Use of a Designed Peptide Array To Infer Dissociation Trends for Nontryptic Peptides in Quadrupole Ion Trap and Quadrupole Time-of-Flight Mass Spectrometry

Gaucher, Sara P.; Morrow, Jeffrey A.; Faulon, Jean-Loup M.

doi:10.1021/ac070557y

Title: Use of a Designed Peptide Array To Infer Dissociation Trends for Nontryptic Peptides in Quadrupole Ion Trap and Quadrupole Time-of-Flight Mass Spectrometry

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Abstract

Observed peptide gas-phase fragmentation patterns are a complex function of many variables. In order to systematically probe this phenomenon, an array of 40 peptides was synthesized for study. The array of sequences was designed to hold certain variables (peptide length) constant and randomize or balance others (peptide amino acid distribution and position). A high-quality tandem mass spectrometry (MS/MS) data set was acquired for each peptide for all observed charge states on multiple MS instruments, quadrupole-time-of-flight and quadrupole ion trap. The data were analyzed as a function of total charge state and number of mobile protons. Previously known dissociation trends were observed, validating our approach. In addition, the general influence of basic amino acids on dissociation could be determined because, in contrast to the more widely studied tryptic peptides, the amino acids H, K, and R were positionally distributed. Interestingly, our results suggest that cleavage at all basic amino acids is suppressed when a mobile proton is available. Cleavage at H becomes favored only under conditions where a partially mobile proton is present, a caveat to the previously reported trend of enhanced cleavage at H. In conclusion, all acquired data were used as a benchmark to determine how well these sequencesmore »« less

Authors:

Gaucher, Sara P. ^[1]; Morrow, Jeffrey A. ^[1]; Faulon, Jean-Loup M. ^[1]

Sandia National Lab. (SNL-CA), Livermore, CA (United States); Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Publication Date:: Fri Sep 14 00:00:00 EDT 2007

Research Org.:: Sandia National Lab. (SNL-CA), Livermore, CA (United States); Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Sponsoring Org.:: USDOE National Nuclear Security Administration (NNSA)

OSTI Identifier:: 1426955

Report Number(s):: SAND-2007-1450J
Journal ID: ISSN 0003-2700; 526822

Grant/Contract Number:: AC04-94AL85000

Resource Type:: Accepted Manuscript

Journal Name:: Analytical Chemistry

Additional Journal Information:: Journal Volume: 79; Journal Issue: 20; Journal ID: ISSN 0003-2700

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats


                    Gaucher, Sara P., Morrow, Jeffrey A., and Faulon, Jean-Loup M. Use of a Designed Peptide Array To Infer Dissociation Trends for Nontryptic Peptides in Quadrupole Ion Trap and Quadrupole Time-of-Flight Mass Spectrometry.  United States: N. p., 2007. 
Web.  doi:10.1021/ac070557y.

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                    Gaucher, Sara P., Morrow, Jeffrey A., & Faulon, Jean-Loup M. Use of a Designed Peptide Array To Infer Dissociation Trends for Nontryptic Peptides in Quadrupole Ion Trap and Quadrupole Time-of-Flight Mass Spectrometry.  United States.  https://doi.org/10.1021/ac070557y

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                    Gaucher, Sara P., Morrow, Jeffrey A., and Faulon, Jean-Loup M. Fri .  
"Use of a Designed Peptide Array To Infer Dissociation Trends for Nontryptic Peptides in Quadrupole Ion Trap and Quadrupole Time-of-Flight Mass Spectrometry".  United States.  https://doi.org/10.1021/ac070557y.  https://www.osti.gov/servlets/purl/1426955.

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@article{osti_1426955,

  title        = {Use of a Designed Peptide Array To Infer Dissociation Trends for Nontryptic Peptides in Quadrupole Ion Trap and Quadrupole Time-of-Flight Mass Spectrometry},

  author       = {Gaucher, Sara P. and Morrow, Jeffrey A. and Faulon, Jean-Loup M.},

  abstractNote = {Observed peptide gas-phase fragmentation patterns are a complex function of many variables. In order to systematically probe this phenomenon, an array of 40 peptides was synthesized for study. The array of sequences was designed to hold certain variables (peptide length) constant and randomize or balance others (peptide amino acid distribution and position). A high-quality tandem mass spectrometry (MS/MS) data set was acquired for each peptide for all observed charge states on multiple MS instruments, quadrupole-time-of-flight and quadrupole ion trap. The data were analyzed as a function of total charge state and number of mobile protons. Previously known dissociation trends were observed, validating our approach. In addition, the general influence of basic amino acids on dissociation could be determined because, in contrast to the more widely studied tryptic peptides, the amino acids H, K, and R were positionally distributed. Interestingly, our results suggest that cleavage at all basic amino acids is suppressed when a mobile proton is available. Cleavage at H becomes favored only under conditions where a partially mobile proton is present, a caveat to the previously reported trend of enhanced cleavage at H. In conclusion, all acquired data were used as a benchmark to determine how well these sequences would have been identified in a database search using a common algorithm, Mascot.},

  doi          = {10.1021/ac070557y},

  journal      = {Analytical Chemistry},

  number       = 20,

  volume       = 79,

  place        = {United States},

  year         = {Fri Sep 14 00:00:00 EDT 2007},

  month        = {Fri Sep 14 00:00:00 EDT 2007}

}

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