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
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Spermidine activates mitochondrial trifunctional protein and improves antitumor immunity in mice
Muna Al-Habsi,Kenji Chamoto,Ken Matsumoto,Norimichi Nomura,Baihao Zhang,Yuki Sugiura,Kazuhiro Sonomura,Aprilia Maharani,Yuka Nakajima,Yibo Wu,Yayoi Nomura,Rosemary J. Menzies,Masaki Tajima,Koji Kitaoka,Y. Haku,Sara Delghandi,Keiko Yurimoto,Fumihiko Matsuda,So Iwata,Toshihiko Ogura,Sidonia Fagarasan,Tasuku Honjo +21 more
TL;DR: T cell-specific deletion of the MTP α subunit abolished enhancement of programmed cell death protein 1 (PD-1) blockade immunotherapy by SPD, indicating that MTP is required for SPD-dependent T cell activation.
Journal ArticleDOI
jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions
TL;DR: JTraML as mentioned in this paper is a Java API for the Proteomics Standards Initiative TraML data standard, which provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions.
Journal ArticleDOI
Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.
TL;DR: A fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework that implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory.
Journal ArticleDOI
Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments
Paul Daly,Paul Daly,Jolanda M. van Munster,Jolanda M. van Munster,Martin J. Blythe,Roger Ibbett,Matthew Kokolski,Sanyasi Gaddipati,Erika Lindquist,Vasanth R. Singan,Kerrie Barry,Anna Lipzen,Chew Yee Ngan,Christopher J. Petzold,Leanne Jade G. Chan,Steven T. Pullan,Steven T. Pullan,Stéphane Delmas,Stéphane Delmas,Paul R. Waldron,Igor V. Grigoriev,Gregory A. Tucker,Blake A. Simmons,David B. Archer +23 more
TL;DR: The authors investigated the responses of Aspergillus niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics.
Journal ArticleDOI
Towards clinical applications of selected reaction monitoring for plasma protein biomarker studies.
TL;DR: This review focuses on the recent adoption of selected reaction monitoring of plasma proteins in the path to clinical use for a broad range of diseases including cancer, cardiovascular disease, genetic disorders and various metabolic disorders.
References
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Statistical significance for genomewide studies
John D. Storey,Robert Tibshirani +1 more
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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TL;DR: SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system and is applied to the relative quantitation of changes in protein expression during the process of muscle cell differentiation.
Journal ArticleDOI
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
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Journal ArticleDOI
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TL;DR: A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample, and it is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications.
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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