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
Reads0
Chats0
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
More filters
Journal ArticleDOI
DIANA - algorithmic improvements for analysis of data-independent acquisition MS data
Johan Teleman,Hannes L. Röst,George Rosenberger,Uwe Schmitt,Lars Malmström,Johan Malmström,Fredrik Levander +6 more
TL;DR: The algorithm DIANA and the classifier PyProphet are presented, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis, and are capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset.
Journal ArticleDOI
A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring
TL;DR: A computer program is developed that calculates nonredundant theoretical SRM assays, also known as unique ion signatures (UIS), for a given proteomic background and expects that the consideration of information content will become a standard step in SRM assay design and analysis, facilitated by the SRMCollider.
Journal ArticleDOI
B cell-derived GABA elicits IL-10 + macrophages to limit anti-tumour immunity
Baihao Zhang,Alexis Vogelzang,Michio Miyajima,Yuki Sugiura,Yibo Wu,Kenji Chamoto,Rei Nakano,Ryusuke Hatae,Rosemary J. Menzies,Kazuhiro Sonomura,Nozomi Hojo,Taisaku Ogawa,Wakana Kobayashi,Yumi Tsutsui,Sachiko Yamamoto,Mikako Maruya,Seiko Narushima,Keiichiro Suzuki,Hiroshi Sugiya,Kosaku Murakami,Motomu Hashimoto,Hideki Ueno,Takashi Kobayashi,Katsuhiro Ito,Tomoko Hirano,Katsuyuki Shiroguchi,Fumihiko Matsuda,Makoto Suematsu,Tasuku Honjo,Sidonia Fagarasan +29 more
TL;DR: This article showed that B cell-derived GABA promotes monocyte differentiation into anti-inflammatory macrophages that secrete interleukin-10 and inhibit CD8+ T cell killer function.
Journal ArticleDOI
Ultrasensitive aptamer-based multiplexed electrochemical detection by coupling distinguishable signal tags with catalytic recycling of DNase I.
TL;DR: Experimental results revealed that the multiplexed electrochemical aptasensor enabled the simultaneous monitoring of ATP and cocaine in a single run with wide working ranges and low detection limits.
Journal ArticleDOI
Mass spectrometry-based proteomics for systems biology.
TL;DR: Recent contributions of MS to systems biology are reviewed and several examples that illustrate the importance of mass spectrometry to elucidate the components and interactions of molecular networks are discussed.
References
More filters
Journal ArticleDOI
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.
Journal ArticleDOI
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.
Shao En Ong,Blagoy Blagoev,Irina Kratchmarova,Dan B. Kristensen,Hanno Steen,Akhilesh Pandey,Matthias Mann +6 more
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.
TL;DR: A statistical model is presented to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST, demonstrating that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides.
Journal ArticleDOI
A statistical model for identifying proteins by tandem mass spectrometry.
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).
Related Papers (5)
Selected reaction monitoring for quantitative proteomics: a tutorial
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma
Terri A. Addona,Susan E. Abbatiello,Birgit Schilling,Steven J. Skates,D. R. Mani,David M. Bunk,Clifford H. Spiegelman,Lisa J. Zimmerman,Amy-Joan L. Ham,Hasmik Keshishian,Steven C. Hall,Simon Allen,Ronald K. Blackman,Christoph H. Borchers,Charles Buck,Helene L. Cardasis,Michael P. Cusack,Nathan G. Dodder,Bradford W. Gibson,Jason M. Held,Tara Hiltke,Angela M. Jackson,Eric B. Johansen,Christopher R. Kinsinger,Jing Li,Mehdi Mesri,Thomas A. Neubert,Richard K. Niles,Trenton C. Pulsipher,David F. Ransohoff,Henry Rodriguez,Paul A. Rudnick,Derek Smith,David L. Tabb,Tony J. Tegeler,Asokan Mulayath Variyath,Lorenzo Vega-Montoto,Asa Wahlander,Sofia Waldemarson,Mu Wang,Jeffrey R. Whiteaker,Lei Zhao,N. Leigh Anderson,Susan J. Fisher,Daniel C. Liebler,Amanda G. Paulovich,Fred E. Regnier,Paul Tempst,Steven A. Carr +48 more