P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

Abstract

The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart ( https://pmart.labworks.org ) is a new interactive web-based software environment that enables domain scientists to perform quality-control processing, statistics, and exploration of large-complex proteomics data sets without requiring statistical programming. P-Mart is developed in a manner that allows researchers to perform analyses via a series of modules, explore the results using interactive visualization, and finalize the analyses with a collection of output files documenting all stages of the analysis and a report to allow reproduction of the analysis.

Keywords: exploratory data analysis; proteomics; reproducibility; software; statistics; visualization; web service.

Figure 1.

Opening page of P-Mart, which offers analyses of personal data or existing CPTAC data. Video tutorials are available from this page at http://bit.ly/PMartPNNL to train users on multiple aspects of the software.

Figure 2.

P-Mart user interface showing the selections made for the example MERS-Co dataset upload.

Figure 3.

Module selection in P-Mart allows the user to add and removed existing capabilities easily and allows new capabilities in R to be easily added to P-Mart.

Figure 4.

P-Mart quality-assessment tools to evaluate the quality of samples (top) and adequate statistical coverage of peptides (bottom). Each module allows the user to modify the parameters to be more or less strict in the selection criteria.

Figure 5.

P-Mart Trelliscope features allow customization of the metrics that will be displayed with each plot (top) and the capability to sort, filter, and search based on parameters of interest.

Figure 6.

P-Mart Trelliscope gives a visual display of each protein that was selected based on user interaction (Figure 5) and allows the interactive evaluation of the proteins through links to public resources, such as UniProt.

Figure 7.

Example of the report yielded at the end of the P-Mart analysis.

Figure 8.

P-Mart download is available at the end of the report. On the right is the collection of data that are available to the user, including normalized data, protein-level data, and all statistics that were performed.