The Coming Age of Complete, Accurate, and Ubiquitous Proteomes
TLDR
Developments discussed in this Perspective will soon enable complete proteome analysis of mammalian cells, as well, with profound impact on biology and biomedicine.About:
This article is published in Molecular Cell.The article was published on 2013-02-21 and is currently open access. It has received 332 citations till now.read more
Citations
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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
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
TL;DR: A new intensity determination and normalization procedure called MaxLFQ is developed that is fully compatible with any peptide or protein separation prior to LC-MS analysis, which accurately detects the mixing ratio over the entire protein expression range, with greater precision for abundant proteins.
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Mass-spectrometric exploration of proteome structure and function
TL;DR: Powerful mass-spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes.
Journal ArticleDOI
A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances
Marco Y. Hein,Nina C. Hubner,Ina Poser,Juergen Cox,Nagarjuna Nagaraj,Yusuke Toyoda,Igor A. Gak,Ina Weisswange,Joerg Mansfeld,Frank Buchholz,Anthony A. Hyman,Matthias Mann +11 more
TL;DR: This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quantitative network analysis, revealing that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology.
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Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues
Roland Bruderer,Oliver M. Bernhardt,Tejas Gandhi,Saša M. Miladinović,Lin-Yang Cheng,Simon Messner,Tobias Ehrenberger,Vito R T Zanotelli,Yulia Butscheid,Claudia Escher,Olga Vitek,Oliver Rinner,Lukas Reiter +12 more
TL;DR: It is shown that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins, implying that DIA should be the preferred method for quantitative protein profiling.
References
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High resolution two-dimensional electrophoresis of proteins.
TL;DR: This technique provides a method for estimation of the number of proteins made by any biological system and can resolve proteins differing in a single charge and consequently can be used in the analysis of in vivo modifications resulting in a change in charge.
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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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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.
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Universal sample preparation method for proteome analysis
TL;DR: A method is described, filter-aided sample preparation (FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry–based proteomics and allows single-run analyses of organelles and an unprecedented depth of proteome coverage.
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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.
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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