Applications of Peptide Retention Time in Proteomic Data Analysis

  • Chen ShaoEmail author
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 845)


In proteomic studies, liquid chromatography is commonly used to separate peptide mixtures prior to mass spectrometry (MS) detection. As an independent dimension of information from the information provided by the MS, peptide retention time information has been proven to be able to aid proteomic data analysis in many aspects. So far, some popular software has offered options for this information for MS data acquisition and analysis. This chapter is a brief review of current methodologies of retention time prediction and application in proteomic analysis.


Retention time Peptide identification Quality control 


  1. 1.
    Baczek T, Kaliszan R (2009) Predictions of peptides’ retention times in reversed-phase liquid chromatography as a new supportive tool to improve protein identification in proteomics. Proteomics 9:835–847PubMedCrossRefGoogle Scholar
  2. 2.
    Browne CA, Bennett HPJ, Solomon S (1982) The isolation of peptides by high-performance liquid chromatography using predicted elution positions. Anal Biochem 124:201–208PubMedCrossRefGoogle Scholar
  3. 3.
    Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372PubMedCrossRefGoogle Scholar
  4. 4.
    Dasari S, Wilmarth PA, Rustvold DL, Riviere MA, Nagalla SR, David LL (2007) Reliable detection of deamidated peptides from lens crystallin proteins using changes in reversed-phase elution times and parent ion masses. J Proteome Res 6:3819–3826PubMedCrossRefGoogle Scholar
  5. 5.
    Dwivedi RC, Spicer V, Harder M, Antonovici M, Ens W, Standing KG, Wilkins JA, Krokhin OV (2008) Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal Chem 80:7036–7042PubMedCrossRefGoogle Scholar
  6. 6.
    Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O (2012) Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12:1111–1121PubMedCrossRefPubMedCentralGoogle Scholar
  7. 7.
    Fu Y, Xiu LY, Jia W, Ye D, Sun RX, Qian XH, He SM (2011) DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data. Mol Cell Proteomics 10(5):M110–000455Google Scholar
  8. 8.
    Gallien S, Peterman S, Kiyonami R, Souady J, Duriez E, Schoen A, Domon B (2012) Highly multiplexed targeted proteomics using precise control of peptide retention time. Proteomics 12:1122–1133PubMedCrossRefGoogle Scholar
  9. 9.
    Guo D, Mant CT, Taneja AK, Parker JMR, Hodges RS (1986) Prediction of peptide retention times in reversed-phase highperformance liquid chromatography I. Determination of retention coefficients of amino acid residues of model synthetic peptides. J Chromatogr 359:499–517CrossRefGoogle Scholar
  10. 10.
    Henneman AA, Palmblad M (2013) Retention time prediction and protein identification. Methods Mol Biol 1007:101–118PubMedCrossRefGoogle Scholar
  11. 11.
    Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA (2006) PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5:1927–1941PubMedCrossRefGoogle Scholar
  12. 12.
    Kawakami T, Tateishi K, Yamano Y, Ishikawa T, Kuroki K, Nishimura T (2005) Protein identification from product ion spectra of peptides validated by correlation between measured and predicted elution times in liquid chromatography/mass spectrometry. Proteomics 5:856–864PubMedCrossRefGoogle Scholar
  13. 13.
    Kim J, Petritis K, Shen Y, Camp DG 2nd, Moore RJ, Smith RD (2007) Phosphopeptide elution times in reversed-phase liquid chromatography. J Chromatogr A 1172:9–18PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Kiyonami R, Schoen A, Zabrouskov V (2010) On-the-Fly retention time shift correction for multiple targeted peptide quantification by LC-MS/MS. Thermo Fisher Scientific Application note: 503Google Scholar
  15. 15.
    Klammer AA, Yi X, MacCoss MJ, Noble WS (2007) Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Anal Chem 79:6111–6118PubMedCrossRefGoogle Scholar
  16. 16.
    Krokhin OV (2006) Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal Chem 78:7785–7795PubMedCrossRefGoogle Scholar
  17. 17.
    Krokhin OV (2012) Peptide retention prediction in reversed-phase chromatography: proteomic applications. Expert Rev Proteomics 9:1–4PubMedCrossRefGoogle Scholar
  18. 18.
    Krokhin OV, Spicer V (2009) Peptide retention standards and hydrophobicity indexes in reversed-phase high-performance liquid chromatography of peptides. Anal Chem 81:9522–9530PubMedCrossRefGoogle Scholar
  19. 19.
    Krokhin OV, Craig R, Spicer V, Ens W, Standing KG, Beavis RC, Wilkins JA (2004) 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. Mol Cell Proteomics 3:908–919PubMedCrossRefGoogle Scholar
  20. 20.
    May D, Liu Y, Law W, Fitzgibbon M, Wang H, Hanash S, McIntosh M (2008) Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments. J Proteome Res 7:5148–5156PubMedCrossRefGoogle Scholar
  21. 21.
    Meek JL (1980) Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. Proc Natl Acad Sci USA 77:1632–1636PubMedCrossRefPubMedCentralGoogle Scholar
  22. 22.
    Meek JL, Rossetti ZL (1981) Factors affecting retention and resolution of peptides in high-performance liquid chromatography. J Chromatogr 211:15–28CrossRefGoogle Scholar
  23. 23.
    Moruz L, Tomazela D, Kall L (2010) Training, selection, and robust calibration of retention time models for targeted proteomics. J Proteome Res 9:5209–5216PubMedCrossRefGoogle Scholar
  24. 24.
    Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Muller M (2007) SuperHirn—a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7:3470–3480PubMedCrossRefGoogle Scholar
  25. 25.
    Nagaraj N, Mann M (2011) Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome. J Proteome Res 10:637–645PubMedCrossRefGoogle Scholar
  26. 26.
    Norbeck AD, Monroe ME, Adkins JN, Anderson KK, Daly DS, Smith RD (2005) The utility of accurate mass and LC elution time information in the analysis of complex proteomes. J Am Soc Mass Spectrom 16:1239–1249PubMedCrossRefPubMedCentralGoogle Scholar
  27. 27.
    Petritis K, Kangas LJ, Yan B, Monroe ME, Strittmatter EF, Qian WJ, Adkins JN, Moore RJ, Xu Y, Lipton MS, Camp DG 2nd, Smith RD (2006) Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal Chem 78:5026–5039PubMedCrossRefPubMedCentralGoogle Scholar
  28. 28.
    Petyuk VA, Qian WJ, Chin MH, Wang H, Livesay EA, Monroe ME, Adkins JN, Jaitly N, Anderson DJ, Camp DG 2nd, Smith DJ, Smith RD (2007) Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. Genome Res 17:328–336PubMedCrossRefPubMedCentralGoogle Scholar
  29. 29.
    Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O (2009) Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. J Proteome Res 8:4109–4115PubMedCrossRefGoogle Scholar
  30. 30.
    Picotti P, Aebersold R (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9:555–566PubMedCrossRefGoogle Scholar
  31. 31.
    Sakamoto Y, Kawakami N, Sasagawa T (1988) Prediction of peptide retention times. J Chromatogr 442:69–79PubMedCrossRefGoogle Scholar
  32. 32.
    Savitski MM, Nielsen ML, Zubarev RA (2006) ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol Cell Proteomics 5:935–948PubMedCrossRefGoogle Scholar
  33. 33.
    Shen Y, Kim J, Strittmatter EF, Jacobs JM, Camp DG 2nd, Fang R, Tolie N, Moore RJ, Smith RD (2005) Characterization of the human blood plasma proteome. Proteomics 5:4034–4045PubMedCrossRefGoogle Scholar
  34. 34.
    Smith RD, Anderson GA, Lipton MS, Pasa-Tolic L, Shen Y, Conrads TP, Veenstra TD, Udseth HR (2002) An accurate mass tag strategy proteome measurements. Proteomics 2:513–523PubMedCrossRefGoogle Scholar
  35. 35.
    Smith R, Ventura D, Prince JT (2013) LC-MS alignment in theory and practice: a comprehensive algorithmic review. Brief Bioinform doi: 10.1093/bib/bbt080Google Scholar
  36. 36.
    Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 6:1809–1817PubMedCrossRefGoogle Scholar
  37. 37.
    Stanley JR, Adkins JN, Slysz GW, Monroe ME, Purvine SO, Karpievitch YV, Anderson GA, Smith RD, Dabney AR (2011) A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics. Anal Chem 83:6135–6140PubMedCrossRefPubMedCentralGoogle Scholar
  38. 38.
    Strittmatter EF, Ferguson PL, Tang K, Smith RD (2003) Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J Am Soc Mass Spectrom 14:980–991PubMedCrossRefGoogle Scholar
  39. 39.
    Strittmatter EF, Kangas LJ, Petritis K, Mottaz HM, Anderson GA, Shen Y, Jacobs JM, Camp DG 2nd, Smith RD (2004) Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J Proteome Res 3:760–769PubMedCrossRefGoogle Scholar
  40. 40.
    Sun W, Zhang L, Yang R, Shao C, Zhang Z, Gao Y (2009) Improving peptide identification using an empirical peptide retention time database. Rapid Commun Mass Spectrom 23:109–118PubMedCrossRefGoogle Scholar
  41. 41.
    Tolmachev AV, Monroe ME, Purvine SO, Moore RJ, Jaitly N, Adkins JN, Anderson GA, Smith RD (2008) Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments. Anal Chem 80:8514–8525PubMedCrossRefPubMedCentralGoogle Scholar
  42. 42.
    Xie H, Gilar M, Gebler JC (2009) Characterization of protein impurities and site-specific modifications using peptide mapping with liquid chromatography and data independent acquisition mass spectrometry. Anal Chem 81:5699–5708PubMedCrossRefGoogle Scholar
  43. 43.
    Yanofsky CM, Kearney RE, Lesimple S, Bergeron JJ, Boismenu D, Carrillo B, Bell AW (2008) A Bayesian approach to peptide identification using accurate mass and time tags from LC-FTICR-MS proteomics experiments. Conf Proc IEEE Eng Med Biol Soc 2008:3775–3778PubMedGoogle Scholar
  44. 44.
    Zimmer JS, Monroe ME, Qian WJ, Smith RD (2006) Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev 25:450–482PubMedCrossRefPubMedCentralGoogle Scholar
  45. 45.
    Zybailov B, Sun Q, van Wijk KJ (2009) Workflow for large scale detection and validation of peptide modifications by RPLC-LTQ-Orbitrap: application to the Arabidopsis thaliana leaf proteome and an online modified peptide library. Anal Chem 81:8015–8024PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.National Key Laboratory of Medical Molecular Biology, Department of PathophysiologyInstitute of Basic Medical Sciences, Chinese Academy of Medical SciencesBeijingChina

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