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

Authors

Liya Ming, Qingdao University
Yang Zou, Qingdao University
Yiming Zhao, Qingdao University
Luna Zhang, Qingdao University
Ningning He, Qingdao University
Zhen Chen, Qingdao University
Shawn S.C. Li, Schulich School of Medicine & DentistryFollow
Lei Li, Qingdao University
Dhami, Schulich School of Medicine & Dentistry
Xing Li, Schulich School of Medicine & Dentistry
Masaaki Miyaji, JSR Micro
Gilles Lajoie, Schulich School of Medicine & Dentistry
Benjamin Chen, UT Southwestern Medical Center
Shawn Shun Cheng Li, Schulich School of Medicine & DentistryFollow

Document Type

Article

Publication Date

8-1-2020

Journal

Proteomics

Volume

20

Issue

15-16

URL with Digital Object Identifier

10.1002/pmic.202000061

Abstract

A large number of post-translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot-gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non-modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide-spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large-scale proteomics datasets generated by liquid chromatography-MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL-3 license.