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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Journal ArticleDOI
Proteomic identification of early urinary-biomarkers of acute kidney injury in preterm infants
TL;DR: In this article, the authors identify novel urinary biomarkers of acute kidney injury using proteomic techniques, and verify and validate that the candidates can serve as early predictive biomarkers for AKI.
Journal ArticleDOI
RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans
Marko Jovanovic,Lukas Reiter,Alejandra M. Clark,Manuel Weiss,Paola Picotti,Hubert Rehrauer,Andreas P. Frei,Lukas J. Neukomm,Ethan J. Kaufman,Bernd Wollscheid,Martin J. Simard,Eric A. Miska,Ruedi Aebersold,André P. Gerber,Michael O. Hengartner +14 more
TL;DR: Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.
Journal ArticleDOI
Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments.
Tsung-Heng Tsai,Meena Choi,Balazs Banfai,Yansheng Liu,Brendan MacLean,Tom Dunkley,Olga Vitek +6 more
TL;DR: An automated statistical approach that automatically detects spectral features with inconsistent patterns of protein abundance can improve the estimation accuracy, sensitivity and specificity of detecting differentially abundant proteins, and reproducibility of conclusions across different data processing tools.
Journal ArticleDOI
Imatinib-Induced Changes in Protein Expression and ATP-Binding Affinities of Kinases in Chronic Myelocytic Leukemia Cells.
Weili Miao,Lei Guo,Yinsheng Wang +2 more
TL;DR: A parallel-reaction monitoring (PRM)-based targeted proteomic method to monitor the alterations in protein expression of kinases in K-562 chronic myelocytic leukemia (CML) cells elicited by treatment with imatinib, an ABL kinase inhibitor approved by the FDA for CML treatment.
Journal ArticleDOI
Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration.
Marc Bachofner,Tobias Speicher,Roman L. Bogorad,Sukalp Muzumdar,Carina Patrizia Derrer,Fabrizio Hürlimann,Friederike Böhm,Paolo Nanni,Tobias Kockmann,Tobias Kockmann,Ekaterina Kachaylo,Michael Meyer,Susagna Padrissa-Altés,Rolf Graf,Daniel G. Anderson,Victor Koteliansky,Ulrich auf dem Keller,Sabine Werner +17 more
TL;DR: It is demonstrated that Nedd4-1 is required for efficient internalization of major growth factor receptors involved in liver regeneration and their downstream mitogenic signaling, and the importance of posttranslational regulation of growth factor signaling in this process is highlighted.
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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