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J Proteome Res. 2019 Feb 1;18(2):678-686. doi: 10.1021/acs.jproteome.8b00732. Epub 2018 Dec 14.

MSstatsQC 2.0: R/Bioconductor Package for Statistical Quality Control of Mass Spectrometry-Based Proteomics Experiments.

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Department of Statistics , Muğla Sitki Koçman University , Muğla 48000 , Turkey.
College of Computer Science , Northeastern University , Boston , Massachusetts 02115 , United States.
Proteomics Unit, Centre de Regulaci Genmica, Barcelona Institute of Science and Technology , Universitat Pompeu Fabra , 08002 Barcelona , Spain.
Biognosys , 8952 Schlieren , Switzerland.


MSstatsQC is an R/Bioconductor package for statistical monitoring of longitudinal system suitability and quality control in mass spectrometry-based proteomics. MSstatsQC was initially designed for targeted selected reaction monitoring experiments. This paper presents an extension, MSstatsQC 2.0, that supports experiments with global data-dependent and data-independent acquisition. The extension implements data processing and analyses that are specific to these acquisition types. It relies on state-of-the-art methods of statistical process control to detect deviations from optimal performance of various metrics (such as intensity and retention time of chromatographic peaks) and to summarize the results across multiple metrics and analytes. Additionally, the web-based graphical user interface MSstatsQCgui, implemented as a separate R/Bioconductor package, provides a user-friendly way to visualize and report the results from MSstatsQC 2.0.


proteomics; quality control; software; statistical process control

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