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

Abstract

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

Parallel Multi-Omics in High-Risk Subjects for the Identification of Integrated Biomarker Signatures of Type 1 Diabetes

“…See Supplementary Table S1 for demographic, serology, OGTT, and other information/parameters. Samples from all subjects were divided into four equal aliquots that were individually subjected to proteomics, metabolomics, lipidomics, and transcriptomics (miRNAs) analyses (i.e., parallel quadra-omics) that were performed in collaboration with the Miami Integrative Metabolomics Research Center (lipidomics) [ 58 ], Pacific Northwest National Laboratories (proteomics) [ 59 ], Ocean Ridge Biosciences (transcriptomics) [ 60 ], and the Stedman Metabolomics Laboratory at Duke University Medical Center (metabolomics) [ 61 ].…”

Molecular networks in Network Medicine: Development and applications

“…In every step of a data analysis procedure, it is advisable to identify outliers (Bittremieux, Meysman, Martens, Valkenborg, & Laukens, 2016;Kauffmann & Huber, 2010;Norton, Vaquero-Garcia, Lahens, Grant, & Barash, 2018;Stanfill et al, 2018), including samples or features with an abnormal number of missing values, samples that display substantially different distributions in their quantitative features, or samples that do not cluster with the rest of their group. Such cases need to be handled carefully; if the outlying nature of a sample cannot be corrected (through appropriate missing data imputation and data normalization, or after correction of mis-annotated samples), the offending sample might be better removed completely for the subsequent data analysis.…”

Rapidly Assessing the Quality of Targeted Proteomics Experiments Through Monitoring Stable-isotope Labeled Standards

“…For experiments that contain many samples, and where the time between data acquisition and data analysis is long, this QC/QA step should not be delayed; rather QC/QA should happen immediately upon data acquisition to give feedback as soon as possible to the instrument operator 28 . To fill this need in targeted proteomics studies, we created Q4SRM which can analyze the heavy labeled reference peptides in an LC-SRM-MS data file within one minute.…”