PMart Web Application: Marketplace for Interactive Analysis of Panomics Data

• Published in: Journal of proteome research Vol. 23; no. 8; pp. 3310 - 3317
• Main Authors: Stratton, Kelly G., Claborne, Daniel M., Degnan, David J., Richardson, Rachel E., White, Amanda M., McCue, Lee Ann, Webb-Robertson, Bobbie-Jo M., Bramer, Lisa M.
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 02.08.2024
• Subjects: Computational Biology - methods; Humans; Internet; Lipidomics - methods; Mass Spectrometry - methods; Metabolomics - methods; Metabolomics - statistics & numerical data; Multiomics; Proteomics - methods; Proteomics - statistics & numerical data; Software; User-Computer Interface; visualization; exploratory data analysis; software; proteomics; RNA-seq; metabolomics; reproducibility; web service; lipidomics; statistics
• DOI: 10.1021/acs.jproteome.3c00512
• ISSN: 1535-3893; 1535-3907

PMart is a web-based tool for reproducible quality control, exploratory data analysis, statistical analysis, and interactive visualization of ‘omics data, based on the functionality of the pmartR R package. The newly improved user interface supports more ‘omics data types, additional statistical capabilities, and enhanced options for creating downloadable graphics. PMart supports the analysis of label-free and isobaric-labeled (e.g., TMT, iTRAQ) proteomics, nuclear magnetic resonance (NMR) and mass-spectrometry (MS)-based metabolomics, MS-based lipidomics, and ribonucleic acid sequencing (RNA-seq) transcriptomics data. At the end of a PMart session, a report is available that summarizes the processing steps performed and includes the pmartR R package functions used to execute the data processing. In addition, built-in safeguards in the backend code prevent users from utilizing methods that are inappropriate based on omics data type. PMart is a user-friendly interface for conducting exploratory data analysis and statistical comparisons of omics data without programming.