A graphical user interface is the best choice for smaller projects. The main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. To start identifying peptides and proteins using SearchGUI, download the latest version, unzip the downloaded file, and double-click on the SearchGUI-X.Y.Z.jar file. To visualize and analyze the search results we recommend PeptideShaker.įor developer access to the search results we recommend the use of compomics-utilities. To start using SearchGUI, unzip the downloaded file, and double-click the SearchGUI-X.Y.Z.jar file. SearchGUI is a a highly adaptable open-source common interface for configuring and running proteomics search and de novo engines, currently supporting X! Tandem, MyriMatch, MS Amanda, MS-GF+, OMSSA, Comet, Tide, Andromeda, MetaMorpheus, Novor and DirecTag. (Click on figure to see the full size version) If you use SearchGUI as part of a publication, please refer to the most recent publication.Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L: SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.Barsnes H and Vaudel M: SearchGUI: a highly adaptable common interface for proteomics search and de novo engines.TopDiff (Top-down mass spectrometry-based identification of Differentially expressed proteoforms) is a tool to compare proteoform abundances and to find differentially expressed proteoforms. The TopMG algorithm uses mass graphs, approximate spectrum-based filtering methods, a Markov chain Monte Carlo method, and can identify proteoforms with multiple variable PTMs and other alterations, for example, histone proteoforms and phosphorylations.Ĥ. TopMG (Top-down mass spectrometry-based proteoform identification using Mass Graphs) is a tool to identify ultra-modified proteoforms using protein sequence database searches in tandem mass spectra (MS/MS) data. The TopPIC algorithm uses spectral alignment, a generation function, and indices to increase the speed.ģ. TopPIC (Top-down mass spectrometry-based Proteoform Identification and Characterization) is a tool for the identification and characterization of proteoforms by searching a protein sequence database. TopFD (TOP-Down Mass Spectrometry-Based Proteoform Identification and Characterization) is a tool to deconvolute spectrum grouping spectral peaks into isotopomers to monoisotopic neutral masses and to compute proteoform features from LC-MS or CE-MS data.Ģ. : TopPIC Suite contains the following tools:ġ. Coli, Saccharomyces cerevisiae, Bos taurus, Mus musculus, Neurospora crassa, Canis lupus familiaris, Gallus gallus, Caldicelluosiruptor kristjanssonii, Thermotoga petrophilia, Clostridium termitidis, Pseudomonas aeruginosa, Caldicellulosiruptor saccharoylticus, Acinetobacter baumannii, Thermoanaerobacter thermohydrosulfuricus, Ralstonia eutropha, Clostridium butryricum, Pseudomonas putida, Thermobifida fusca, Yarrowia lioplytica, and Clostridium thermocellum. And, can predict retention for the following chemical modifications: N-terminal cyclization for Gln and Cys alkylated with Iodoacetamide, Methionine oxidation, six types of alkylation chemistries for Cys, TMT, and iTRAQ labels. The SSRCalc algorithm uses retention coefficients summation of the individual amino acids and computes retention coefficients for amino acids at the N-terminal of the peptide, at the C-terminal of the peptide, peptide lengths, hydrophobicity, the nearest-neighbor effect for charged residues, and peptide propensity to form amphipathic helical structures. : SSRCalc (Sequence-Specific Retention Calculator), SSRCalcQ (see links below) are a tools to predict peptides’ behavior in reversed-phase HPLC data, such as prediction of retention filtering, method development for targeted (SRM) and data-independent (SWATH, MSE) in LC-MS, and analytical applications of peptide RP-HPLC.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |