Peptide Ion Fragmentation

Proteomics is an emerging technology that promises instant diagnoses of disease based upon characteristic molecular "markers." The primary analytical tool is tandem mass spectrometry. Conventional mass spectrometry merely provides the mass of an unknown peptide, while tandem mass spectrometry shatters that peptide ion and reveals the masses of the fragments. The fragments are believed to be characteristic of their parent peptide, but procedures for inferring the parent’s identity are only partly successful, hindering progress in analytical proteomics.

Intended Impact

Reliable, routine identification of proteins and peptides will lead to clinically successful diagnostics based upon analytical proteomics.

Objective

Improved understanding of the underlying physics and chemistry of peptide ion fragmentation will lead to more robust procedures for inferring the identity of a peptide ion from the masses and abundances of its fragments.

Goals

Apply and develop quantum chemistry tools to solve mechanistic problems encountered in the NIST mass spectrometry data center, or elsewhere. Solutions should be broadly applicable, not specific to just a few peptides.

Research Activities and Technical Approach

Peptide ion fragmentation is essentially a problem in organic chemistry, for which current theoretical methods are generally adequate. The challenge is that peptides are large molecules with a nearly intractable number of degrees of freedom and innumerable structural and chemical variations. Highly simplified models (e.g., Coulomb models for triply-charged ions) are tried first, because they are most likely to yield general results. Increasingly detailed models, based upon molecular mechanics and quantum chemistry, are applied as necessary to obtain explanations and predictions that are technologically relevant. The top priority for FY09 is to prepare printed publications describing the achievements of former NRC postdoctoral associates.

Publications

Kinsinger, C.R., Irikura, K.K., MacKerell, A.D., “A Force Field for Peptide-Ions in the Gas Phase", 230th ACS National Meeting, Washington, DC; August 31, 2005.

Irikura, K.K., “Quantum Chemistry for Mass Spectrometric Applications”, NIST-wide Mass Spectrometry Meeting, NIST, Gaithersburg; September 22, 2004.

Merle, J.K., Irikura, K.K., “Kinetic and Mechanistic Studies of Peptide Fragmentation in Mass Spectrometry”, NIST Sigma Xi 13th Annual Postdoctoral Poster Session; February 2006.

Kinsinger, C.R., Irikura, K.K., “Toward Improved Predictions of Peptide Fragmentation using Quantum Chemical Calculations”, Second US Human Proteome Organization (HUPO) Conference, Boston, MA; March 12, 2006.

Merle, J.K., Irikura, K.K., “Mechanistic Studies of Peptide Fragmentation in Mass Spectrometry”, ASMS National Meeting, Seattle, WA; May 2006.

Kinsinger, C.R., Irikura, K.K., “Quantum Mechanical Studies of Neutral Losses from Peptides with Glutamine in the N-terminal Position”, 54th American Society for Mass Spectrometry (ASMS) Conference, Seattle, WA; May 31, 2006.

Merle, J.K., Kinsinger, C.R., Irikura, K.K., “Computational Prediction of Peptide Fragmentation Mechanisms in Tandem Mass Spectrometry”, 31st Reaction Mechanism Conference, University of Maryland, College Park, MD; June 2006.

Merle, J.K., Irikura, K.K., “Mechanistic Studies of Proton Transfer Reactions in Peptides”, 17th International Mass Spectrometry Conference, Prague, Czech Republic; August 2006.

Merle, J.K., Irikura, K.K., “Computational Prediction of Peptide Fragmentation Mechanisms in Tandem Mass Spectrometry”, Gordon Research Conference on Gaseous Ions: Structures, Energetics & Reactions, Ventura, CA; Feb. 27, 2007.

• SEMOT (Semi-empirical molecular orbital theory) is too approximate for the mobile proton model.
  
• Force-field Monte Carlo, with Hartree-Fock but avoiding SEMOT, works for geometry optimization.
  
• Mechanisms for selected fragmentation reactions.
  
• Coulomb model for triply-charged ions.