A 'proteomic ruler' for protein copy number and concentration estimation without spike-in standards
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TLDR
This work shows that the MS signal of histones can be used as a “proteomic ruler” because it is proportional to the amount of DNA in the sample, which in turn depends on the number of cells, and adds an absolute scale to the MS readout and allows estimation of the copy numbers of individual proteins per cell.About:
This article is published in Molecular & Cellular Proteomics.The article was published on 2014-09-15 and is currently open access. It has received 495 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
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.
TL;DR: 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.
Journal ArticleDOI
On the Dependency of Cellular Protein Levels on mRNA Abundance.
TL;DR: It is concluded that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
Journal ArticleDOI
A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation
Avinash Patel,Hyun O. Lee,Louise Jawerth,Shovamayee Maharana,Marcus Jahnel,Marco Y. Hein,Stoyno S. Stoynov,Julia Mahamid,Shambaditya Saha,Titus M. Franzmann,Andrej Pozniakovski,Ina Poser,Nicola Maghelli,Loic Royer,Martin Weigert,Eugene W. Myers,Stephan W. Grill,David N. Drechsel,Anthony A. Hyman,Simon Alberti +19 more
TL;DR: It is proposed that liquid-like compartments carry the trade-off between functionality and risk of aggregation and that aberrant phase transitions within liquid- like compartments lie at the heart of ALS and, presumably, other age-related diseases.
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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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
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.
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
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.
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