Abstract
The instrument instructions for a selected reaction monitoring experiment contain the basic programming needed to detect the set of peptides that will act as the quantitative surrogate for each protein being measured. The overarching goal of the design process is find the best peptides to monitor and optimize the collision induced dissociation conditions to give the best signal for those peptides. The general stages are finding an initial set of candidate peptides for initial testing, optimizing the conditions for those candidates, selecting the best of the optimized group, and validating the proper detection of the correct peptides. A six step approach is used to go through these stages.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wysocki VH, Tsaprailis G, Smith LL, Breci LA (2000) Mobile and localized protons: a framework for understanding peptide dissociation. J Mass Spectrom 35:1399–1406
Gucinski AC, Dodds ED, Li W, Wysocki VH (2010) Understanding and exploiting peptide fragment ion intensities using experimental and informatic approaches. Methods Mol Biol 604:73–94
Harrison AG, Csizmadia IG, Tang TH (2000) Structure and fragmentation of b2 ions in peptide mass spectra. J Am Soc Mass Spectrom 11:427–436
Harrison AG (2009) To b or not to b: the ongoing saga of peptide b ions. Mass Spectrom Rev 28:640–654
Lau KW, Hart SR, Lynch JA, Wong SC, Hubbard SJ, Gaskell SJ (2009) Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides. Rapid Commun Mass Spectrom 23:1508–14
Kinter M, Sherman NE (2000) Protein sequencing and identification using tandem mass spectrometry. Wiley, New York
Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10:R130
Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R (2006) The PeptideAtlas project. Nucleic Acids Res 34:D655–D658
Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins D (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539
Spicer V, Yamchuk A, Cortens J, Sousa S, Ens W, Standing KG, Wilkins JA, Krokhin OV (2007) Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. Anal Chem 79:8762–8768
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). Designing a Selected Reaction Monitoring Method. 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_3
Download citation
DOI: https://doi.org/10.1007/978-1-4614-8666-4_3
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)