Abstract
Selected reaction monitoring mass spectrometry (SRM-MS) becomes an essential tool for targeted protein quantification. Quantitative data has two forms—relative and absolute quantification.
Most of the quantifications in SRM-MS utilize stable isotope labeling (SIL) either at the peptide level, or at the protein level, as an internal standard. There are two types of SIL techniques—one that is achieved metabolically in vivo like stable isotope labeling by amino acids in cell culture (SILAC) and others that are achieved chemically or enzymatically in vitro such as isotope-coded affinity tag (ICAT) and isobaric tags for relative and absolute quantification (iTRAQ). In relative quantification, the relative changes in terms of fold change or protein abundance between two samples or states are measured with SRM-MS using various label-free or label-based techniques, including SILAC, ICAT, iTRAQ, mTRAQ, and 18O-labeling. In absolute quantification, the exact amount of substance in question—ng/mL of a protein in serum or copy number of a protein in a cell—is determined using absolute quantification (AQUA), QconCAT, or protein standard absolute quantification (PSAQ) labeling techniques.
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
Addona TA, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009;27:633–41.
Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods. 2005;2:587–9.
Bondarenko PV, Chelius D, Shaler TA. Identification and relative quantification of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem. 2002;74:4741–9.
Brun V, Dupuis A, Adrait A, Marcellin M, et al. Isotope-labeled protein standards: towards absolute quantitative proteomics. Mol Cell Proteomics. 2007;6:2139–49.
Calderon-Celis F, Encinar JR, Sanz-Medel A. Standardization approaches in absolute quantitative proteomics with mass spectrometry. Mass Spec Rev. 2018;37:715–37.
Chahrour O, Cobice D, Malone J. Stable isotope labeling methods in mass spectrometry-based quantitative proteomics. J Pharma Biomed Anal. 2015;113:2–20.
Chelius D, Bondarenko PV. Quantitative profiling of protein in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res. 2002;1:317–23.
Choi S, Kim J, Yea K, Suh PG, Kim J, Ryu SH. Targeted label-free quantitative analysis of secretory proteins from adipocytes in response to oxidative stress. Anal Biochem. 2010;401:196–202.
Conrads TP, Alving K, Veenstra TD, Belov ME, Anderson GA, Anderson DJ, Lipton MS, Pasa-Tolic L, Udesh HR, Chrisler WB, Thrall BD, Smith RD. Quantitative analysis of bacterial and mammalian proteomics using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal Chem. 2001;73:2132–9.
DeSouza LV, Taylor AM, Li W, Minkoff MS, Romaschin AD, Colgan TJ, Siu KWM. Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues. J Proteome Res. 2008;7:3525–54.
FDA. Bioanalytical method validation, guidance for industry. Rockville: United States Food and Drug Administration (FDA); 2018.
Gerber SA, Rush J, Stemman O, Krischner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A. 2003;100:6940–5.
Hoofnagle AN, Becker JO, Oda MN, Cavigiolio, G, et al. Multiple reaction monitoring-mass spectrometric assays can accurately measure many protein concentrations in complex mixtures. Clin Chem. 2012;58:777–81.
Holman SW, Sims FG, Eyers CE. The use of selected reaction monitoring in quantitative proteomics. Bioanalysis. 2012;4:1763–86.
Huillet C, Adrait A, Lebert D, Picard G, Trauchessec M, Louwagie M, Dupuis A, Hittinger L, Ghaleh B, Corvoisier PL, Jaquinod M, Garin J, Bruley C, Brun V. Accurate quantification of cardiovascular biomarkers in serum using protein standard absolute quantification (PSAQ™) and selected reaction monitoring. Mol Cell Proteomics. 2012;11:1–12. https://doi.org/10.1074/mcp.M111.008235.
Jovanovic M, Reiter L, Picotti P, Lange V, Bogan E, Hurschler BA, Blenkiron C, Lehrbach NJ, Ding XC, Weiss M, Schrimpf SP, Miska EA, Groβans H, Aebersold R, Hengartner MO. A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nat Methods. 2010;7:837–42.
Kettenbach AN, Rush J, Gerber SA. Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc. 2011;6:175–86.
Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods. 2005;35:265–73.
Kuzyk MA, Parker CE, Domanski D, Borchers CH. Development of MRM-based assays for the absolute quantification of plasma proteins. In: Backvall H, Lehtio J, editors. The low molecular weight proteome: methods and protocols, Methods in molecular biology, vol. 1023. New York: Springer; 2013.
Langen H, Takacs B, Evers S, Berndt P, et al. Two-dimensional map of the proteome of Haemophilus influenza. Electrophoresis. 2000;21:411–29.
Langenfeld E, Zanger UM, Jung K, Meyer HE, et al. Mass spectrometry-based absolute quantification of microsomal cytochrome P450 2D6 in human liver. Proteomics. 2009;9:2313–23.
Lawless C, Holman SW, Brownridge P, Lanthaler K, et al. Direct and absolute quantification of over 1800 yeast proteins via selected reaction monitoring. Mol Cell Proteomics. 2016;15:1309–22.
Li J, Zhou L, Wang H, Yan H, Li N, Zhai R, Jiao F, Hao F, Jin Z, Tian F, Peng B, Zhang Y, Qian X. A new sample preparation method for the absolute quantification of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry. Analyst. 2015;140:1281–90.
Liu H, Sadygov RG, Yates JR. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004;76:4193–201.
Mayya V, Rezual K, Wu L, Fong MB, et al. Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol Cell Proteomics. 2006;5:1146–57.
Mirzaei H, McBee JK, Watta J, Aebersold R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics. 2008;7:813–23.
Mohammed Y, Pan J, Zhang S, Han J, et al. ExSTA: external standard addition method for accurate high-throughput quantitation in targeted proteomics experiments. Proteomics Clin Appl. 2018;12:1600180.
Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, Sluyter SCV, Haynes AP. Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics. 2011;11:535–53.
Oda Y, Huang K, Cross FR, Cowburn D, et al. Accurate quantification of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A. 1999;96:6591–6.
Oeckl P, Steinacker P, Otto M. Comparison of internal standard approaches for SRM analysis of alpha-synuclein in cerebrospinal fluid. J Proteome. 2018;17:516–23.
Ong S, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol. 2005;1:252–62.
Ong SE, Blagoev B, Kratchmarova I, Kristensen DB. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002;1:376–86.
Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods. 2012;9:555–66.
Picotti P, Bodenmiller B, Mueller LN, Domon B, et al. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell. 2009;138:795–806.
Pino LK, Searle BC, Huang EL, Noble WS, et al. Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories. Anal Chem. 2018;90:13112–7.
Rangiah K, Tippornwong M, Sangar V, Austin D, Tetreault MP, Rustgi AK, Blair IA, Yu KH. Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. J Proteome Res. 2009;8:5153–64.
Selevsek N, Chang CY, Gillet LC, Navarro P, et al. Reproducible and consistent quantification of the Saccharomyces cerevisiae by SWATH-mass spectrometry. Mol Cell Proteomics. 2015;14:739–49.
Sohn A, Kim H, Yeo I, Kim Y, et al. Fully validated SRM-MS-based method for absolute quantification of PIVKA-II in human serum: clinical applications for patients with HCC. J Pharm Biomed Anal. 2018;156:142–6.
Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A. 2007;104:5860–5.
Xu P, Duong DM, Seyfried NT, Cheng D, et al. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell. 2009;137:133–45.
Ye X, Luke B, Andresson T, Blonder J. 18O stable isotope labeling in MS-based proteomics. Brief Funct Genomic Proteomic. 2009;8:136–44.
Zhao Y, Jia W, Sun W, Guo L, Wei J, Ying W, Ying W, Zhang Y, Xie Y, Jiang Y, He F, Qian X. Combination of improved 18O incorporation and multiple reaction monitoring: a universal strategy for absolute quantitative verification of serum candidate biomarkers of liver cancer. J Proteome Res. 2010;9:3319–27.
Zhou Y, Shan Y, Zhang L, Zhang Y. Recent advantages in stable isotope labeling based techniques for proteome relative quantification. J Chromatogr A. 2014;1365:1–11.
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, et al. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2006;5:2339–47.
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Hossain, M. (2020). Quantification by SRM-MS. In: Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics. Springer, Cham. https://doi.org/10.1007/978-3-030-53433-2_6
Download citation
DOI: https://doi.org/10.1007/978-3-030-53433-2_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-53432-5
Online ISBN: 978-3-030-53433-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)