Journal ArticleDOI
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.
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TLDR
An updated protocol covering the most important basic computational workflows for mass-spectrometry-based proteomics data analysis, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques is presented.Abstract:
MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda This protocol update describes an adaptation of an existing protocol that substantially modifies the technique Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs) The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores The software is written in C# and is freely available at http://wwwmaxquantorgread more
Citations
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The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol,Attila Csordas,Jingwen Bai,Manuel Bernal-Llinares,Suresh Hewapathirana,Deepti J. Kundu,Avinash Inuganti,Johannes Griss,Johannes Griss,Gerhard Mayer,Martin Eisenacher,Enrique Perez,Julian Uszkoreit,Julianus Pfeuffer,Timo Sachsenberg,Şule Yılmaz,Shivani Tiwary,Juergen Cox,Enrique Audain,Mathias Walzer,Andrew F. Jarnuczak,Tobias Ternent,Alvis Brazma,Juan Antonio Vizcaíno +23 more
TL;DR: Key statistics on the current data contents and volume of downloads are outlined, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas are outlined.
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Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma
Qiang Gao,Hongwen Zhu,Liangqing Dong,Weiwei Shi,Ran Chen,Zhijian Song,Chen Huang,Junqiang Li,Xiaowei Dong,Yanting Zhou,Qian Liu,Lijie Ma,Xiaoying Wang,Jian Zhou,Yansheng Liu,Emily S. Boja,Ana I. Robles,Weiping Ma,Pei Wang,Yize Li,Li Ding,Bo Wen,Bing Zhang,Henry Rodriguez,Daming Gao,Hu Zhou,Jia Fan +26 more
TL;DR: The first proteogenomic characterization of hepatitis B virus-related hepatocellular carcinoma using paired tumor and adjacent liver tissues from 159 patients provides a valuable resource that significantly expands the knowledge of HBV-related HCC and may eventually benefit clinical practice.
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SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation.
TL;DR: This work develops Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to identify distinct human cancer cell types based on their proteomes and uses it to quantify over a thousand proteins in differentiating mouse embryonic stem cells.
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An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes.
Dorte B. Bekker-Jensen,Christian D. Kelstrup,Tanveer S. Batth,Sara Larsen,Christa Haldrup,Jesper B. Bramsen,Karina Dalsgaard Sørensen,Søren Høyer,Torben F. Ørntoft,Claus L. Andersen,Michael L. Nielsen,Jesper V. Olsen +11 more
TL;DR: A classical two-dimensional high-resolution reversed-phase peptide fractionation scheme is modified and optimized to provide sufficient peak capacity to saturate the sequencing speed of modern MS instruments.
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Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells.
Ying Zhu,Paul D. Piehowski,Rui Zhao,Jing Chen,Yufeng Shen,Ronald J. Moore,Anil K. Shukla,Vladislav A. Petyuk,Martha Campbell-Thompson,Clayton E. Mathews,Richard D. Smith,Wei-Jun Qian,Ryan T. Kelly +12 more
TL;DR: A robotically controlled chip-based nanodroplet processing platform is established and its ability to profile the proteome from 10–100 mammalian cells is demonstrated, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.
References
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Journal ArticleDOI
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.
Journal ArticleDOI
Global quantification of mammalian gene expression control
Björn Schwanhäusser,Dorothea Busse,Na Li,Gunnar Dittmar,Johannes Schuchhardt,Jana Wolf,Wei Chen,Matthias Selbach +7 more
TL;DR: Using a quantitative model, the first genome-scale prediction of synthesis rates of mRNAs and proteins is obtained and it is found that the cellular abundance of proteins is predominantly controlled at the level of translation.
Journal ArticleDOI
The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova,Tikira Temu,Pavel Sinitcyn,Arthur Carlson,Marco Y. Hein,Tamar Geiger,Matthias Mann,Jürgen Cox +7 more
TL;DR: The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
Journal ArticleDOI
Andromeda: a peptide search engine integrated into the MaxQuant environment
Jürgen Cox,Nadin Neuhauser,Annette Michalski,Richard A. Scheltema,Jesper V. Olsen,Matthias Mann +5 more
TL;DR: A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.
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.
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Yasset Perez-Riverol,Attila Csordas,Jingwen Bai,Manuel Bernal-Llinares,Suresh Hewapathirana,Deepti J. Kundu,Avinash Inuganti,Johannes Griss,Johannes Griss,Gerhard Mayer,Martin Eisenacher,Enrique Perez,Julian Uszkoreit,Julianus Pfeuffer,Timo Sachsenberg,Şule Yılmaz,Shivani Tiwary,Juergen Cox,Enrique Audain,Mathias Walzer,Andrew F. Jarnuczak,Tobias Ternent,Alvis Brazma,Juan Antonio Vizcaíno +23 more