biostudies-literatureUnknownTsantilas KANIA NIH HHSNIGMS NIH HHSA thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to veribioRxiv : the preprint server for biology2024.04.12.589318https://www.ebi.ac.uk/biostudies/studies/S-EPMC11030400biostudies-literatureA framework for quality control in quantitative proteomics.PMC11030400P30 AG013280F31 AG069420T32 AG066574RF1 AG053959U19 AG065156R24 GM141156Johnson RSHuang EHoofnagle ANPark JMacCoss MJRiffle MBereman MSMacLean BXTsantilas KAPlubell DLSharma VMerrihew GEEckels JCanterbury JDRobbins JEWu CCSpencer SEfalseA framework for quality control in quantitative proteomics.A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to veri2024-01-01T00:00:00Z2024 Aug2026-04-08T18:31:51.295Z2026-04-08T09:40:41.859ZS-EPMC110304003864509810.1101/2024.04.12.589318