Skvortsov V S, Alekseychuk N N, Khudyakov D V, Mikurova A V, Rybina A V, Novikova S E, Tikhonova O V
Institute of Biomedical Chemistry, Moscow, Russia.
Biomed Khim. 2015 Nov-Dec;61(6):770-6. doi: 10.18097/PBMC20156106770.
ProteoCat is a computer program has been designed to help researchers in the planning of large-scale proteomic experiments. The central part of this program is the subprogram of hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases AspN and GluC). For the peptides obtained after virtual hydrolysis or loaded from data file a number of properties important in mass-spectrometric experiments can be calculated or predicted. The data can be analyzed or filtered to reduce a set of peptides. The program is using new and improved modification of our methods developed to predict pI and probability of peptide detection; pI can also be predicted for a number of popular pKa's scales, proposed by other investigators. The algorithm for prediction of peptide retention time was realized similar to the algorithm used in the program SSRCalc. ProteoCat can estimate the coverage of amino acid sequences of proteins under defined limitation on peptides detection, as well as the possibility of assembly of peptide fragments with user-defined size of "sticky" ends. The program has a graphical user interface, written on JAVA and available at http://www.ibmc.msk.ru/LPCIT/ProteoCat.
ProteoCat是一个专门设计用于帮助研究人员规划大规模蛋白质组学实验的计算机程序。该程序的核心部分是水解模拟子程序，它支持4种蛋白酶（胰蛋白酶、赖氨酸C、天冬氨酸内肽酶和谷氨酸内肽酶）。对于虚拟水解后获得或从数据文件中加载的肽段，可以计算或预测质谱实验中一些重要的属性。可以对数据进行分析或过滤，以减少肽段集。该程序采用了我们开发的预测肽段pI和检测概率的新的改进方法；对于其他研究人员提出的一些流行的pKa标度，也可以预测pI。肽段保留时间的预测算法与SSRCalc程序中使用的算法类似。ProteoCat可以在肽段检测的定义限制下估计蛋白质氨基酸序列的覆盖率，以及组装具有用户定义大小“粘性”末端的肽段片段的可能性。该程序有一个用JAVA编写的图形用户界面，可在http://www.ibmc.msk.ru/LPCIT/ProteoCat上获取。
