Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data

• DOI: 10.1074/mcp.ra118.000648
• Publication Date: 2018-04-17T21:40:12Z
• Authors: Bryan A. Stanfill; Ernesto S. Nakayasu; Lisa M. Bramer; Allison M. Thompson; Charles K. Ansong; Therese R. Clauss; Marina A. Gritsenko; Matthew E. Monroe; Ronald J. Moore; Daniel J. Orton; Paul D. Piehowski; Athena A. Schepmoes; Richard D. Smith; Bobbie-Jo M. Webb...; Thomas O. Metz
• Keywords: Proteomics; Quality Control; 0301 basic medicine; Cohort Studies; User-Computer Interface; 03 medical and health sciences; ROC Curve; Computer Systems; Tandem Mass Spectrometry; Isotope Labeling; Humans; Databases, Protein; Peptides; Oxidation-Reduction; Algorithms

Liquid chromatography-mass spectrometry (LC-MS)-based proteomics studies of large sample cohorts can easily require from months to years complete. Acquiring consistent, high-quality data in such large-scale is challenging because normal variations instrumentation performance over time, as well artifacts introduced by the samples themselves, those collection, storage and processing. Existing quality control methods for primarily focus on post-hoc analysis remove low-quality that would degrade downstream statistics; they are not designed evaluate near real-time, which allow interventions soon deviations detected. In addition flagging analyses demonstrate outlier behavior, evaluating how structure changes time aide understanding typical instrument or identify issues a degradation need cleaning and/or re-calibration. To address this gap proteomics, we developed Quality Control Analysis Real-Time (QC-ART), tool acquired dynamically flag potential with quality. QC-ART has similar accuracy standard additional benefit real-time analysis. We utility identifying both LC-MS-based plasma subset The Environmental Determinants Diabetes Young cohort. also present case where facilitated identification oxidative modifications, often underappreciated proteomic experiments.