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

Degnan, David J.; Bramer, Lisa M.; White, Amanda M.; Zhou, Mowei; Bilbao, Aivett; McCue, Lee Ann

doi:10.1021/acs.jproteome.0c00857

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

Journal Article · Thu Mar 04 04:00:00 EST 2021 · Journal of Proteome Research

DOI:https://doi.org/10.1021/acs.jproteome.0c00857· OSTI ID:1782588

^[1]; ^[1]; White, Amanda M. ^[1]; ^[1]; ^[1]; ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

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 MS data is hindered by proprietary proteomics visualization software designed for particular workflows and academic software that lack visualization tools. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search tools, labelling 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) is available for easy local installation.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1782588

Report Number(s):: PNNL-SA-157638

Journal Information:: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 4 Vol. 20; ISSN 1535-3893

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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