This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We continue to maintain an internet based bioinformatic resource for protein mass spectrometry. These tools ca be found at the universal resource locator www.rockefeller.edu/labheads/chait/tools.php and include: ProFound ProFound is a tool for searching a 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. ProteinInfo ProteinInfo is a collection of tools for retrieval and analysis of protein sequences. The capabilities of the analysis tools include peptide mapping, mass spectrometric fragmentation analysis, disulfide mapping, etc. PeptideMap PeptideMap is a tool for finding modifications on polypeptide sequences. The modifications can be affecting single amino acids (e.g. phoshorylation or oxidation) or cross-linking two amino acids (e.g. disulfide bonds or chemical cross-linking reagents). PepFrag PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum. X! Tandem X! Tandem is a tool for identifying proteins from a collection of peptide sequences that matches tandem mass spectra. X! Hunter X! Hunter is a tool for identifying proteins that matches tandem mass spectra to a library of spectra that have been confidently assigned to a particular peptide sequence. GPMDB GPMDB is a database of tandem mass spectra and their assigned peptide sequences. It is designed to aid in the difficult process of validating peptide MS/MS spectra. (A manuscript describing the Global Protein Macine is in press: D. Feny?, J. Eriksson and R.C. Beavis, """"""""Mass Spectrometric Protein Identification Using the Global Proteome Machine"""""""", Methods in Molecular Biology, Computational Biology, Ed. D. Feny?, Humana Press, Totowa, NJ, in press 2010.) NCDIR Strain Database The National Center for Dynamic Interactome Research (NCDIR) Strain Database
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