Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

By Lyris M F Godoy, Jesper V. Olsen, Jüergen Cox, M. L. Nielsen, N. Hubner, F. Fröhlich, T. Walther, Matthias Mann. Nature, 2008

926 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/1f3cd993e370ab6da5039e30cb9dbd013a8e0ad7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Spectroscopy

Citations in the corpus

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* (2011, background): “…reconstruction of protein interaction networks,(14–16) or the comprehensive characterization of proteomes of model organisms such as Drosophila (17), C. elegans (18), and S. cerevisiae (19) via extensive fractionation of the proteome sample and the mass spectro-metric measurement of each fraction.”
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* (2012, background): “Those represent essentially the complete yeast proteome observable by mass spectrometry (30) and constitute therefore a realistic proteomic background.”
Deep proteome and transcriptome mapping of a human cancer cell line (2011, background): “These advances had allowed us to quantify an essentially complete proteome of the model organism yeast as judged by comparison with genomic tagging methods (de Godoy et al, 2008).”
Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy (2011, methodology): “All mass spectrometry experiments were performed on an EASY-nLC connected to a hybrid LTQ–Orbitrap classic (Thermo Fisher Scientific) equipped with a nanoelectrospray ion source (Proxeon Biosystems) essentially as previously described (39) with some modifications.”
The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics (2010, positive): “Data Processing and Protein Identiﬁcation MS data were processed using MaxQuant 1.0.11.2 (Cox and Mann, 2008) using the default settings (slice peaks: true; recalibrate: true; correct mass errors: true; max. peptide FDR: 0.01; max. peptide FPR: 0.1; max. protein FDR: 0.01; min. peptide length: 6; pe”
Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry* (2009, neutral): “Protein Identification False Discovery Rates for”