Establishing Quality Control Metrics for Large-Scale Plasma Proteomic Sample Preparation.

Autor: Oliver NC; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States., Choi MJ; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States., Arul AB; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States., Whitaker MD; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States., Robinson RAS; Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.; Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States.; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.; Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, United States.; Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.
Jazyk: angličtina
Zdroj: ACS measurement science au [ACS Meas Sci Au] 2024 Apr 29; Vol. 4 (4), pp. 442-451. Date of Electronic Publication: 2024 Apr 29 (Print Publication: 2024).
DOI: 10.1021/acsmeasuresciau.3c00070
Abstrakt: Large-scale plasma proteomics studies have been transformed due to the multiplexing and automation of sample preparation workflows. However, these workflows can suffer from reproducibility issues, a lack of standardized quality control (QC) metrics, and the assessment of variation before liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The incorporation of robust QC metrics in sample preparation workflows ensures better reproducibility, lower assay variation, and better-informed decisions for troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of patient samples ( N = 808) using tandem mass tag (TMT) 16-plex batches ( N = 58). The proteomic workflow consisted of protein depletion, protein digestion, TMT labeling, and fractionation. Five QC sample types (QC std , QC dig , QC pool , QC TMT , and QC BSA ) were created to measure the performance of sample preparation prior to the final LC-MS/MS analysis. We measured <10% CV for individual sample preparation steps in the proteomic workflow based on data from various QC sample steps. The establishment of robust measures for QC of sample preparation steps allowed for greater confidence in prepared samples for subsequent LC-MS/MS analysis. This study also provides recommendations for standardized QC metrics that can assist with future large-scale cohort sample preparation workflows.
Competing Interests: The authors declare no competing financial interest.
(© 2024 The Authors. Published by American Chemical Society.)
Databáze: MEDLINE
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