Multicenter experiment for quality control of peptide-centric LC–MS/MS analysis — A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers

• The LC–MS/MS performance of 6 laboratories was evaluated during 6 months.
• QC metrics were evaluated to check performance of shotgun proteomics workflows.
• Protein identification repeatability overtime is overall fair, IQR: 69.2–72.4%.
• Lack of systematic LC–MS quality assessment can drop identifications down to 30%.

Proteomic technologies based on mass spectrometry (MS) have greatly evolved in the past years, and nowadays it is possible to routinely identify thousands of peptides from complex biological samples in a single LC–MS/MS experiment. Despite the advancements in proteomic technologies, the scientific community still faces important challenges in terms of depth and reproducibility of proteomics analyses. Here, we present a multicenter study designed to evaluate long-term performance of LC–MS/MS platforms within the Spanish Proteomics Facilities Network (ProteoRed-ISCIII). The study was performed under well-established standard operating procedures, and demonstrated that it is possible to attain qualitative and quantitative reproducibility over time. Our study highlights the importance of deploying quality assessment metrics routinely in individual laboratories and in multi-laboratory studies. The mass spectrometry data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000205.This article is part of a Special Issue entitled: HUPO 2014.

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