Abstract
Recent advances in mass spectrometry based proteomic techniques and publicly available large proteomic repositories are being exploited to characterize the proteome of multiple organisms. While humongous amount of proteomic data is being acquired and analyzed, many biological questions still remain unanswered. Proteotypic peptides which uniquely represent target proteins or a protein isoform are used as an alternative strategy for protein identification in the field of immunological methods and targeted proteomic techniques. Using different computational approaches, resources and techniques used in the identification of proteotypic peptides of target proteins is discussed here.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, Sokal I, Yan P, Schoenherr RM, Zhao L, Voytovich UJ, Kelly-Spratt KS, Krasnoselsky A, Gafken PR, Hogan JM, Jones LA, Wang P, Amon L, Chodosh LA, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol 29(7):625–634. doi:10.1038/nbt.1900
Cohen Freue GV, Meredith A, Smith D, Bergman A, Sasaki M, Lam KK, Hollander Z, Opushneva N, Takhar M, Lin D, Wilson-McManus J, Balshaw R, Keown PA, Borchers CH, McManus B, Ng RT, McMaster WR, Biomarkers in T, the NCECPoOFCoET (2013) Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. PLoS Comput Biol 9(4), e1002963. doi:10.1371/journal.pcbi.1002963
Huttenhain R, Malmstrom J, Picotti P, Aebersold R (2009) Perspectives of targeted mass spectrometry for protein biomarker verification. Curr Opin Chem Biol 13(5-6):518–525. doi:10.1016/j.cbpa.2009.09.014
Brewis IA, Brennan P (2010) Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol 80:1–44. doi:10.1016/B978-0-12-381264-3.00001-1
Percy AJ, Chambers AG, Yang J, Hardie DB, Borchers CH (2014) Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. Biochim Biophys Acta 1844(5):917–926. doi:10.1016/j.bbapap.2013.06.008
Lange V, Picotti P, Domon B, Aebersold R (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4:222. doi:10.1038/msb.2008.61
Picotti P, Aebersold R (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9(6):555–566. doi:10.1038/nmeth.2015
Dittrich J, Becker S, Hecht M, Ceglarek U (2015) Sample preparation strategies for targeted proteomics via proteotypic peptides in human blood using liquid chromatography tandem mass spectrometry. Proteomics Clin Appl 9(1-2):5–16. doi:10.1002/prca.201400121
Vandemoortele G, Staes A, Gonnelli G, Samyn N, De Sutter D, Vandermarliere E, Timmerman E, Gevaert K, Martens L, Eyckerman S (2016) An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics. Sci Rep 6:27220. doi:10.1038/srep27220
Deutsch EW, Lam H, Aebersold R (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 9(5):429–434. doi:10.1038/embor.2008.56
Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD (2016) Advances in targeted proteomics and applications to biomedical research. Proteomics. doi:10.1002/pmic.201500449
Song X, Amirkhani A, Wu JX, Pascovici D, Zaw T, Xavier D, Clarke SJ, Molloy MP (2016) Analytical performance of nanoLC-SRM using non-depleted human plasma over an 18-month period. Proteomics. doi:10.1002/pmic.201500507
Liebler DC, Zimmerman LJ (2013) Targeted quantitation of proteins by mass spectrometry. Biochemistry 52(22):3797–3806. doi:10.1021/bi400110b
Chambers AG, Percy AJ, Yang J, Borchers CH (2015) Multiple reaction monitoring enables precise quantification of 97 proteins in dried blood spots. Mol Cell Proteomics 14(11):3094–3104. doi:10.1074/mcp.O115.049957
Craig R, Cortens JP, Beavis RC (2005) The use of proteotypic peptide libraries for protein identification. Rapid Commun Mass Spectrom 19(13):1844–1850. doi:10.1002/rcm.1992
Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL (2015) Trans-proteomic pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl 9(7-8):745–754. doi:10.1002/prca.201400164
Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL (2013) The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res 12(1):162–171. doi:10.1021/pr301012j
Vizcaino JA, Foster JM, Martens L (2010) Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J Proteomics 73(11):2136–2146. doi:10.1016/j.jprot.2010.06.008
Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA (2009) Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 8(2):787–797. doi:10.1021/pr800538n
Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Huttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL (2012) PASSEL: the PeptideAtlas SRMexperiment library. Proteomics 12(8):1170–1175. doi:10.1002/pmic.201100515
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. doi:10.1101/gr.1239303
Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 25(1):125–131. doi:10.1038/nbt1275
Webb-Robertson BJ, Cannon WR, Oehmen CS, Shah AR, Gurumoorthi V, Lipton MS, Waters KM (2010) A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics 26(13):1677–1683
Fusaro VA, Mani DR, Mesirov JP, Carr SA (2009) Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol 27(2):190–198. doi:10.1038/nbt.1524
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Keerthikumar, S., Mathivanan, S. (2017). Proteotypic Peptides and Their Applications. In: Keerthikumar, S., Mathivanan, S. (eds) Proteome Bioinformatics. Methods in Molecular Biology, vol 1549. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6740-7_8
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6740-7_8
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6738-4
Online ISBN: 978-1-4939-6740-7
eBook Packages: Springer Protocols