Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry
Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry
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DOI：
10.1016/j.jprot.2012.06.031
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发表时间：
2012-12-05
影响因子：
3.3
通讯作者：
Simpson, Richard J.
中科院分区：
文献类型：
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作者：
Mathivanan, Suresh;Ji, Hong;Simpson, Richard J.
由突变基因编码的分泌蛋白（突变蛋白）是生物标志物的特别丰富的来源，不仅是癌症分泌组的组分，而且实际上与肿瘤发生有关。蛋白质组学驱动的生物标志物发现研究的挑战之一是，由于现有蛋白质组学数据库中缺乏突变肽信息，大部分分泌的突变蛋白不能通过质谱法直接鉴定和定量。在这里，我们使用整合的基因组学和蛋白质组学策略（称为iMASp -突变和分泌蛋白的鉴定），在来自一组18个人结直肠癌（CRC）细胞系的集体分泌组中鉴定了112个推定的突变胰蛋白酶肽（对应于57种蛋白质）。该iMASp的核心是创建人类蛋白质突变体数据库（HPMD），针对该数据库搜索实验来源的分泌组肽谱。通过RT-PCR和从那些CRC细胞中提取的RNA的cDNA测序确认了八种鉴定的突变的胰蛋白酶肽，其中突变通过质谱法鉴定。iMASp技术有望改善蛋白质组学和基因组突变数据之间的联系，从而为靶向具有突变氨基酸的胰蛋白酶肽作为潜在的癌症生物标志物候选者提供有效的工具。(C)2012爱思唯尔有限公司版权所有。
Secreted proteins encoded by mutated genes (mutant proteins) are a particularly rich source of biomarkers being not only components of the cancer secretome but also actually implicated in tumorigenesis. One of the challenges of proteomics-driven biomarker discovery research is that the bulk of secreted mutant proteins cannot be identified directly and quantified by mass spectrometry due to the lack of mutated peptide information in extant proteomics databases. Here we identify, using an integrated genomics and proteomics strategy (referred to iMASp - identification of Mutated And Secreted proteins), 112 putative mutated tryptic peptides (corresponding to 57 proteins) in the collective secretomes derived from a panel of 18 human colorectal cancer (CRC) cell lines. Central to this iMASp was the creation of Human Protein Mutant Database (HPMD), against which experimentally-derived secretome peptide spectra were searched. Eight of the identified mutated tryptic peptides were confirmed by RT-PCR and cDNA sequencing of RNA extracted from those CRC cells from which the mutation was identified by mass spectrometry. The iMASp technology promises to improve the link between proteomics and genomic mutation data thereby providing an effective tool for targeting tryptic peptides with mutated amino acids as potential cancer biomarker candidates.This article is part of a Special Issue entitled: Integrated omics. (C) 2012 Elsevier B.V. All rights reserved.