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Databases

  • MIAPEGelDB  •  MIAPEGelDB helps end-users to write MIAPE documents (minimum information to report when describing or publishing a proteomics experiment), through a self-documenting web interface. The produced documents are stored in a database, and thus remain easily accessible by anybody through a stable URL unique for each document. [less]
  • SWISS-2DPAGE  •  The SWISS-2DPAGE database assembles data on proteins identified on various 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data and bibliographical references. In addition several 2-D PAGE and SDS-PAGE images are provided, showing the experimentally determined location of the protein, as well as a theoretical region where the protein might be found in the gel. [less]
  • World-2DPAGE Constellation  •  Entry point to the World2D-PAGE Repository, the World-2DPAGE Portal (a dynamic portal to simultaneously query world-wide gel-based proteomics databases), Swiss-2DPAGE, Make2D-DB II, MiapeGelDB, Melanie Viewer, 2D-PAGE Submission Process and the 2D-PAGE list of resources.  [less]
  • World-2DPAGE Repository  •  World-2DPAGE is a public repository, standards compliant, for gel-based proteomics data published in the literature [less]

Tools

  • AACompIdent  •  Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques. [less]
  • EasyProt  •  EasyProt is a platform for mass spectrometry data processing, protein identification, quantification and unexpected PTM characterization. It provides a graphical interface to perform a large part of the proteomic data analysis workflow. Protein identification is based on OLAV scoring schemes and protein quantification is implemented (isobaric labeling and label-free). Features: peak list processing, isotopic correction, spectra filtering, charge-state deconvolution and spectra merging.  [less]
  • FindMod  •  Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides. The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest. [less]
  • FindPept  •  Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage. [less]
  • GlycoMod  •  Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides. [less]
  • Glycoviewer  •  Visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG).  [less]
  • ImageMaster / Melanie  •  Melanie offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels. [less]
  • InsPecT  •  InsPecT is an MS/MS database search tool, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, InsPecT implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.  [less]
  • IsotopIdent  •  Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.  [less]
  • Make2D-DB II  •  Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web. [less]
  • MALDIPepQuant  •  A tool to quantify MALDI peptides (SILAC) from Phenyx output [less]
  • Mascot  •  Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. Mascot integrates all of the proven methods of searching: Peptide Mass Fingerprint (the only experimental data are peptide mass values), Sequence Query (peptide mass data are combined with amino acid sequence and composition information), MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides.  [less]
  • MSight  •  MSight: An image analysis software for liquid chromatography-mass spectrometry. MSight is a tool specifically developed for the representation of mass spectra along with data from a separation step. It provides simple ways to navigate through very large volumes of data, with the ability to display small regions for closer scrutiny.  [less]
  • MzJava  •  MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.  [less]
  • PepFrag  •  PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.  [less]
  • pIcarver  •  A tool to visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies [less]
  • ProFound  •  Tool for searching protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map.  [less]
  • ProteinProspector  •  Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments, including MS-Fit, MS-Pattern, MS-Digest, etc. [less]
  • QuickMod  •  QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides. The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and the fit of the spectral alignment is assigned a similarity score. In a second step the most likely attachment position of the modification is determined.  [less]
  • SmileMS  •  LC-MSMS software for small molecule identification, can search both low and high mass precision libraries. Users can search on multiple libraries simultaneously, including privately built ones. [less]
  • xComb  •  Computes all possible crosslinks based on proteins of interest (max. 30 proteins) for further interrogation using standard search engine (e.g. Phenyx, Mascot, Sequest, OMSSA, X!Tandem) [less]
  • xQuest  •  xQuest is a search engine for cross-linked peptides from complex samples. xQuest works with small and large protein databases and features flexible fragment ion assignment, advanced scoring, and interactive evaluation tools.  [less]