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.
Programma ProteoCat prednaznachena dlia pomoshchi issledovateliam pri planirovanii shirokomasshtabnykh proteomnykh éksperimentov. Tsentral'noĭ chast'iu programmy iavliaetsia modul' simuliatsiigidroliza, podderzhivaiushchiĭ 4 proteazy (tripsin, lizin S, éndoproteinazy AspN i GluC). Dlia poluchennykh v rezul'tate virtual'nogo gidroliza ili zagruzhennykh peptidov rasschityvaetsia ili predskazyvaetsia riad vazhnykh dlia mass-spektrometricheskogo éksperimenta svoĭstv, po kotorym dannye mogut byt' proanalizirovany i otfil'trovany. Dlia predskazaniia pI i otsenki veroiatnosti detektsii peptida v programme ispol'zovany novye uluchshennye modifikatsii opisannykh ranee sobstvennykh metodov; pI takzhe mozhet byt' predskazano po riadu populiarnykh shkal pKa, predlozhennykh drugimi issledovateliami. Predskazanie vremeni uderzhaniia peptida realizovano v vide algoritma analogichnogo ispol'zuemomu v programme SSRCalc. Ispol'zuia ProteoCat mozhno otsenit' stepen' pokrytiia aminokislotnoĭ posledovatel'nosti analiziruemykh belkov pri zadannykh ogranicheniiakh na detektsiiu peptidov, a takzhe vozmozhnost' sborki protiazhennykh peptidov iz fragmentov s ustanovlennymi pol'zovatelem minimal'nymi razmerami “lipkikh” kontsov. Programma imeet graficheskiĭ interfeĭs, napisana na iazyke JAVA i dostupna po adresu http://www.ibmc.msk.ru/LPCIT/ProteoCat.
Keywords: covering of protein sequence; mass spectrometry; peptide properties prediction; protein hydrolysis.