Selected reaction monitoring for quantitative proteomics: a tutorial
TLDR
This tutorial explains the application of SRM for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions, and normalization and various factors affecting sensitivity and accuracy are discussed.Abstract:
Systems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. Selected reaction monitoring (SRM)—also called multiple reaction monitoring—is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable quantification of analytes of low abundance in complex mixtures. In an SRM experiment, a predefined precursor ion and one of its fragments are selected by the two mass filters of a triple quadrupole instrument and monitored over time for precise quantification. A series of transitions (precursor/fragment ion pairs) in combination with the retention time of the targeted peptide can constitute a definitive assay. Typically, a large number of peptides are quantified during a single LC-MS experiment. This tutorial explains the application of SRM for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions. Furthermore, normalization and various factors affecting sensitivity and accuracy are discussed.read more
Citations
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Tissue-based map of the human proteome
Mathias Uhlén,Mathias Uhlén,Linn Fagerberg,Björn M. Hallström,Cecilia Lindskog,Per Oksvold,Adil Mardinoglu,Åsa Sivertsson,Caroline Kampf,Evelina Sjöstedt,Evelina Sjöstedt,Anna Asplund,IngMarie Olsson,Karolina Edlund,Emma Lundberg,Sanjay Navani,Cristina Al-Khalili Szigyarto,Jacob Odeberg,Dijana Djureinovic,Jenny Ottosson Takanen,Sophia Hober,Tove Alm,Per-Henrik Edqvist,Holger Berling,Hanna Tegel,Jan Mulder,Johan Rockberg,Peter Nilsson,Jochen M. Schwenk,Marica Hamsten,Kalle von Feilitzen,Mattias Forsberg,Lukas Persson,Fredric Johansson,Martin Zwahlen,Gunnar von Heijne,Jens Nielsen,Jens Nielsen,Fredrik Pontén +38 more
TL;DR: In this paper, a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level.
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Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
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TL;DR: A new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest is presented, using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method.
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Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens
Matthew M. Gubin,Xiuli Zhang,Heiko Schuster,Etienne Caron,Jeffrey P. Ward,Takuro Noguchi,Yulia Ivanova,Jasreet Hundal,Cora D. Arthur,Willem Jan Krebber,Gwenn E. Mulder,Mireille Toebes,Matthew D. Vesely,Samuel S. K. Lam,Alan J. Korman,James P. Allison,Gordon J. Freeman,Arlene H. Sharpe,Erika L. Pearce,Ton N. Schumacher,Ruedi Aebersold,Hans-Georg Rammensee,Cornelis J. M. Melief,Elaine R. Mardis,William E. Gillanders,Maxim N. Artyomov,Robert D. Schreiber +26 more
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Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
TL;DR: How SRM is applied in proteomics is described, recent advances are reviewed, present selected applications and a perspective on the future of this powerful technology is provided.
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TL;DR: The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis.
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