Identification and characterization with peptide mass fingerprinting data
Aldente - Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion. Download the stand-alone version
FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.
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
GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)
Mascot - Peptide mass fingerprint from Matrix Science Ltd., London
PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK
ProFound - Search known protein sequences with peptide mass information from Rockefeller and NY Universities [or from Genomic Solutions]
ProteinProspector - UCSF tools for peptide masses data (MS-Fit, MS-Pattern, MS-Digest, etc.)
Identification and characterization with MS/MS data
Popitam - Identification and characterization tool for peptides with unexpected modifications (e.g. post-translational modifications or mutations) by tandem mass spectrometry
Phenyx - Protein and peptide identification/characterization from MS/MS data from GeneBio, Switzerland
Mascot - Sequence query and MS/MS ion search from Matrix Science Ltd., London
OMSSA - MS/MS peptide spectra identification by searching libraries of known protein sequences
PepFrag - Search known protein sequences with peptide fragment mass information from Rockefeller and NY Universities [or from Genomic Solutions]
ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.)
xQuest - search machine to identify cross-linked peptides from complex samples and large protein sequence databases
Identification with isoelectric point, molecular weight and/or amino acid composition
AACompIdent - Identify a protein by its amino acid composition
AACompSim - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries
TagIdent - Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw
MultiIdent - Identify proteins with isoelectric point (pI), molecular weight (Mw), amino acid composition, sequence tag and peptide mass fingerprinting data
Other prediction or characterization tools
ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
GlycanMass - Calculate the mass of an oligosaccharide structure
PeptideCutter - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
PeptideMass - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence
IsotopIdent - Predicts the theoretical isotopic distribution of a peptide, protein, polynucleotide or chemical compound
SeqLogo
- Sequence logos at the Immunomedicine Group, Facultad de Medicina, U.C.M, Spain (The Molecular Immunology Foundation (MIF) does not exist anymore)