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Showing 20 records out of 27 total
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Categories: proteomics, (protein sequences and identification, proteomics experiment, function analysis) - Software type(s): website - tool
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.
Categories: proteomics, (protein sequences and identification, proteomics experiment, protein modifications), glycomics - Software type(s): website - tool
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.
Categories: proteomics, glycomics - Software type(s): website - database
GlyTouCan is the international glycan structure repository. It is an uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s).
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
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.
Categories: proteomics, (proteomics experiment), genomics, (characterisation/annotation) - Software type(s): website - tool
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.
Categories: proteomics, (proteomics experiment) - Software type(s): website, GUI - tool
A tool to quantify MALDI peptides (SILAC) from Phenyx output
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
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.
Categories: proteomics, (proteomics experiment), imaging - Software type(s): website, GUI - tool
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.
Categories: proteomics, (proteomics experiment), glycomics - Software type(s): CLI, API - tool
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.
Categories: proteomics - Software type(s): website - database
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.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.
Categories: proteomics, glycomics - Software type(s): website, GUI - tool
PepSweetener supports the manual annotation of MS data for intact glycopeptides. It displays an interactive map of all theoretical glycopeptides that match the molecular masses of queried precursor ions. Ion matching can be performed in two modes: simple when the search space spans the combination of all tryptic peptides including N-glycosites in the human proteome, and advanced when the search space is custom-built by specifying peptides and glycans.
Categories: proteomics, (function analysis) - Software type(s): website - tool
PeptideCutter predicts potential substrate cleavage sites, cleaved by proteases or chemicals in a given protein sequence. The tool returns the query sequence with the possible cleavage sites mapped on it and/or a table of cleavage site positions.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - tool
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.
Categories: proteomics, (proteomics experiment) - Software type(s): website, GUI - tool
A tool to visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
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.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments, including MS-Fit, MS-Pattern, MS-Digest, etc.
Categories: proteomics, (proteomics experiment, protein modifications) - Software type(s): CLI, GUI - tool
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.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
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.
Categories: proteomics, (proteomics experiment) - Software type(s): website - database
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.
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