To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues. Therefore, we conducted a thorough comparative analysis on data sets in PeptideAtlas Tiered Human Integrated Search Proteome (THISP, 2017-03 release), including neXtProt (2017-01 release), to systematically investigate the possibility of unique peptides in missing proteins (PE2-4), unique peptides in dubious proteins, and variant peptides affected by isobaric substitutions, causing doubtful identification results. In this study, we considered eleven isobaric substitutions. From our analysis, we found <5% of the unique peptides of missing proteins and >6% of variant peptides became shared with peptides of PE1 proteins after isobaric substitutions.

中文翻译：

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解码同量异位取代基在鉴定人类蛋白质组中缺失的蛋白质和变异肽中的作用

为了确认缺失蛋白质的存在，我们需要在基于自下而上质谱的蛋白质组学实验中，鉴定出至少两种独特的肽，其缺失蛋白质的长度为9-40个氨基酸。但是，由于等压取代，质量修饰，替代剪接同工型或单个氨基酸变体（SAAV），即使是高可信度的鉴定，所鉴定出的缺失蛋白质的独特肽也可能与通常观察到的蛋白质的肽相吻合。 。除了上述缺失蛋白的独特肽外，由于上述问题，鉴定出的变异肽（含SAAV的肽）也可以映射到其他蛋白的肽。因此，我们对PeptideAtlas分层人类集成搜索蛋白质组（THISP，2017-03版）中的数据集进行了全面的比较分析，包括neXtProt（2017-01版），以系统地研究缺失蛋白（PE2-4）中独特肽，可疑蛋白中独特肽以及受同量异位取代影响的变异肽的可能性，从而导致可疑的鉴定结果。在这项研究中，我们考虑了11个同量异位取代基。从我们的分析中，我们发现异戊酸取代后，<5％的缺失蛋白独特肽和> 6％的变异肽与PE1蛋白肽共享。