Skip to main content

Bioinformatics Tools to Define the Proteomic State of the Cell


EMSL Project ID
9603

Abstract

During the next three years we intend to enhance mass spectrometry-based proteomic analysis by building a new generation of tools for peptide identification. The accurate identification of protein complexes in the majority of mass spectrometry-based techniques relies on accurate identification of peptides by tandem mass spectrometry (MS/MS). Currently, approximately 90-85% of MS/MS spectra cannot be identified with a peptide for a number of reasons.
In this project, we will develop statistical models that will more accurately describe the various aspects of the identification process. This will include statistical mechanical models in the case of peptide fragmentation, and sophisticated conditional probability networks in the case of utilizing the fragmentation patterns in scoring spectra. We will develop computational evolutionary methods specifically suited for solving the combinatorial problem of identifying post-translational modifications to peptides. The result of the development will be to increase the number of identified peptides from the currently level of approximately 10% to a level exceeding 25%.

Project Details

Project type
Capability Research
Start Date
2005-10-01
End Date
2008-10-05
Status
Closed

Team

Principal Investigator

William Cannon
Institution
Pacific Northwest National Laboratory

Team Members

Jason McDermott
Institution
Pacific Northwest National Laboratory

Vladislav Petyuk
Institution
Pacific Northwest National Laboratory

Danny Taasevigen
Institution
Pacific Northwest National Laboratory

Gordon Anderson
Institution
Pacific Northwest National Laboratory

Christopher Oehmen
Institution
Pacific Northwest National Laboratory

Douglas Baxter
Institution
Environmental Molecular Sciences Laboratory

Alejandro Heredia-Langner
Institution
Pacific Northwest National Laboratory

Kristin Jarman
Institution
Pacific Northwest National Laboratory

Joel Malard
Institution
SIMUCAD Design Automation

Related Publications

Brian H. Lower, Roberto D. Lins, Tjerk P. Straatsma, Michael F. Hochella Jr., and Steven K. Lower (2007). "In vitro evolution of a peptide with a hematite binding motif," Nano Lett.: In review.
Cannon WR, and BM Webb-Robertson. 2007. "Computational Proteomics: High-throughput Analysis for Systems Biology." In Biocomputing 2007. Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3 - 7 January 2007, ed. RB Altman, AK Dunker, L Hunter, T Murray & TE Klein, pp. 403-408. World Scientific Publishing Company, Singapore, Singapore.
Cannon WR, DJ Taasevigen, DJ Baxter, and J Laskin. 2007. "Evaluation of the Influence of Amino Acid Composition on the Propensity for Collision-Induced Dissociation of Model Peptides Using Molecular Dynamics Simulations." Journal of the American Society for Mass Spectrometry 18(9):1625-1637.
Cannon WR, KH Jarman, BM Webb-Robertson, DJ Baxter, CS Oehmen, KD Jarman, A Heredia-Langner, KJ Auberry, and GA Anderson. 2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4(5):1687-1698.
Deric R. Learman, Haakrho J. Yi, Steven D. Brown, Stanton L. Martin, Gill G. Geesey, Ann M. Stevens, and Michael F. Hochella, Jr. (2008). Shewanella oneidensis MR-1 LuxS involvement in biofilm development and sulfur metabolism. Appl. Environ. Microbiol. (in review).
Kaiser NK, G Skulason, CR Weisbrod, S Wu, K Zhang, DC Prior, MA Buschbach, GA Anderson, and JE Bruce. 2008. "Restrained Ion Population Transfer: A Novel Ion Transfer Method for Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(12):1955-1964.
Learman DR, H Yi, SD Brown, SL Martin, GG Geesey, AM Stevens, and MF Hochella. 2009. "Involvement of Shewanella oneidensis MR-1 LuxS in Biofilm Development and Sulfur Metabolism." Applied and Environmental Microbiology 75(5):1301-1307. doi:10.1128/AEM.01393-08
Lower B.H., Lins R.D., Oestreicher Z., Straatsma T.P., Hochella M.F., Jr., Shi L., and Lower S.K. (2008) In vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype. Environmental Science and Technology 42, 3821-3827.
Oehmen CS, and DJ Baxter. 2013. "ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems." Bioinformatics 29(6):797-8. doi:10.1093/bioinformatics/btt013
Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra William R. Cannon and Mitchell M. Rawlins J. Phys. Chem. C, Publication Date (Web): November 25, 2009 DOI: 10.1021/jp905049d
Saumyaditya Bose, Michael F. Hochella Jr., Yuri A. Gorby, David W. Kennedy, David E. McCready, Andrew S. Madden, and Brian H. Lower (2009). Bioreduction of Hematite Nanoparticles by the Dissimilatory Iron Reducing Bacterium Shewanella oneidensis MR-1. Geochimica et Cosmochimica Acta (in press).