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. 2025 Sep 5;24(9):4816-4824.
doi: 10.1021/acs.jproteome.5c00119. Epub 2025 Aug 19.

QSample: An Automated System for Rapid Monitoring of Quality Indicators in Proteomics Samples

Roger Olivella  1   2 , Cristina Chiva  1   2 , Marc Serret  1   2 , Antoni Hermoso  1   2 , Eva Borràs  1   2 , Guadalupe Espadas  1   2 , Julia Morales-Sanfrutos  1   2 , Olga Pastor  1   2 , Amanda Solé  1   2 , Julia Ponomarenko  1   2 , Eduard Sabidó  1   2
Affiliations

QSample: An Automated System for Rapid Monitoring of Quality Indicators in Proteomics Samples

Roger Olivella et al. J Proteome Res. .

Abstract

Mass spectrometry-based proteomics is an essential technique in contemporary biomedicine, offering quantitative, sensitive, and rapid analysis of proteomes. Recent advancements in mass spectrometry have enabled the acquisition of data from increasingly large-scale experiments, often conducted in core facilities and research infrastructures. While automated tools exist to assess instrument performance using predefined control samples, the analysis of experimental samples typically occurs postacquisition, which can delay decision-making and lead to potential data integrity issues. To address these challenges, we developed QSample, an open-source automated system for rapidly monitoring quality indicators in proteomics samples during data collection. QSample enhances the quality control framework by facilitating prompt actions and fast decision-making, ensuring that proteomics core facilities deliver data that adhere to best research practices.

Keywords: automation; data analysis; mass spectrometry; nextflow; web application.

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Figures

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1
General structure of QSample, with a file transfer function (Rawocop), a bioinformatics pipeline (Atlas), and a web server for visualizing key quality indicators of samples associated with specific applications and grouped by request or experiment.
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Scheme of the main bioinformatics pipelines supported by QSample, including data-dependent and data-independent acquisition file structures.
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Main plots of the QSample web server automatically generated to display the key quality indicators of each sample within a request.
See this image and copyright information in PMC

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