Proteoforms and their expanding role in laboratory medicine

Abstract

The term “proteoforms” describes the range of different structures of a protein product of a single gene, including variations in amino acid sequence and post-translational modifications. This diversity in protein structure contributes to the biological complexity observed in living organisms. As the concentration of a particular proteoform may increase or decrease in abnormal physiological states, proteoforms have long been used in medicine as biomarkers of health and disease. Notably, the analytical approaches used to analyze proteoforms have evolved considerably over the years. While ligand binding methods continue to play a large role in proteoform measurement in the clinical laboratory, unanticipated or unknown post-translational modifications and sequence variants can upend even extensively tested and vetted assays that have successfully made it through the medical regulatory process. As an alternate approach, mass spectrometry—with its high molecular selectivity—has become an essential tool in detection, characterization, and quantification of proteoforms in biological fluids and tissues. This review explores the analytical techniques used for proteoform detection and quantification, with an emphasis on mass spectrometry and its various applications in clinical research and patient care including, revealing new biomarker targets, helping improve the design of contemporary ligand binding in vitro diagnostics, and as mass spectrometric laboratory developed tests used in routine patient care.

The Integration of Data from Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis

“…This would provide, for example, a novel overview of the diversity and versatility of proteoforms underlying plant phenotypical responses to environmental stresses [ 38 ]. It also represents a tremendous opportunity for isoform-resolved investigations in translational research, since proteoforms have been long used in medicine as health and disease biomarkers [ 44 ]. This approach would also be beneficial for non-model species, for which a sequenced genome is not available.…”

Analytical validation of the PROphet test for treatment decision-making guidance in metastatic non-small cell lung cancer

“…Advances in proteomic profiling technologies have helped to better handle this complexity, leading to a deeper examination of the plasma proteome and enabling the discovery of new blood-based biomarkers 37,40 ; (ii) proteins exist in a range of different structures due to splicing, variations in amino acid sequence, protein complex formation, or post-translational modification. This diversity in protein structure, termed proteoform [41][42][43] , may introduce noise when measuring proteins in a given proteomic platform, as well as when comparing between platforms; (iii) human blood samples are highly heterogeneous owing to clinical, biological and environmental variability. Given these challenges, it is important to perform a thorough assessment of the biomarker discovery platform of choice, as well as to explore its analytical validity.…”

Proteomic Profiling and Pathway Analysis of Acid Stress-Induced Vasorelaxation of Mesenteric Arteries In Vitro

“…Proteoforms are variations in proteins arising from a single gene via multiple mechanisms, such as alternative splicing and post-translation modifications [41]. The proteoforms vary in their expression patterns in physiological states, and thus, have been used as biomarkers of health and diseases [42]. The variations observed in the proteoforms of actin could be indicative of impairment in muscular contractility under acid stress and could have importance as biomarkers and need further investigation.…”