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Proteomics Tools

Posttranslational Modification Tools

Protein Identification Tools

A variety of web-based programs are available to search protein databases using peptide fragment size or sequence information obtained from mass spectrometry.

Peptide Search at EMBL
Mascot
MOWSE
ProteinProspector
Profound (short form at PROWL)
PROWL
PeptIdent at ExPASy
Lutefisk Downloadable software for MS/MS analysis
SEQUEST. SEAQUEST tips. SEAQUEST Interpretation

JavaScript Protein Digest. Predicts peptide fragment sizes of digests.
Protein cleavage at NIH. Predicts peptide fragment size and matches masses.
PeptideMass at ExPASy. cleaves a protein with a chosen enzyme, and computes the masses of the generated peptides.

Posttranslational Modification Tools

FindMod at ExPASy. FindMod is a tool that can predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides.
GlycoMod at ExPASy. A tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses.
Delta Mass listing of mass differences caused by modifications to aa or aa substitutions.
Scansite search a protein and predict phosphorylation sites
GlycanMass at ExPASy. A tool which allows you to calculate the mass of an oligosaccharide structure.

NetPhos 2.0 Prediction Server. Predicts serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.

Phosphoprotein database. Annotated 2DE images of phosphoproteins.
Protein Phosphorylation Site Database.

Protein Structure

Dali Comparison of protein structures in 3D
AGADIR An algorithm to predict the helical content of peptides
FOLD-X A tool to calculate the folding pathways of proteins and the effect of a point mutation on the stability of a protein
PredictProtein sequence analysis, and structure prediction
SSCP Secondary structural content prediction from amino acid composition

Specific Proteomics Tools

Amino Acid Structures at i-mass.
Amino Acid residue masses at i-mass. Table of average and monoisotopic masses of amino acids.
Search for protein by molecular mass at NCBI. Hints
MS BLAST at EMBL. identify protein from several short sequences
Compute pI/Mw tool at ExPASy. computation of the theoretical pI (isoelectric point) and Mw (molecular weight).
TagIdent at ExPASy. List of proteins from pI and MW.
iProClass software for retrieving/matching protein sequences
PROPSEARCH Compositional search using a sequence
SMART Simple Modular Architecture Research Tool: domain annotation in proteins
Amino acid table
Amino acid table