An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS.

Molecular & Cellular Proteomics : MCP
O V KrokhinJ A Wilkins

Abstract

The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests. These peptides were measured in HPLC-MALDI MS runs, with peptide identities confirmed by MS/MS. The model relies on summation of the retention coefficients of the individual amino acids, as in previous approaches, but additional terms are introduced that depend on the retention coefficients for amino acids at the N-terminal of the peptide. In the 17-protein mixture, optimization of two sets of coefficients, along with additional compensation for peptide length and hydrophobicity, yielded a linear dependence of retention time on hydrophobicity, with an R2 value about 0.94. The predictive capability of the model was used to distinguish peptides with close m/z values and for detailed peptide mapping of selected proteins. Its applicability was tested on columns of different sizes, from nano- to narrow-bore, and for direct sample injection, or injection via a pre-column. It can be used for accurate prediction of retention times for tryptic peptides on reversed-phase (300-A pore size) columns of different sizes with a linear water-ACN gradient and with TFA as t...Continue Reading

References

Jun 17, 1988·Journal of Chromatography·Y SakamotoT Sasagawa
Mar 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·J L Meek
Jul 15, 1999·Nature Biotechnology·A J LinkJ R Yates
May 18, 2000·Analytical Chemistry·A ShevchenkoK G Standing
May 8, 2001·Analytical Chemistry·T JohnsonJ Gobom
Jun 8, 2001·Annual Review of Biochemistry·M MannA Pandey
Nov 20, 2001·Chemical Reviews·R Aebersold, D R Goodlett
Nov 28, 2001·Analytical Chemistry·A N KrutchinskyB T Chait
Mar 20, 2003·Journal of Proteome Research·Tomas RejtarBarry L Karger
May 31, 2003·Molecular & Cellular Proteomics : MCP·Oleg KrokhinKenneth G Standing
Jul 3, 2003·Journal of the American Society for Mass Spectrometry·Ruedi Aebersold

❮ Previous
Next ❯

Citations

Aug 1, 2012·Journal of the American Society for Mass Spectrometry·Konstantinos ThalassinosScott J Geromanos
Apr 10, 2007·Journal of the American Society for Mass Spectrometry·Yi-Min SheJohn B Westmore
Aug 19, 2008·Journal of the American Society for Mass Spectrometry·Ryan M DanellChristoph H Borchers
May 18, 2005·Drug Discovery Today·Selene K Swanson, Michael P Washburn
Dec 1, 2010·Analytical Chemistry·Suzanne E KulevichLloyd M Smith
Mar 23, 2011·Journal of Proteome Research·Stephen J ValentineDavid E Clemmer
Jul 17, 2009·Journal of Proteome Research·Carly A SherwoodDaniel B Martin
Jul 16, 2009·Journal of Proteome Research·Amelia PetersonDaniel B Martin
May 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Derek J BaileyJoshua J Coon
Nov 5, 2008·The Journal of Biological Chemistry·David M BlodgettAnthony Carruthers
Jul 29, 2010·Molecular & Cellular Proteomics : MCP·Reiko KiyonamiBruno Domon
Nov 18, 2008·Molecular & Cellular Proteomics : MCP·Jennifer A MeadConrad Bessant
Jul 25, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Marshall Bern, David Goldberg
Jul 19, 2012·Omics : a Journal of Integrative Biology·Jun FanConrad Bessant
Jul 19, 2008·Annual Review of Analytical Chemistry·David A Egas, Mary J Wirth
Apr 21, 2009·Proteome Science·Geert ZegelsXaveer W M Van Ostade
Nov 15, 2006·Genome Biology·Nichole L KingRuedi Aebersold
Jun 19, 2010·Se pu = Chinese journal of chromatography·Chen Shao, Youhe Gao
Aug 11, 2012·Bioanalysis·Stephen W HolmanClaire E Eyers
Dec 19, 2012·Bioanalysis·James W HowardColin S Creaser
Aug 26, 2014·Nature Methods·Jonathan D WorboysClaus Jørgensen
Jun 11, 2011·Journal of Proteomics·Yasset Perez-RiverolVladimir Besada
Jul 8, 2005·Expert Review of Proteomics·Rainer CramerEckhard Nordhoff
Jan 23, 2016·Analytical Chemistry·Yuko FukuyamaKoichi Tanaka
Jan 19, 2016·Journal of Proteome Research·Stephen W HolmanClaire E Eyers
Jan 23, 2016·Mass Spectrometry Reviews·Luminita Moruz, Lukas Käll
Nov 20, 2009·Rapid Communications in Mass Spectrometry : RCM·Wantao YingMark E McComb
Jan 22, 2013·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Xuehui JiangOleg V Krokhin

❮ Previous
Next ❯

Related Concepts

Related Feeds

ASBMB Publications

The American Society for Biochemistry and Molecular Biology (ASBMB) includes the Journal of Biological Chemistry, Molecular & Cellular Proteomics, and the Journal of Lipid Research. Discover the latest research from ASBMB here.