Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
J Proteomics. 2012 Dec 5;76 Spec No.:141-9. doi: 10.1016/j.jprot.2012.06.031. Epub 2012 Jul 13.
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.
分泌蛋白由突变基因编码（突变蛋白）是生物标志物的一个特别丰富的来源，不仅是癌症分泌组的组成部分，而且实际上也与肿瘤发生有关。蛋白质组学驱动的生物标志物发现研究的一个挑战是，由于现有蛋白质组学数据库中缺乏突变肽信息，大量分泌的突变蛋白不能直接通过质谱进行鉴定和定量。在这里，我们使用集成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 18 个人结直肠癌细胞系的集体分泌组中鉴定出 112 个潜在的突变胰蛋白酶肽（对应于 57 种蛋白质）。iMASp 的核心是创建人类蛋白质突变数据库（HPMD），根据该数据库搜索实验衍生的分泌肽谱。从通过质谱鉴定突变的 CRC 细胞中提取 RNA 并通过 RT-PCR 和 cDNA 测序验证了 8 个鉴定出的突变胰蛋白酶肽。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癌症生物标志物候选物提供有效的工具。本文是一个特刊的一部分，题为：综合组学。
