Abstract

Protein identification is an important problem in many proteomics projects, including studies of post-translational modifications, protein-protein interactions, and protein functions. This grant proposal focuses on the computational aspect of tandem mass spectrometry (MS-MS), a technology of choice in many proteomics projects. Computational analysis is often a bottleneck in applying this technology for protein identification since the corresponding combinatorial problems remain largely unsolved. In close collaboration with leading mass-spectrometry groups we propose to develop new algorithms and software for identification of mutated and modified proteins, de-novo protein sequencing, DXMS, and gene validation via mass-spectrometry. We also propose to implement MS-ALIGNMENT, MS-SEQUENCING, and MS-GENESEARCH software tools as a web server available for mass-spectrometry researchers.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Research Project (R01)
Project #
5R01RR016522-02
Application #
6652527
Study Section
Special Emphasis Panel (ZRG1-SSS-H (01))
Program Officer
Sheeley, Douglas
Project Start
2002-09-01
Project End
2005-08-31
Budget Start
2003-09-01
Budget End
2004-08-31
Support Year
2
Fiscal Year
2003
Total Cost
$620,503
Indirect Cost

  Institution

Name
University of California San Diego
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093

  Publications

Gupta, Nitin; Bark, Steven J; Lu, Weiya D et al. (2010) Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing. J Proteome Res 9:5065-75
Gupta, Nitin; Hixson, Kim K; Culley, David E et al. (2010) Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics 10:2833-44
Hook, Vivian; Bark, Steven; Gupta, Nitin et al. (2010) Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. AAPS J 12:635-45
Gupta, Nitin; Pevzner, Pavel A (2009) False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res 8:4173-81
Kim, Sangtae; Gupta, Nitin; Bandeira, Nuno et al. (2009) Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics 8:53-69
Castellana, Natalie E; Payne, Samuel H; Shen, Zhouxin et al. (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A 105:21034-8
Gupta, Nitin; Benhamida, Jamal; Bhargava, Vipul et al. (2008) Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res 18:1133-42
Frank, Ari M; Pesavento, James J; Mizzen, Craig A et al. (2008) Interpreting top-down mass spectra using spectral alignment. Anal Chem 80:2499-505
Bandeira, Nuno; Pham, Victoria; Pevzner, Pavel et al. (2008) Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol 26:1336-8
Ng, Julio; Pevzner, Pavel A (2008) Algorithm for identification of fusion proteins via mass spectrometry. J Proteome Res 7:89-95

Showing the most recent 10 out of 37 publications