Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples

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• 作者：Na Su ; Chengpu Zhang ; Yao Zhang ; Zhiqiang Wang ; Fengxu Fan ; Mingzhi Zhao ; Feilin Wu ; Yuan Gao ; Yanchang Li ; Lingsheng Chen ; Miaomiao Tian ; Tao Zhang ; Bo Wen ; Na Sensang ; Zhi Xiong ; Songfeng Wu ; Siqi Liu ; Pengyuan Yang ; Bei Zhen ; Yunping Zhu ; Fuchu He ; Ping Xu
• 刊名：Journal of Proteome Research
• 出版年：2015
• 出版时间：September 4, 2015
• 年：2015
• 卷：14
• 期：9
• 页码：3680-3692
• 全文大小：783K
• ISSN：1535-3907

文摘

As part of the Chromosome-Centric Human Proteome Project (C-HPP) mission, laboratories all over the world have tried to map the entire missing proteins (MPs) since 2012. On the basis of the first and second Chinese Chromosome Proteome Database (CCPD 1.0 and 2.0) studies, we developed systematic enrichment strategies to identify MPs that fell into four classes: (1) low molecular weight (LMW) proteins, (2) membrane proteins, (3) proteins that contained various post-translational modifications (PTMs), and (4) nucleic acid-associated proteins. Of 8845 proteins identified in 7 data sets, 79 proteins were classified as MPs. Among data sets derived from different enrichment strategies, data sets for LMW and PTM yielded the most novel MPs. In addition, we found that some MPs were identified in multiple-data sets, which implied that tandem enrichments methods might improve the ability to identify MPs. Moreover, low expression at the transcription level was the major cause of the 鈥渕issing鈥?of these MPs; however, MPs with higher expression level also evaded identification, most likely due to other characteristics such as LMW, high hydrophobicity and PTM. By combining a stringent manual check of the MS₂ spectra with peptides synthesis verification, we confirmed 30 MPs (neXtProt PE2 鈭?PE4) and 6 potential MPs (neXtProt PE5) with authentic MS evidence. By integrating our large-scale data sets of CCPD 2.0, the number of identified proteins has increased considerably beyond simulation saturation. Here, we show that special enrichment strategies can break through the data saturation bottleneck, which could increase the efficiency of MP identification in future C-HPP studies. All 7 data sets have been uploaded to ProteomeXchange with the identifier PXD002255.