Abstract
The application of a selected reaction monitoring method in a complete, multiplexed assay is achieved by combining multiple descriptors. Care must be taken to find an optimal number of targets so that proper sampling of the chromatographic experiment is still obtained. The final challenge is then analyzing the data to determine the signals for the respective peptides and calculating an amount of each protein. Internal standards and housekeeping proteins facilitate this process.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Anderson L, Hunter CL (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5:573–588
Keshishian H, Addona T, Burgess M, Mani DR, Shi X, Kuhn E, Sabatine MS, Gerszten RE, Carr SA (2009) Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 8:2339–2349
Kikuchi T, Hassanein M, Amann JM, Liu Q, Slebos RJ, Rahman SM, Kaufman JM, Zhang X, Hoeksema MD, Harris BK, Li M, Shyr Y, Gonzalez AL, Zimmerman LJ, Liebler DC, Massion PP, Carbone DP (2012) In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers. Mol Cell Proteomics 11:916–932
Barnidge DR, Goodmanson MK, Klee GG, Muddiman DC (2004) Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-MS/MS using protein cleavage and isotope dilution mass spectrometry. J Proteome Res 3:644–652
Williams DK, Muddiman DC (2009) Absolute quantification of C-reactive protein in human plasma derived from patients with epithelial ovarian cancer utilizing protein cleavage isotope dilution mass spectrometry. J Proteome Res 8:1085–1090
Rindler PM, Plafker SM, Szweda LI, Kinter M (2013) High dietary fat selectively increases catalase expression within cardiac mitochondria. J Biol Chem 288:1979–1990
Crewe C, Kinter M, Szweda LI (2013) Immediate inhibition of pyruvate dehydrogenase: An initiating event in high dietary fat-induced loss of metabolic flexibility in the heart (Submitted)
Shuford CM, Li Q, Sun YH, Chen HC, Wang J, Shi R, Sederoff RR, Chiang VL, Muddiman DC (2012) Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry. J Proteome Res 11:3390–3404
Kinter CS, Lundie JM, Patel H, Rindler PM, Szweda LI, Kinter M (2012) A quantitative proteomic profile of the Nrf2-mediated antioxidant response of macrophages to oxidized LDL determined by multiplexed selected reaction monitoring. PLoS One 7:e50016
Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100:6940–6945
Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW (2004) Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 3:235–244
Hanke S, Besir H, Oesterhelt D, Mann M (2008) Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res 7:1118–1130
Rivers J, Simpson DM, Robertson DH, Gaskell SJ, Beynon RJ (2007) Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol Cell Proteomics 6:1416–1427
Ludwig C, Claassen M, Schmidt A, Aebersold R (2012) Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Mol Cell Proteomics 11:M111.013987
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this chapter
Cite this chapter
Kinter, M., Kinter, C.S. (2013). Sample Analysis and Data Processing. In: Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics. SpringerBriefs in Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8666-4_5
Download citation
DOI: https://doi.org/10.1007/978-1-4614-8666-4_5
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-8665-7
Online ISBN: 978-1-4614-8666-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)