QSample: an automated system for rapid monitoring of quality indicators in proteomics samples

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.

We acknowledge support of the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S grant funded by MCIN/AEI/10.13039/501100011033) and PID2020-115092GB-I00 funded by AEI/10.13039/501100011033 and the Generalitat de Catalunya through the CERCA programme and the Departament de Recerca i Universitats (2021-SGR2021-01225). We also acknowledge financial support from the Core for Life Challenge Projects program, and we specially thank An Staes, Teresa Maia, and Sara Dufour from the VIB Proteomics Core and the rest of the Core for Life Proteomics Working Group for their feedback and fruitful discussion. The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech).