Journal
JOURNAL OF PROTEOME RESEARCH
Volume 20, Issue 4, Pages 2014-2020Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.0c00857
Keywords
proteomics web application; tandem mass spectrometry; peptide database search; bottom-up; top-down
Categories
Funding
- Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility - Office of Biological and Environmental Research [DE-AC05-76RL01830]
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Visual examination of mass spectrometry data is crucial for evaluating data quality and aiding data exploration. However, the limitations of proteomics visualization software make visual inspection of LC-MS data challenging. PSpecteR, an open-source and interactive R Shiny web application, supports various proteomics data processing steps and overcomes these limitations.
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.
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