A guided tour of the Trans‐Proteomic Pipeline
Eric W. Deutsch,Luis Mendoza,David Shteynberg,Terry Farrah,Henry H N Lam,Natalie Tasman,Zhi Sun,Erik Nilsson,Brian S. Pratt,Bryan J. Prazen,Jimmy K. Eng,Daniel Martin,Alexey I. Nesvizhskii,Ruedi Aebersold +13 more
TLDR
The full workflow of the TPP is described, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.Abstract:
The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.read more
Citations
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Journal ArticleDOI
Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion
Wan-ting He,Haoqiang Wan,Lichen Hu,Pengda Chen,Xin Wang,Zhe Huang,Zhang-Hua Yang,Chuan-Qi Zhong,Jiahuai Han +8 more
TL;DR: It is reported that gasdermin D (GSDMD) is another crucial component of inflammasomes and the presence of GSDMD protein in nigericin-induced NLRP3 inflammaomes is discovered by a quantitative mass spectrometry-based analysis.
Journal ArticleDOI
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Dattatreya Mellacheruvu,Zachary Wright,Amber L. Couzens,Jean-Philippe Lambert,Nicole St-Denis,Tuo Li,Yana Miteva,Simon Hauri,Mihaela E. Sardiu,Teck Yew Low,Vincentius A. Halim,Vincentius A. Halim,Richard D. Bagshaw,Nina C. Hubner,Abdallah Al-Hakim,Annie Bouchard,Denis Faubert,Damian Fermin,Wade H. Dunham,Marilyn Goudreault,Zhen Yuan Lin,Beatriz Gonzalez Badillo,Tony Pawson,Daniel Durocher,Benoit Coulombe,Ruedi Aebersold,Ruedi Aebersold,Giulio Superti-Furga,Jacques Colinge,Albert J. R. Heck,Hyungwon Choi,Matthias Gstaiger,Shabaz Mohammed,Ileana M. Cristea,Keiryn L. Bennett,Michael P. Washburn,Michael P. Washburn,Brian Raught,Rob M. Ewing,Rob M. Ewing,Anne-Claude Gingras,Alexey I. Nesvizhskii +41 more
TL;DR: The contaminant repository for affinity purification (the CRAPome) is presented and its use for scoring protein-protein interactions is described and aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol.
Journal ArticleDOI
Protein Analysis by Shotgun/Bottom-up Proteomics
TL;DR: The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis.
Journal ArticleDOI
MS-GF+ makes progress towards a universal database search tool for proteomics.
Sangtae Kim,Pavel A. Pevzner +1 more
TL;DR: A database search tool MS-GF+ is presented that is sensitive (it identifies more peptides than most other database search tools) and universal (it works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols), and improves upon the performance of tools specifically designed for these applications.
Journal ArticleDOI
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Andy T. Kong,Felipe da Veiga Leprevost,Dmitry M. Avtonomov,Dattatreya Mellacheruvu,Alexey I. Nesvizhskii +4 more
TL;DR: A fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables a more than 100-fold improvement in speed over most existing proteome database search tools.
References
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Jiirgen Cox,Matthias Mann +1 more
TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
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Probability-based protein identification by searching sequence databases using mass spectrometry data.
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
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Mass spectrometry-based proteomics
Ruedi Aebersold,Matthias Mann +1 more
TL;DR: The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
Journal ArticleDOI
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
TL;DR: The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.
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.