Published in Nat Genet on February 18, 2003
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol (2008) 3.53
Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J (2004) 3.50
Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol Syst Biol (2005) 3.48
Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc Natl Acad Sci U S A (2009) 2.94
GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem (2003) 2.74
Mass spectrometry-based proteomics in cell biology. J Cell Biol (2010) 2.66
Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol (2004) 2.26
Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol Cell Biol (2003) 2.08
Target identification and mechanism of action in chemical biology and drug discovery. Nat Chem Biol (2013) 2.01
Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit. Genes Dev (2009) 1.91
Systems biology of innate immunity. Immunol Rev (2009) 1.87
Targets of the Gal4 transcription activator in functional transcription complexes. Mol Cell Biol (2005) 1.68
The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol (2009) 1.64
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci U S A (2007) 1.60
Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J Proteome Res (2008) 1.53
Association of calcineurin with the COPI protein Sec28 and the COPII protein Sec13 revealed by quantitative proteomics. PLoS One (2011) 1.52
Advances in protein complex analysis using mass spectrometry. J Physiol (2004) 1.51
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol (2006) 1.45
Dynamic changes in protein-protein interaction and protein phosphorylation probed with amine-reactive isotope tag. Mol Cell Proteomics (2005) 1.39
Mediator coordinates PIC assembly with recruitment of CHD1. Genes Dev (2011) 1.28
Advances in proteomic workflows for systems biology. Curr Opin Biotechnol (2007) 1.26
Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes. Protein Sci (2005) 1.23
Revealing novel telomere proteins using in vivo cross-linking, tandem affinity purification, and label-free quantitative LC-FTICR-MS. Mol Cell Proteomics (2010) 1.22
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21
SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. J Proteome Res (2012) 1.20
Mitogen-induced recruitment of ERK and MSK to SRE promoter complexes by ternary complex factor Elk-1. Nucleic Acids Res (2008) 1.18
Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell (2011) 1.18
Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol Cell Biol (2004) 1.17
Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genet (2012) 1.13
Mass spectrometry-based approaches toward absolute quantitative proteomics. Curr Genomics (2008) 1.10
Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics (2014) 1.07
Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics (2011) 1.05
Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes. Mol Cell Biol (2008) 1.01
Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2. Mol Cell Biol (2004) 0.99
Proteomics of the peroxisome. Biochim Biophys Acta (2006) 0.97
Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev (2005) 0.97
Exploring the spatial and temporal organization of a cell's proteome. J Struct Biol (2010) 0.97
Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. J Neurosci (2013) 0.96
Multiple sequence-specific DNA-binding proteins mediate estrogen receptor signaling through a tethering pathway. Mol Endocrinol (2011) 0.95
Atbf1 is required for the Pit1 gene early activation. Proc Natl Acad Sci U S A (2008) 0.94
Dicer-dependent and -independent Argonaute2 protein interaction networks in mammalian cells. Mol Cell Proteomics (2012) 0.94
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics (2012) 0.92
Triple SILAC to determine stimulus specific interactions in the Wnt pathway. J Proteome Res (2011) 0.91
Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J (2004) 0.90
A profile of differentially abundant proteins at the yeast cell periphery during pseudohyphal growth. J Biol Chem (2010) 0.90
Systematic prediction of human membrane receptor interactions. Proteomics (2009) 0.90
Protein footprinting in a complex milieu: identifying the interaction surfaces of the chemotaxis adaptor protein CheW. J Mol Biol (2011) 0.89
ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. Nucleic Acids Res (2015) 0.87
Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res (2009) 0.86
Proteomic studies of Syk-interacting proteins using a novel amine-specific isotope tag and GFP nanotrap. J Am Soc Mass Spectrom (2011) 0.86
Genomics meets proteomics: identifying the culprits in disease. Hum Genet (2013) 0.86
Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry. J Am Soc Mass Spectrom (2010) 0.85
SynCAM1, a synaptic adhesion molecule, is expressed in astrocytes and contributes to erbB4 receptor-mediated control of female sexual development. Endocrinology (2011) 0.84
Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Bioorg Med Chem (2006) 0.83
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proc Natl Acad Sci U S A (2013) 0.83
Quantitative neuroproteomics of the synapse. Methods Mol Biol (2010) 0.82
In vitro transcription and immobilized template analysis of preinitiation complexes. Curr Protoc Mol Biol (2012) 0.82
Proteomic analysis demonstrates activator- and chromatin-specific recruitment to promoters. J Biol Chem (2012) 0.82
PICquant: a quantitative platform to measure differential peptide abundance using dual-isotopic labeling with 12C6- and 13C6-phenyl isocyanate. Anal Chem (2010) 0.81
Proteomic analyses to identify novel therapeutic targets for the treatment of advanced prostate cancer. Cellscience (2006) 0.81
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). Biochem Cell Biol (2008) 0.81
Streamline proteomic approach for characterizing protein-protein interaction network in a RAD52 protein complex. J Proteome Res (2009) 0.81
Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis. Nucleic Acids Res (2012) 0.80
CTGC motifs within the HIV core promoter specify Tat-responsive pre-initiation complexes. Retrovirology (2012) 0.80
The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci (2012) 0.79
Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2. Mol Cell Proteomics (2009) 0.79
Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clin Proteomics (2008) 0.79
Proteomic-based identification of CD4-interacting proteins in human primary macrophages. PLoS One (2011) 0.79
Measuring dissociation rate constants of protein complexes through subunit exchange: experimental design and theoretical modeling. PLoS One (2011) 0.78
APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res (2016) 0.77
Matching isotopic distributions from metabolically labeled samples. Bioinformatics (2008) 0.77
RABA (reductive alkylation by acetone): a novel stable isotope labeling approach for quantitative proteomics. J Am Soc Mass Spectrom (2009) 0.77
An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. EMBO J (2015) 0.77
Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling. Mol Cell Proteomics (2017) 0.75
Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy. Methods Mol Biol (2016) 0.75
A database of optimized proteomic quantitative methods for 284 human drug disposition related proteins for applications in PBPK modeling. CPT Pharmacometrics Syst Pharmacol (2017) 0.75
Proteomics in the investigation of HIV-1 interactions with host proteins. Proteomics Clin Appl (2015) 0.75
Proteomic insights into cardiac cell death and survival. Proteomics Clin Appl (2008) 0.75
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
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
A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe (2010) 4.98
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
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
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res (2006) 4.32
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
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
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
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
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
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics (2006) 3.32
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
The B7 family member B7-H6 is a tumor cell ligand for the activating natural killer cell receptor NKp30 in humans. J Exp Med (2009) 3.17
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics (2008) 3.13
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
Genetic basis of proteome variation in yeast. Nat Genet (2007) 3.04
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
A data integration methodology for systems biology. Proc Natl Acad Sci U S A (2005) 2.93
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
MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics (2008) 2.89
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol Microbiol (2007) 2.87
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
Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol (2009) 2.70
Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biol (2007) 2.68
Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol (2006) 2.66
Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell Biol (2004) 2.65
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
Experimental protein mixture for validating tandem mass spectral analysis. OMICS (2002) 2.54
A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet (2004) 2.54
Code developments to improve the efficiency of automated MS/MS spectra interpretation. J Proteome Res (2003) 2.53
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet (2009) 2.44