This R package provides functionality for quality control processing, statistical analysis and visualization of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level; isobaric labeled or unlabled), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be compared against each other, filtering of feature and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons of groups of interest (ANOVA and/or independence of missing data tests). Example data to be used with this packages can be found in pmartRdata.
devtools::install_github("pmartR/pmartR")To get started, see the package documentation and function reference located here.
Example peptide (both unlabeled and isobaric labeled), protein, metabolite and lipid data are available in the pmartRdata package available on Github, here
To cite this package, please use the following:
Stratton KG, Webb-Robertson BJ, McCue LA, Stanfill B, Claborne D, Godinez I, Johansen T, Thompson AM, Burnum-Johnson KE, Waters KM, Bramer LM. pmartR: quality control and statistics for mass spectrometry-based biological data. Journal of proteome research. 2019 Jan 14;18(3):1418-25.