In-depth analysis of HeLa cell proteome

The tryptic peptide mixture from HeLa cells was fractionated using a High pH Reversed-Phase Peptide Fractionation Kit (Thermo Fisher Scientific). Each peptide fraction was subjected to LC-MS/MS in triplicate using a Q Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 liquid chromatograph (Thermo Fisher Scientific). LC-MS/MS data were integrated on a Progenesis QI for proteomics software (Waters), followed by sequence database search of the MS/MS data using Mascot software (Matrix Science). The search results showed identification of the total of 6151 protein groups, filtered at 1% false discovery rate (FDR) peptide threshold.

采用高pH反相肽分级试剂盒（High pH Reversed-Phase Peptide Fractionation Kit，赛默飞世尔科技（Thermo Fisher Scientific））对海拉细胞（HeLa cells）的胰酶消化肽混合物进行分级分离。采用配备UltiMate 3000液相色谱仪的Q Exactive Orbitrap质谱仪（赛默飞世尔科技），对每个肽分级组分进行三次重复的液相色谱-串联质谱（LC-MS/MS）分析。液相色谱-串联质谱（LC-MS/MS）数据通过蛋白质组学分析软件Progenesis QI（沃特斯（Waters））完成整合，随后使用Mascot软件（Matrix Science）对串联质谱（MS/MS）数据进行序列数据库检索。检索结果共鉴定得到6151个蛋白质群组，并以1%的肽段假发现率（FDR）作为过滤阈值。