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 #
5R01RR016522-03
Application #
6787190
Study Section
Special Emphasis Panel (ZRG1-SSS-H (01))
Program Officer
Sheeley, Douglas
Project Start
2002-09-01
Project End
2006-08-31
Budget Start
2004-09-01
Budget End
2006-08-31
Support Year
3
Fiscal Year
2004
Total Cost
$628,165
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
Payne, Samuel H; Yau, Margaret; Smolka, Marcus B et al. (2008) Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res 7:3373-81
Albuquerque, Claudio P; Smolka, Marcus B; Payne, Samuel H et al. (2008) A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 7:1389-96
Bandeira, Nuno; Olsen, Jesper V; Mann, Jesper V et al. (2008) Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics 24:i416-23
Kim, Sangtae; Gupta, Nitin; Pevzner, Pavel A (2008) Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 7:3354-63
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

Showing the most recent 10 out of 37 publications