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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.
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.
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.
GlycoSuiteDB is a curated and annotated glycan database
A tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines
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.
A tool to quantify MALDI peptides (SILAC) from Phenyx output
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.
The MassSearch server takes as input a set of weights determined from a mass spectrometry experiment and uses them to search for the best matching protein in various databases.
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.
The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST.
PaxDb contains estimated abundance values for a large number of proteins in several different species. Furthermore, it contains information about inter-species variation of protein abundances.
PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.
Predict potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and/or a table of cleavage site positions.
Cleave a protein sequence with a chosen enzyme/protease, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants.
A tool to visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies
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.
Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments, including MS-Fit, MS-Pattern, MS-Digest, etc.
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.
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.