MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments

Liquid chromatography coupled with
bottom-up mass spectrometry
(LC-MS/MS)-based proteomics is a versatile technology for identifying
and quantifying proteins in complex biological mixtures. Postidentification,
analysis of changes in protein abundances between conditions requires
increasingly complex and specialized statistical methods. Many of
these methods, in particular the family of open-source Bioconductor
packages MSstats, are implemented in a coding language
such as R. To make the methods in MSstats accessible
to users with limited programming and statistical background, we have
created MSstatsShiny, an R-Shiny graphical user interface
(GUI) integrated with MSstats, MSstatsTMT, and MSstatsPTM. The GUI provides a point and click
analysis pipeline applicable to a wide variety of proteomics experimental
types, including label-free data-dependent acquisitions (DDAs) or
data-independent acquisitions (DIAs), or tandem mass tag (TMT)-based
TMT-DDAs, answering questions such as relative changes in the abundance
of peptides, proteins, or post-translational modifications (PTMs).
To support reproducible research, the application saves user’s
selections and builds an R script that programmatically recreates
the analysis. MSstatsShiny can be installed locally
via Github and Bioconductor, or utilized on the cloud at www.msstatsshiny.com. We
illustrate the utility of the platform using two experimental data
sets (MassIVE IDs MSV000086623 and MSV000085565).