable tool for PTM discovery in liquid chromatography-MS/MS proteomics.
• The package simplifies the assessment of PTM assignments from complex datasets.
• MMS2plot is freely available for use in the scientific community.