Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project.
Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project.
复制标题
DOI：
10.1021/pr300825v
复制
发表时间：
2013-01
影响因子：
4.4
通讯作者：
Takashi Shiromizu;J. Adachi;S. Watanabe;T. Murakami;T. Kuga;S. Muraoka;T. Tomonaga
中科院分区：
文献类型：
--
作者：
Takashi Shiromizu;J. Adachi;S. Watanabe;T. Murakami;T. Kuga;S. Muraoka;T. Tomonaga
以染色体为中心的人类蛋白质组计划（C-HPP）是一项为每条染色体创建带注释的蛋白质组目录的国际努力。C-HPP项目的第一步是找到每条染色体上编码的所有蛋白质表达的证据。C-HPP还优先考虑特定的蛋白质亚群，例如具有翻译后修饰（PTMs）的蛋白质亚群和低丰度的蛋白质亚群。作为C-HPP的参与者，我们整合了来自染色体独立生物标志物发现研究的蛋白质组学和磷酸化蛋白质组学分析结果，以创建基于染色体的蛋白质和磷酸化位点列表。整合来自5个独立结直肠癌（CRC）样本（3种临床组织和2种细胞系）的数据，鉴定出11278个蛋白，包括8305个磷酸化蛋白和28205个磷酸化位点；所有这些都是以染色体为基础进行分类的。总的来说，在neXtProt数据库中鉴定了3033个“缺失蛋白”，即目前缺乏质谱证据的蛋白，以及在PhosphoSitePlus数据库中未登记的12,852个未知磷酸化位点。我们深入的磷蛋白组学研究代表了C-HPP的重大贡献。质谱蛋白质组学数据已存入ProteomeXchange Consortium，数据集标识符为PXD000089。
The Chromosome-Centric Human Proteome Project (C-HPP) is an international effort for creating an annotated proteomic catalog for each chromosome. The first step of the C-HPP project is to find evidence of expression of all proteins encoded on each chromosome. C-HPP also prioritizes particular protein subsets, such as those with post-translational modifications (PTMs) and those found in low abundance. As participants in C-HPP, we integrated proteomic and phosphoproteomic analysis results from chromosome-independent biomarker discovery research to create a chromosome-based list of proteins and phosphorylation sites. Data were integrated from five independent colorectal cancer (CRC) samples (three types of clinical tissue and two types of cell lines) and lead to the identification of 11,278 proteins, including 8,305 phosphoproteins and 28,205 phosphorylation sites; all of these were categorized on a chromosome-by-chromosome basis. In total, 3,033 "missing proteins", i.e., proteins that currently lack evidence by mass spectrometry, in the neXtProt database and 12,852 unknown phosphorylation sites not registered in the PhosphoSitePlus database were identified. Our in-depth phosphoproteomic study represents a significant contribution to C-HPP. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000089.