The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs

Abstract

Protein mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics. In contrast to immunoassays with indirect readouts, MS quantifications are multiplexed and include identification of proteoforms in a direct manner. Although widely used for routine measurements of drugs and metabolites, the number of clinical MS-based protein applications is limited. In this paper, we share our experience and aim to take away the concerns that have kept laboratory medicine from implementing quantitative protein MS. To ensure added value of new medical tests and guarantee accurate test results, five key elements of test evaluation have been established by a working group within the European Federation for Clinical Chemistry and Laboratory Medicine. Moreover, it is emphasized to identify clinical gaps in the contemporary clinical pathways before test development is started. We demonstrate that quantitative protein MS tests that provide an additional layer of clinical information have robust performance and meet long-term desirable analytical performance specifications as exemplified by our own experience. Yet, the adoption of quantitative protein MS tests into medical laboratories is seriously hampered due to its complexity, lack of robotization and high initial investment costs. Successful and widespread implementation in medical laboratories requires uptake and automation of this next generation protein technology by the In-Vitro Diagnostics industry. Also, training curricula of lab workers and lab specialists should include education on enabling technologies for transitioning to precision medicine by quantitative protein MS tests.

Mass Spectrometry for the Monitoring of Lipoprotein Oxidations by Myeloperoxidase in Cardiovascular Diseases

“…Therefore, it has been proposed to use biological variation data from intraindividual and interindividual variations to establish goals for imprecision, bias, and total allowable error of the method. If the biological data sought are not available, analytical performance specifications should be set based on the “state-of-the-art” performance and the purpose and mode of the test in the clinical pathway [ 87 ]. Concerning LC-MS based protein quantitation, analytical coefficient of variation (CV) less than 10% can be possible [ 87 ].…”

“…If the biological data sought are not available, analytical performance specifications should be set based on the “state-of-the-art” performance and the purpose and mode of the test in the clinical pathway [ 87 ]. Concerning LC-MS based protein quantitation, analytical coefficient of variation (CV) less than 10% can be possible [ 87 ]. EMA and FDA guidelines for validation of LC-MS/MS methods even allows 15% and 20% at the lower limit of quantification (LLOQ) [ 88 ].…”

“…If MS was first used for small molecules, it has been now well established as a protein quantification tool [ 90 ]. Its field of application is vast and varied, from monoclonal immunoglobulins detection to resolving quantification for example [ 86 , 87 ]. Multiplexing technologies such as LC-MS/MS allow the measurement of molecular marker patterns that confer significantly more information than the measurement of a single parameter alone [ 91 ].…”

“…Sample preparation must be optimized to solve potential interferences ( Figure 3 ). Standard procedure for protein digestion implies denaturation and reduction in the proteins, followed by alkylation of free thiol groups [ 87 ]. When proteins are completely unfolded, they are easily accessible by the trypsin for homogeneous digestion at the carboxyl side of the amino acids lysine (K) or arginine (R).…”

Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade

“…Targeted MRM assays represent a logical choice for the analytical validation of biomarker candidates identified by discovery proteomics. Validation of MRM assays are well established and guidance documents are available [174][175][176]. Resources for developing targeted MRM assays include the NCI's Clinical Proteomic Tumor Consortium assay portal and SRMAtlas [177].…”