Yale Cancer Biology Institute, Yale University, West Haven, Connecticut, USA.
Department of Pharmacology, School of Medicine, Yale University, New Haven, Connecticut, USA.
Proteomics. 2022 Feb;22(4):e2100316. doi: 10.1002/pmic.202100316. Epub 2021 Dec 23.
Protein post-translational modifications (PTMs) generate an enormous, but as yet undetermined, expansion of the produced proteoforms. In this Viewpoint, we firstly reviewed the concepts of proteoform and peptidoform. We show that many of the current PTM biological investigation and annotation studies largely follow a PTM site-specific rather than proteoform-specific approach. We further illustrate a potentially useful matching strategy in which a particular "modified peptidoform" is matched to the corresponding "unmodified peptidoform" as a reference for the quantitative analysis between samples and conditions. We suggest this strategy has the potential to provide more directly relevant information to learn the PTM site-specific biological functions. Accordingly, we advocate for the wider use of the nomenclature "peptidoform" in future bottom-up proteomic studies.
蛋白质翻译后修饰（PTMs）产生了大量的、但尚未确定的、已产生的蛋白质变体。在本观点中，我们首先回顾了蛋白质变体和肽段变体的概念。我们表明，目前许多 PTM 生物学研究和注释研究在很大程度上遵循 PTM 位点特异性，而不是蛋白质变体特异性的方法。我们进一步说明了一种潜在有用的匹配策略，其中特定的“修饰肽段变体”与相应的“未修饰肽段变体”相匹配，作为样品和条件之间定量分析的参考。我们认为这种策略有可能提供更直接相关的信息，以了解 PTM 位点特异性的生物学功能。因此，我们主张在未来的从头蛋白质组学研究中更广泛地使用“肽段变体”这一名词。
