PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R

• Published in: Journal of proteome research 2021-04, Vol.20 (4), p.2014-2020
• Main Authors: Degnan, David J, Bramer, Lisa M, White, Amanda M, Zhou, Mowei, Bilbao, Aivett, McCue, Lee Ann
• Format: Article
• Language: English
• Subjects: KNOWLEDGE MANAGEMENT AND PRESERVATION
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.0c00857

Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of LC–MS data is constrained by proteomics visualization software designed for particular workflows or vendor-specific tools without open-source code. We built PSpecteR, an open-source and interactive R Shiny web application for visualization of LC–MS data, with support for several steps of proteomics data processing, including reading various mass spectrometry files, running open-source database search engines, labeling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open-source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing/pspecter) is available for easy local installation.