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

Description

Last updated on 2025-01-29T20:22:29+00:00 by LN Anderson

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. 

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.

 

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. 

Citation Policy

In efforts to enable discovery, reproducibility, and reuse of PPI-funded project source code in accordance with best practices (as outlined by the FAIR4RS Principles), we ask that all reuse of all project source code materials acknowledge all primary and secondary software citations and corresponding journal articles where applicable.

    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 Background The National Institute of Allergy and Infectious Diseases (NIAID) "Modeling Host...

    1. Datasets

      45

    Last updated on 2024-02-11T22:41:43+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 belonging to the Orthomyxoviridae family is classified as a Category C priority pathogen by the National...

    1. Datasets

      8

    Last updated on 2024-02-11T22:41:43+00:00 by LN Anderson Omics-LHV Profiling of Host Response to MERS-CoV Virus Infection Background Middle East Respiratory Syndrome coronavirus ( MERS-CoV ), part of the Coronaviridae family, is classified as a Category C priority pathogen by the National Institute...

    1. Datasets

      15

    Last updated on 2024-02-11T22:41:43+00:00 by LN Anderson Omics-LHV Profiling of Host Response to West Nile Virus Infection Background West Nile virus ( WNV ) belongs to the mosquito-borne Flaviviridae family and is classified as a Category A priority pathogen by the National Institute of Allergy and...

    1. Datasets

      11

    Last updated on 2024-02-11T22:41:43+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...

    1. Datasets

      5

    Last updated on 2024-02-11T22:41:43+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, belonging to the Flaviviridae family, and is classified as a Category A priority pathogen by the National Institute...

    1. Datasets

      6
    Datasets (41)
    Publications (2)
    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)