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
Systems proteomics of liver mitochondria function
Evan G. Williams,Yibo Wu,Pooja Jha,Sébastien Dubuis,Peter Blattmann,Carmen Argmann,Sander M. Houten,Tiffany Amariuta,Witold Wolski,Nicola Zamboni,Ruedi Aebersold,Ruedi Aebersold,Johan Auwerx +12 more
TL;DR: The characterization of mitochondrial function in a genetic reference panel of recombinant inbred mice showed a frequent lack of correlation of transcript and protein abundance, enabled the identification of genomic variants of mitochondrial enzymes that caused inborn errors in metabolism, and revealed two genes that appear to function in cholesterol metabolism.
Journal ArticleDOI
A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition.
Veronika Vidova,Zdenek Spacil +1 more
TL;DR: A step-by-step tutorial on development of SRM/MRM protein assay intended for researchers without prior experience in proteomics is presented.
Journal ArticleDOI
Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics
Ruth Hüttenhain,Martin Soste,Nathalie Selevsek,Hannes L. Röst,Hannes L. Röst,Atul Sethi,Atul Sethi,Christine Carapito,Terry Farrah,Eric W. Deutsch,Ulrike Kusebauch,Robert L. Moritz,Emma Niméus-Malmström,Oliver Rinner,Ruedi Aebersold,Ruedi Aebersold +15 more
TL;DR: A high-throughput method for the development and refinement of selected reaction monitoring (SRM) assays for human proteins is described and it is demonstrated that these SRM assays allow reproducible quantification by monitoring 34 biomarker candidates across 83 patient plasma samples.
Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition
Jean-Philippe Lambert,Gordana Ivosev,Amber L. Couzens,Brett Larsen,Mikko Taipale,Zhen-Yuan Lin,Quan Zhong,Susan Lindquist,Susan Lindquist,Marc Vidal,Ruedi Aebersold,Ruedi Aebersold,Tony Pawson,Tony Pawson,Ron Bonner,Stephen A. Tate,Anne-Claude Gingras,Anne-Claude Gingras +17 more
TL;DR: In this article, changes to protein interactomes as a result of mutations to the bait protein or addition of a pharmacological inhibitor are robustly monitored with affinity purification coupled with data-independent acquisition-based mass spectrometry and an automated data analysis pipeline.
Journal ArticleDOI
Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS.
Yansheng Liu,Ruth Hüttenhain,Silvia Surinova,Ludovic C Gillet,Jeppe Mouritsen,Roland Brunner,Pedro Navarro,Ruedi Aebersold +7 more
TL;DR: Overall, SWATH‐MS measurements showed a slightly lower sensitivity and a comparable reproducibility to state‐of‐the‐art SRM measurements for targeted quantification of the N‐glycosites in human blood, but a significantly larger number of peptides can be quantified per analysis.
References
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Statistical significance for genomewide studies
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TL;DR: This work proposes an approach to measuring statistical significance in genomewide studies based on the concept of the false discovery rate, which offers a sensible balance between the number of true and false positives that is automatically calibrated and easily interpreted.
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Journal ArticleDOI
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Brendan MacLean,Daniela M. Tomazela,Nicholas J. Shulman,Matthew C. Chambers,Gregory L. Finney,Barbara Frewen,Randall Kern,David L. Tabb,Daniel C. Liebler,Michael J. MacCoss +9 more
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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