Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry

Abstract

Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.

Targeted and Untargeted Proteomics Approaches in Biomarker Development

“…Despite these technological advancements, discovery proteomics workflows often do not account for PTMs, particularly PTMs other than the most abundant ones, such as phosphorylation or glycosylation. Nearly 200 other PTMs of known biological relevance are typically neglected . Of particular importance in the field of cancer immuno‐oncology is protein glycosylation, which is thought to play an essential role in tumor immune evasion and thus a tumor's resistance to cancer immunotherapeutic intervention .…”

“…As such, MS may provide a unique advantage over immunoassays due to the ability to discern the glycosylation status of the putative protein biomarkers. Technologies that would allow large‐scale quantitation of different PTMs in thousands of samples, in a cost‐effective, high throughput, and robust fashion would be highly useful for the field of biomarker discovery . As PTMs are usually sub‐stoichiometric and therefore of low abundance, their in‐depth analysis requires the use of specific enrichment workflows, which—apart from phosphorylation, glycosylation, ubiquitination, acetylation and redox‐modifications—are mostly lacking …”

Why are there proteins in the urine of healthy people?

“…不仅存在[Cys→Dha]修饰的影响, 有报道表明许 多疾病是由修饰水平变化引起的 [28] . 在帕金森综合征 中, 有些蛋白质通过各种修饰以及与其他细胞成分的 相互作用来影响神经元的正常功能 [29] .…”

Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection, characterization and structural modeling

“…7 This is a powerful tool for glycopeptide mapping, although with important technical obstacles such as the weak ionization efficiency of glycopeptides and the important matrix effects in biological uids, which leads to a limited sensitivity. 8 The second approach combines the use of a receptor selective for the protein, for example an antibody or an aptamer, and a lectin capable of recognizing specic carbohydrate structures, [9][10][11][12] although the glycosylation of antibodies complicates the analysis in the most common immune-lectin assays. It is also possible to detect protein-specic glycosylation by articial linking a protein receptor, antibody or aptamer, with a metabolically engineered glycan, mainly with azide-containing sugars.…”