A Standardized Protocol for Assuring the Validity of Proteomics Results from Liquid Chromatography-High-Resolution Mass Spectrometry

Abstract

Significant advances in the technological development of mass spectrometry in the field of proteomics and the generation of extremely large amounts of data require a very critical approach to assure the validity of results. Commonly used procedures involved liquid chromatography followed by high-resolution mass spectrometry measurements. Proteomics analysis is used in many fields including the investigation of the metabolism of biologically active substances in organisms. Thus, there is a need to care about the validity of the obtained results. In this work, we proposed a standardized protocol for proteomic analysis using liquid chromatography-high-resolution mass spectrometry, which covers all of these analytical steps to ensure the validity of the results. For this purpose, we explored the requirements of the ISO/IEC 17025:2017 standard as a reference document for quality control in biochemistry research-based mass spectrometry.

Keywords: ISO 15189:2022; ISO/IEC 17025:2017; mass spectrometry; proteomics; quality control; valid result.

Figure 1

Main steps in ensuring the validity of proteomics results based on the ISO/IEC 17025:2017 standard.

Figure 2

Monitoring the stability of the LC–MS/MS system using a control sample obtained after mixing all of the samples of the measurement series (XIC chromatograms for peptide DAHKSEVAHR m/z = 393.8611 and comparison of selected parameters).

Figure 3

Monitoring the carry-over effect in an LC–MS/MS system using a control sample and a blank sample (XIC chromatograms for peptide DAHKSEVAHR m/z = 393.8611 and comparison of selected parameters).

Figure 4

Shewhart charts for peak width at the baseline for the selected peptide LVNELTEFAK m/z = 582.3193 from the BSA control sample.