Published in Mol Cell Proteomics on November 01, 2008
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
Mass spectrometry and protein analysis. Science (2006) 8.05
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol (2003) 6.86
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol (2008) 6.38
Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics (2005) 6.28
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature (2011) 6.09
Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol (2011) 6.02
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell (2002) 5.70
An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron (2007) 5.35
Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods (2012) 4.93
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics (2007) 4.72
Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol (2007) 4.70
Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol (2005) 4.63
Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc (2009) 4.61
RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A (2011) 4.58
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods (2009) 4.17
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics (2004) 4.15
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature (2009) 4.07
Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem (2004) 4.06
Rewiring of genetic networks in response to DNA damage. Science (2010) 4.03
Identification of cross-linked peptides from large sequence databases. Nat Methods (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J (2012) 3.70
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol (2010) 3.51
Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods (2007) 3.46
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics (2010) 3.44
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A (2012) 3.42
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34
Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol Cell Proteomics (2007) 3.33
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev (2009) 3.31
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics (2008) 3.29
Orm family proteins mediate sphingolipid homeostasis. Nature (2010) 3.29
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell (2012) 3.26
A database of mass spectrometric assays for the yeast proteome. Nat Methods (2008) 3.19
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods (2011) 3.10
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol (2009) 3.09
Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell (2009) 3.03
Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex. Cell (2012) 3.03
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics (2009) 2.96
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today (2004) 2.82
The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics (2007) 2.82
A human proteome detection and quantitation project. Mol Cell Proteomics (2009) 2.80
The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res (2007) 2.77
Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors. Nature (2012) 2.76
Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol (2009) 2.70
Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell Biol (2004) 2.65
The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics (2010) 2.64
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol (2007) 2.59
A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Mol Cell Proteomics (2008) 2.56
PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol Syst Biol (2007) 2.56
Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7. J Cell Biol (2008) 2.56
GATA-1 forms distinct activating and repressive complexes in erythroid cells. EMBO J (2005) 2.56
A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet (2004) 2.54
The study of macromolecular complexes by quantitative proteomics. Nat Genet (2003) 2.44
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet (2009) 2.44
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res (2010) 2.40
Sequential waves of functionally related proteins are expressed when B cells prepare for antibody secretion. Immunity (2003) 2.40
Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet (2012) 2.39
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS (2006) 2.38
Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol (2003) 2.37
Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics (2014) 2.37