Software - Statistical Analysis pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data

pmartR Software Overview

The pmartR package provides a single software tool for QC (filtering and normalization), exploratory data analysis (EDA), and statistical analysis (robust to missing data) and includes numerous visualization capabilities of mass spectrometry (MS) omics data (proteomic, metabolomic, and lipidomic data). The pmartR package provides the necessary capabilities for preparing and performing statistical MS data analysis using simple function calls. Data objects are automatically updated with information about the analysis as it is performed, streamlining the data exploration, QC, and statistical analysis process for the user. It is described in publication pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data and can be found at the Pacific Northwest National Laboratory Developer Community at Zenodo.

Usage

• Example peptide (both unlabeled and isobaric labeled), protein, metabolite and lipid data are available in the pmartRdata package available on Github, and used for illustration purposes in pmartRqc. See supplementary software documentation at 10.5281/zenodo.6554575. 

Dependencies

• It's been noted that there are issues with Rtools for R version 3.5.1.

Programming Language

• R (3.0.0 or newer), HTML, C++

License

pmartR is licensed under BSD-2-Clause license at GitHub and Creative Commons Attribution 4.0 International at the Zenodo citation.

Acknowledgment of Federal Funding

The software described here was funded in whole or in part by the National Institute of Allergy and Infectious Diseases, of the National Institutes of Health under award number U19AI106772, and is a contribution of the "Modeling Host Responses to Understand Severe Human Virus Infections" Project at Pacific Northwest National Laboratory. Data generated by the Omics-LHV Core for proteomics, metabolomics, and lipidomics analyses for were performed at Pacific Northwest National Laboratory in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office, operating under the Battelle Memorial Institute for the DOE under contract number DE-AC05-76RLO1830. 

Cite as

1. Kelly G. Stratton, & Lisa M. Bramer. (2018). pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data (0.10.0). Zenodo. https://doi.org/10.5281/zenodo.6108668
2. Stratton KG, Webb-Robertson BM, 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. J Proteome Res. 2019 Mar 1;18(3):1418-1425. doi: 10.1021/acs.jproteome.8b00760. Epub 2019 Jan 28. PMID: 30638385; PMCID: PMC6750869.