Journal ArticleDOI
mProphet: automated data processing and statistical validation for large-scale SRM experiments
Lukas Reiter,Oliver Rinner,Paola Picotti,Paola Picotti,Ruth Hüttenhain,Martin Beck,Martin Beck,Mi-Youn Brusniak,Michael O. Hengartner,Ruedi Aebersold,Ruedi Aebersold +10 more
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TLDR
In this article, the authors present mProphet, a fully automated system that computes accurate error rates for the identification of targeted peptides in SRM data sets and maximizes specificity and sensitivity by combining relevant features in the data into a statistical model.Abstract:
Selected reaction monitoring (SRM) is a targeted mass spectrometric method that is increasingly used in proteomics for the detection and quantification of sets of preselected proteins at high sensitivity, reproducibility and accuracy. Currently, data from SRM measurements are mostly evaluated subjectively by manual inspection on the basis of ad hoc criteria, precluding the consistent analysis of different data sets and an objective assessment of their error rates. Here we present mProphet, a fully automated system that computes accurate error rates for the identification of targeted peptides in SRM data sets and maximizes specificity and sensitivity by combining relevant features in the data into a statistical model.read more
Citations
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Journal ArticleDOI
Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: Principle and applications.
TL;DR: Various implementation schemes of parallel reaction monitoring (PRM) are described and their benefits and limitations in terms of quantification performance and confidence in analyte identification are discussed.
Journal ArticleDOI
The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium
Rory N Pruitt,Rory N Pruitt,Benjamin Schwessinger,Benjamin Schwessinger,Benjamin Schwessinger,Anna Joe,Anna Joe,Nicholas Thomas,Furong Liu,Markus Albert,Michelle R. Robinson,Leanne Jade G. Chan,Dee Dee Luu,Huamin Chen,Ofir Bahar,Arsalan Daudi,David De Vleesschauwer,Daniel F. Caddell,Weiguo Zhang,Xiuxiang Zhao,Xiang Li,Joshua L. Heazlewood,Deling Ruan,Deling Ruan,Dipali Majumder,Mawsheng Chern,Mawsheng Chern,Hubert Kalbacher,Samriti Midha,Prabhu B. Patil,Ramesh V. Sonti,Christopher J. Petzold,Chang C. Liu,Jennifer S. Brodbelt,Georg Felix,Pamela C. Ronald,Pamela C. Ronald +36 more
TL;DR: The identification of a previously undescribed Xoo protein, called RaxX, is reported, which is required for activation of XA21-mediated immunity, and can be applied to the development of resistant crop varieties and therapeutic reagents that have the potential to block microbial infection of both plants and animals.
Journal ArticleDOI
PASSEL: The PeptideAtlas SRMexperiment library
Terry Farrah,Eric W. Deutsch,Richard Kreisberg,Zhi Sun,David S. Campbell,Luis Mendoza,Ulrike Kusebauch,Mi-Youn Brusniak,Ruth Hüttenhain,Ralph Schiess,Nathalie Selevsek,Ruedi Aebersold,Ruedi Aebersold,Robert L. Moritz +13 more
TL;DR: The PeptideAtlas SRM Experiment Library (PASSEL) allows researchers to easily submit proteomic data sets generated by SRM and will help in the assessment of proteotypic peptide performance in a wide array of samples containing the same peptide, as well as across multiple experimental protocols.
Journal ArticleDOI
Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications.
TL;DR: This work describes and review data‐independent acquisition strategies and their recent use in clinically oriented studies, and provides a detailed guide for the implementation of SWATH‐MS (where SWATH is sequential window acquisition of all theoretical mass spectra)—one of the data‐ independent strategies that have gained wide application of late.
Journal ArticleDOI
Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry
Etienne Caron,Daniel J. Kowalewski,Ching Chiek Koh,Theo Sturm,Heiko Schuster,Ruedi Aebersold,Ruedi Aebersold +6 more
TL;DR: In this article, the authors summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e., SWATH-MS) to identify and quantify MHC-associated peptides.
References
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Journal ArticleDOI
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
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TL;DR: The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM).
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