NameLinkDescription
Aldentehttp://www.expasy.org/tools/aldente/Program for protein identification on the basis of mass spectrometry data
CancerPDFhttp://crdd.osdd.net/raghava/cancerpdf/Database of components of peptidome, associated with cancer
CCMShttp://proteomics.ucsd.edu/software-tools/Website providing access to multiple programs supporting proteomic analyses
Database on Demandhttp://www.ebi.ac.uk/pride/dodProgram generating databases of peptides for application in proteomic studies
Fragment Ion Calculatorhttp://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.htmlProgram calculating masses of fragmentation ions from peptides
GMPDBhttp://gpmdb.rockefeller.edu/Database containing tandem mass spectra of peptides
LabWorm Mass Spectrometryhttps://labworm.com/category/proteomics-metabolomics/mass-spectrometryWebsite providing access to bioinfromatics tools supporting mass spectrometric analysis
MASCOThttp://www.matrixscience.com/Program for protein identification using mass spectrometry data
MS2PIPhttp://iomics.ugent.be/ms2pipProgram for prediction of  CID spectra of peptides
NCBI Peptidomehttp://www.ncbi.nlm.nih.gov/peptidomeDatabase of fragments used for protein indentification via mass spectrometry (proteotypic peptides)
Normalyzerhttp://quantitativeproteomics.org/normalyzerProgram aimed on normalization of quantitative proteomics datasets
OmicTools Mass spectrometryhttp://omictools.com/mass-spectrometry-categoryMetaserver providing access to bioinformatics tools supporting mass spectrometry (e.g. involved in proteomics)
OmicTools Proteomicshttp://omictools.com/proteomics-categoryMetaserver providing access to bioinformatics tools supporting research in proteomics area
OMSSAhttp://pubchem.ncbi.nlm.nih.gov/omssa/Program for protein identification using mass spectrometry data
P4P http://sing-group.org/p4p/?/p4p=true&Tool  for comparison microbial peptidomes
Pacific Northwest National Laboratory websitehttp://ncrr.pnnl.gov/software/Alphabetically_index.stmDownloadable software for proteomics
PANDORAhttp://www.pandora.cs.huji.ac.il/index.phpProgram enabling study a set of proteins that share an annotation; study client own set of proteins including quantitative data; blast a sequence and view the results; match list of mass spectrometry-derived (MS) peptides to the corresponding proteins and analyze these proteins
PepFraghttp://prowl.rockefeller.edu/prowl/pepfrag.htmlProgram for peptide identification based on fragmentation ions. Includes data concerning phosphorylation
peptiCKDdbhttp://www.peptickddb.com/Database of peptides associated with chronic kidney disease
PeptideMaphttp://prowl.rockefeller.edu/prowl/peptidemap.htmlProgram for proteolysis simulation and calculation of masses of resulting peptides
Peptide Related Proteomics Software and Toolshttp://www.peptideresource.com/proteomics.htmlTools enabling identification of proteins and peptides
pFindhttp://pfind.jdl.ac.cn/Program for protein identification on the basis of mass spectrometry data
ProFoundhttp://prowl.rockefeller.edu/prowl-cgi/profound.exeProgram for protein identification on the basis of mass spectrometry data
ProteinProspectorhttp://prospector.ucsf.edu/prospector/mshome.htmProgram for protein identification on the basis of mass spectrometry data
Proteome-pIhttp://isoelectricpointdb.orgDatabase of predicted isoelectric points of proteins
Proteomic tools at EXPASY serverhttp://expasy.org/tools/#proteomeTools enabling identification of proteins and peptides
PROWLhttp://prowl.rockefeller.edu/prowl/prowl.htmlWebsite enabling access to proteomic tools provided by Rockefeller University
SSRCalchttp://hs2.proteome.ca/SSRCalc/SSRCalc.htmlProgram for peptide retention times prediction
Unipepthttp://unipept.ugent.be/apidocsProgram for finding multiple precursors of tryptic peptides, identified by mass spectrometry. Displays e.g. taxonomic lineage of organisms with proteins containing query fragments
Warp2Dhttp://www.nbpp.nl/warp2d.htmlProgram for LC-MS chromatograms aligning >