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MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non-Modified Peptides.
Proteomics ( IF 3.4 ) Pub Date : 2020-07-08 , DOI: 10.1002/pmic.202000061
Liya Ming 1 , Yang Zou 1 , Yiming Zhao 2 , Luna Zhang 2 , Ningning He 1 , Zhen Chen 1 , Shawn S-C Li 3 , Lei Li 1, 2
Affiliation  

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.

中文翻译:

MMS2plot:一个R包,用于可视化多个MS / MS光谱的修饰和未修饰肽组。

蛋白质的大量翻译后修饰(PTM)被掩埋在shot弹枪蛋白质组学数据集中的未分配质谱(MS)光谱中。由于修饰的肽片段相对于相应的未修饰的版本而言丰度低,因此至关重要的是开发一种工具,以便能够基于MS / MS光谱轻松评估PTM的分配。这样的工具将优选具有允许比较经修饰的和未经修饰的肽对或基团之间的碎片离子光谱和保留时间的能力。本文介绍了MMS2plot,它是一种R包,用于可视化多种肽的肽谱匹配(PSM)。MMS2plot具有批处理模式,并以矢量图形文件格式生成输出图像,从而便于评估和发布PSM分配。MMS2plot有望在由液相色谱MS / MS生成的大规模蛋白质组学数据集中的PTM发现中发挥重要作用。MMS2plot软件包可通过GPL-3许可在https://github.com/lileir/MMS2plot免费获得。
更新日期:2020-08-18
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