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MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.

ABSTRACT:

Motivation

Multiple factors can impact accuracy and reproducibility of mass spectrometry data. There is a need to integrate quality assessment and control into data analytic workflows.

Results

The MsQuality package calculates 43 low-level quality metrics based on the controlled mzQC vocabulary defined by the HUPO-PSI on a single mass spectrometry-based measurement of a sample. It helps to identify low-quality measurements and track data quality. Its use of community-standard quality metrics facilitates comparability of quality assessment and control (QA/QC) criteria across datasets.

Availability and implementation

The R package MsQuality is available through Bioconductor at https://bioconductor.org/packages/MsQuality.

SUBMITTER: Naake T

PROVIDER: S-EPMC10580266 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.

Naake Thomas T Rainer Johannes J Huber Wolfgang W

Bioinformatics (Oxford, England) 20231001 10

<h4>Motivation</h4>Multiple factors can impact accuracy and reproducibility of mass spectrometry data. There is a need to integrate quality assessment and control into data analytic workflows.<h4>Results</h4>The MsQuality package calculates 43 low-level quality metrics based on the controlled mzQC vocabulary defined by the HUPO-PSI on a single mass spectrometry-based measurement of a sample. It helps to identify low-quality measurements and track data quality. Its use of community-standard quali ...[more]

PMID: 37812234

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