This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We continue to maintain an internet based bioinformatic resource for protein mass spectrometry. WE also maintain the databases used to search for proteins and insert specialized databases upon request by our users. 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 Machine 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
| Manning, Lois R; Popowicz, Anthony M; Padovan, Julio C et al. (2017) Gel filtration of dilute human embryonic hemoglobins reveals basis for their increased oxygen binding. Anal Biochem 519:38-41 |
| Boice, Michael; Salloum, Darin; Mourcin, Frederic et al. (2016) Loss of the HVEM Tumor Suppressor in Lymphoma and Restoration by Modified CAR-T Cells. Cell 167:405-418.e13 |
| Chait, Brian T; Cadene, Martine; Olinares, Paul Dominic et al. (2016) Revealing Higher Order Protein Structure Using Mass Spectrometry. J Am Soc Mass Spectrom 27:952-65 |
| Krutchinsky, Andrew N; Padovan, Júlio C; Cohen, Herbert et al. (2015) Maximizing ion transmission from atmospheric pressure into the vacuum of mass spectrometers with a novel electrospray interface. J Am Soc Mass Spectrom 26:649-58 |
| Mast, Fred D; Rachubinski, Richard A; Aitchison, John D (2015) Signaling dynamics and peroxisomes. Curr Opin Cell Biol 35:131-6 |
| Krutchinsky, Andrew N; Padovan, Júlio C; Cohen, Herbert et al. (2015) Optimizing electrospray interfaces using slowly diverging conical duct (ConDuct) electrodes. J Am Soc Mass Spectrom 26:659-67 |
| Oricchio, Elisa; Papapetrou, Eirini P; Lafaille, Fabien et al. (2014) A cell engineering strategy to enhance the safety of stem cell therapies. Cell Rep 8:1677-1685 |
| Zhong, Yu; Morris, Deanna H; Jin, Lin et al. (2014) Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels. J Biol Chem 289:26021-37 |
| Indiani, Chiara; O'Donnell, Mike (2013) A proposal: Source of single strand DNA that elicits the SOS response. Front Biosci (Landmark Ed) 18:312-23 |
| Di Virgilio, Michela; Callen, Elsa; Yamane, Arito et al. (2013) Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching. Science 339:711-5 |
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