![Sample our Medicine, Dentistry, Nursing & Allied Health journals, sign in here to start your FREE access for 14 days]({"type":"image" , "src" : "/sda/5944/TOC-Subject-Sample-2021-Medicine-Dentistry-Nursing-Allied-Health.jpg"})
Abstract
Today, proteomics usually compares clinical samples by use of bottom-up profiling with high resolution mass spectrometry, where all protein products of a single gene are considered as an integral whole. At the same time, proteomics of proteoforms, which considers the variety of protein species, offers the potential to discover valuable biomarkers. Proteoforms are protein species that arise as a consequence of genetic polymorphisms, alternative splicing, post-translational modifications and other less-explored molecular events. The comprehensive observation of proteoforms has been an exclusive privilege of top-down proteomics. Here, we review the possibilities of a bottom-up approach to address the microheterogeneity of the human proteome. Special focus is given to shotgun proteomics and structure-based bioinformatics as a source of hypothetical proteoforms, which can potentially be verified by targeted mass spectrometry to determine the relevance of proteoforms to diseases.
Financial & competing interests disclosure
This work was supported by the Russian Fund for Basic Research, grant #12-04-33109. The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.
No writing assistance was utilized in the production of this manuscript.
Key issues
Proteoform profiling, the proteoformics, is a new direction of proteomics to unravel biologically and clinically relevant proteoforms specific for protein molecules arising from a single protein-coding gene.
Main sources of proteoforms include single amino acid polymorphisms, alternatively spliced protein forms and post-translational modifications (PTM).
Missense mutations in the cancer genome, which lead to amino acid polymorphisms, represent an important source of biomarkers and drug targets.
For alternative splicing, there is a problem in the selection of appropriate proteotypic peptides for distinguishing highly homologous isoforms using bottom-up targeted proteomics.
PTMs, due to their reversibility, are not always reliable biomarkers. In addition, accounting for PTMs in interpreting bottom-up mass spectra significantly increases the false discovery rate.
Overall, highly multiplexed mass-spectrometry assays are needed to detect and quantify various clinically relevant proteoforms, such as PTMs, alternatively spliced species and amino acid polymorphisms.