title: [ProteoСat: a tool for planning of proteomic experiments].
abstract: 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.
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: V S
authors.initials: VS
authors.lastname: Skvortsov
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: N N
authors.initials: NN
authors.lastname: Alekseychuk
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: D V
authors.initials: DV
authors.lastname: Khudyakov
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Mikurova
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Rybina
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: S E
authors.initials: SE
authors.lastname: Novikova
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: O V
authors.initials: OV
authors.lastname: Tikhonova
mesh_terms: D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D010934:Planning Techniques; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*; D012984:Software
chemical_list: D010455:Peptides
keywords: covering of protein sequence; mass spectrometry; peptide properties prediction; protein hydrolysis