New Procedures Enhance Quality Control for Large-Scale Plasma Proteomics Analyses

Proteomics research has undergone a significant transformation with the integration of high-throughput liquid chromatography tandem mass spectrometry (LC–MS/MS) instruments and advanced automated sample preparation techniques. However, when it comes to scaling proteomics experiments for large sample cohorts, robust quality control (QC) procedures are crucial. In a groundbreaking study published in the Journal of the American Society for Mass Spectrometry, lead author Renã A. S. Robinson from Vanderbilt University presents an innovative approach to establishing comprehensive QC protocols for large-scale plasma proteomics analyses (1).

Glowing plasma background | Image Credit: © peshkova - stock.adobe.com

To address the challenges of reproducibility and quantitative accuracy in proteomics experiments involving hundreds to thousands of samples, the research team conducted a plasma proteomics study using tandem mass tag (TMT_pro) 16-plex batches. Over a 10-month data acquisition period, a total of 271 pooled QC LC–MS/MS result files were collected from the analysis of a patient-derived pooled plasma sample, which represented the entire cohort population. This sample was labeled with TMT_zero or TMT_pro reagents, allowing for performance monitoring of the LC–MS/MS instruments and within and across sample batch normalization.

Various analytical metrics, including protein and peptide identifications, peptide spectral matches (PSMs), MS/MS spectra acquisition, average peptide abundance, and retention time of selected tracking peptides, were evaluated to establish a robust LC–MS/MS QC workflow for future cohort studies. These metrics provided valuable insights into instrumental and data analysis variability, aiding in the identification of potential performance issues and enabling real-time troubleshooting.

The study not only outlined the QC procedures specifically tailored for large-scale plasma proteomics analyses but also provided general recommendations on using selected metrics for daily QC checks. By implementing these protocols, researchers can enhance reproducibility, improve quantitative accuracy, and achieve more reliable results in their proteomics investigations.

The establishment of comprehensive QC procedures for large-scale plasma proteomics analyses marks a significant milestone in the field, paving the way for more rigorous and standardized approaches in biomarker discovery, disease research, and personalized medicine. The findings presented in this study offer valuable insights into optimizing LC–MS/MS performance and highlight the importance of robust QC protocols in proteomics research.

Reference

(1) Patterson, K. L.; Arul, A. B.; Choi, M. J; Oliver, N. C.; Whitaker, M. D.; Bodrick, A. C.; Libbuy, J. B.; Hansen, S.; Dumitrescu, L.; Gifford, K. A.; Jefferson, A. L.; Hohman, T. J.; Robinson, R. A. S.; Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses. J. Am. Soc. Mass Spectrom. 2023. DOI: https://doi.org/10.1021/jasms.3c00050