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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Dissertation
Digital data heritage preservation (DHP) modelling and design
Carrion Gordon,Lucia Cristina +1 more
TL;DR: Motto: ’When the origin and heritage of data are lost, data has no meaning’
Journal ArticleDOI
Plasma preparation to measure FDA-approved protein markers by selected reaction monitoring
Olga I. Kiseleva,Yulia A. Romashova,Natalia E. Moskaleva,N. A. Petushkova,N B Teryaeva,Artem Yu. Belyaev,Andrey Lisitsa +6 more
TL;DR: It was shown that commercially designed SRM kits are suitable for SRM detection of well-established plasma/serum biomarkers.
Journal ArticleDOI
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Christopher R. Kinsinger,James A Apffel,Mark S. Baker,Xiaopeng Bian,Christoph H. Borchers,Ralph A. Bradshaw,Mi Youn Brusniak,Daniel W. Chan,Eric W. Deutsch,Bruno Domon,Jeffrey J. Gorman,Rudolf Grimm,William S. Hancock,Henning Hermjakob,David Horn,Christie L. Hunter,Patrik Kolar,Hans Joachim Kraus,Hanno Langen,Rune Linding,Robert L. Moritz,Gilbert S. Omenn,Ron Orlando,Akhilesh Pandey,Peipei Ping,Amir Rahbar,Robert Rivers,Sean L. Seymour,Richard J. Simpson,Douglas J. Slotta,Richard Smith,Stephen E. Stein,David L. Tabb,Danilo A. Tagle,John R. Yates,Henry Rodriguez +35 more
TL;DR: The historic precedents, key discussions, and necessary next steps to enhance the quality of open access data are explored, including an evolving list of comprehensive quality metrics and standards accompanied by software analytics.
Book ChapterDOI
Prediction of Antioxidant Status in Fish Farmed on Selenium Nanoparticles using Neural Network Regression Algorithm
TL;DR: The effect of the different concentrations of Nano-selenium in the diet on the antioxidant status of common carp was investigated through the estimation of antioxidant enzymes activity and some biochemical blood prole to build preliminary prediction models to know the antioxidants status activity.
Patent
Method for analysis of samples in targeted proteomics applications, computer program product and set of reference peptides
TL;DR: In this article, the authors proposed a method for polypeptide analysis based on indexed retention time as peptide specific property and applied it to the analysis of compounds with mass spectrometry.
References
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Journal ArticleDOI
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Journal ArticleDOI
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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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