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

Description

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

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.
Projects (6)

Last updated on 2024-02-11T22:41:43+00:00 by LN Anderson PNNL DataHub NIAID Program Project: Modeling Host Responses to Understand Severe Human Virus Infections, Multi-Omic Viral Dataset Catalog Collection The National Institute of Allergy and Infectious Diseases ( NIAID ) "Modeling Host Responses...

  1. Datasets

    45

Last updated on 2023-11-09T21:18:57+00:00 by LN Anderson Omics-LHV Profiling of Host Response to Influenza A Virus Infection Background Influenza A virus (IAV) is a high risk biological agent, classified as a Category C priority pathogen ( Orthomyxoviridae ) by the National Institute of Allergy and...

  1. Datasets

    8

Last updated on 2023-11-09T21:18:57+00:00 by LN Anderson Omics-LHV Profiling of Host Response to MERS-CoV Virus Infection Background Middle East Respiratory Syndrome coronavirus (MERS-CoV) is classified as a Category C priority pathogen ( Coronaviridae ) by the National Institute of Allergy and...

  1. Datasets

    15

Last updated on 2023-11-09T21:18:57+00:00 by LN Anderson Omics-LHV Profiling of Host Response to West Nile Virus Infection Background West Nile virus (WNV) is classified as a Category B priority pathogen (mosquito-borne Flaviviridae ) by the National Institute of Allergy and Infectious Diseases (...

  1. Datasets

    11

Last updated on 2023-11-09T21:18:57+00:00 by LN Anderson Omics-LHV Profiling of Host Interferon-Stimulated Response to Virus Infection Background The human host Interferon (IFN) alpha, beta, and gamma participate in the body's natural immune response to lethal virus infection and disease. The NIAID...

  1. Datasets

    5

Last updated on 2023-11-09T21:18:57+00:00 by LN Anderson Omics-LHV Profiling of Host Response to Ebola Virus Infection Background Ebola virus (EBOV) is a high risk biological agent, classified as a Category A priority pathogen ( Flaviviridae ) by the National Institute of Allergy and Infectious...

  1. Datasets

    6
Datasets (41)
Publications (1)
People (1)

Biography Kelly is a senior data scientist in the Computational Biology group within the Biological Sciences Division at Pacific Northwest National Laboratory (PNNL). After earning a MS in Biostatistics from the University of Washington in 2012, she worked at a cancer research company for two years...

Data Sources (3)
Methods (1)
Institutions (1)