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
Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis.
Anuli Uzozie,Nathalie Selevsek,Asa Wahlander,Paolo Nanni,Jonas Grossmann,Achim Weber,Federico Buffoli,Giancarlo Marra +7 more
TL;DR: The proteins identified in this study expand the pool of biomarker candidates that can be used to develop a standardized precolonoscopy blood test for the early detection of colorectal tumors.
Journal ArticleDOI
SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
TL;DR: The R/Bioconductor package SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.
Journal ArticleDOI
Tandem mass spectral libraries of peptides and their roles in proteomics research
TL;DR: The historical development of spectral libraries in proteomics is described, the computational procedures behind library building and searching are detailed, the current applications of spectral Libraries are surveyed, and the outstanding challenges are discussed.
Journal ArticleDOI
Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry.
TL;DR: A data-independent acquisition (DIA) workflow that provides superior run-to-run consistency and postacquisition flexibility in comparison to DDA methods is utilized and a novel DIA-based methodology to quantify isobaric, co-eluting histone peptides that lack unique MS2 transitions is developed.
Journal ArticleDOI
Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites.
Manuel Bauer,Erik Ahrné,Anna P. Baron,Timo Glatter,Luca L. Fava,Anna Santamaria,Erich A. Nigg,Alexander Schmidt +7 more
TL;DR: Comparing the performance of conventional DDA, directed, and various targeted MS approaches on two different instruments, namely, a hybrid linear ion trap--Orbitrap and a triple quadrupole instrument found that all methods performed similarly in the absence of background proteins; however, when analyzing whole-cell lysates, targeted methods were at least 5-10 times more sensitive than that of the directed or DDA method.
References
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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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