Published in Nat Rev Mol Cell Biol on August 01, 2007
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Probing cellular protein complexes using single-molecule pull-down. Nature (2011) 3.92
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
RASSF1A elicits apoptosis through an MST2 pathway directing proapoptotic transcription by the p73 tumor suppressor protein. Mol Cell (2007) 3.47
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics (2010) 3.44
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
Proteomics: a pragmatic perspective. Nat Biotechnol (2010) 2.81
Mass spectrometry-based proteomics in cell biology. J Cell Biol (2010) 2.66
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
Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet (2012) 2.39
ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol (2010) 2.22
Quantitative proteomics of the Cav2 channel nano-environments in the mammalian brain. Proc Natl Acad Sci U S A (2010) 1.85
Molecular architecture of human polycomb repressive complex 2. Elife (2012) 1.64
Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry. Mol Cell Proteomics (2008) 1.58
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods (2013) 1.56
Quantitative interaction proteomics using mass spectrometry. Nat Methods (2009) 1.47
A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics (2010) 1.41
The transience of transient overexpression. Nat Methods (2013) 1.41
Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat Methods (2013) 1.41
Charting the molecular network of the drug target Bcr-Abl. Proc Natl Acad Sci U S A (2009) 1.37
Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins. Mol Cell Proteomics (2008) 1.36
Mapping and analysis of phosphorylation sites: a quick guide for cell biologists. Mol Biol Cell (2013) 1.33
PP4R4/KIAA1622 forms a novel stable cytosolic complex with phosphoprotein phosphatase 4. J Biol Chem (2008) 1.31
Single-molecule pull-down for studying protein interactions. Nat Protoc (2012) 1.30
Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics (2010) 1.28
Gemin5 delivers snRNA precursors to the SMN complex for snRNP biogenesis. Mol Cell (2010) 1.27
Mapping the local protein interactome of the NuA3 histone acetyltransferase. Protein Sci (2009) 1.25
Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. Proteomics (2011) 1.24
Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Mol Cell Proteomics (2009) 1.24
Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation. EMBO Rep (2011) 1.24
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
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20
Defining the budding yeast chromatin-associated interactome. Mol Syst Biol (2010) 1.19
A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells. Mol Cell Proteomics (2014) 1.18
Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking. Proc Natl Acad Sci U S A (2007) 1.17
Evolutionary descent of prion genes from the ZIP family of metal ion transporters. PLoS One (2009) 1.17
Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry. Proteome Sci (2010) 1.14
A new cross-linking strategy: protein interaction reporter (PIR) technology for protein-protein interaction studies. Mol Biosyst (2010) 1.14
Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genet (2012) 1.13
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. Mol Cell Proteomics (2010) 1.13
Stringent analysis of gene function and protein-protein interactions using fluorescently tagged genes. Genetics (2011) 1.11
In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers. J Proteome Res (2008) 1.10
Mass spectrometry-based approaches toward absolute quantitative proteomics. Curr Genomics (2008) 1.10
Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Mol Syst Biol (2013) 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
The Pseudomonas aeruginosa N-acylhomoserine lactone quorum sensing molecules target IQGAP1 and modulate epithelial cell migration. PLoS Pathog (2012) 1.05
Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics (2012) 1.04
Quantitative proteomics reveals a dynamic association of proteins to detergent-resistant membranes upon elicitor signaling in tobacco. Mol Cell Proteomics (2009) 1.04
Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Mol Cell Proteomics (2013) 1.04
Computational modeling of mammalian signaling networks. Wiley Interdiscip Rev Syst Biol Med (2010) 1.04
Odin (ANKS1A) is a Src family kinase target in colorectal cancer cells. Cell Commun Signal (2008) 1.03
Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. Mol Cell Proteomics (2011) 1.02
In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med (2010) 1.01
Host-Microbe Protein Interactions during Bacterial Infection. Chem Biol (2015) 1.01
Deciphering preferential interactions within supramolecular protein complexes: the proteasome case. Mol Syst Biol (2015) 1.00
A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies. Anal Chem (2010) 1.00
Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. Mol Syst Biol (2010) 0.99
XLink-DB: database and software tools for storing and visualizing protein interaction topology data. J Proteome Res (2013) 0.99
Androgen receptor requires JunD as a coactivator to switch on an oxidative stress generation pathway in prostate cancer cells. Cancer Res (2010) 0.98
Chronic ethanol feeding affects proteasome-interacting proteins. Proteomics (2009) 0.98
Analysis of stable and transient protein-protein interactions. Methods Mol Biol (2012) 0.98
DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res (2010) 0.98
Systems cell biology. J Cell Biol (2014) 0.97
In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. Plant Cell (2016) 0.96
The proteomic profile of circulating pentraxin 3 (PTX3) complex in sepsis demonstrates the interaction with azurocidin 1 and other components of neutrophil extracellular traps. Mol Cell Proteomics (2012) 0.96
Lesson from the stoichiometry determination of the cohesin complex: a short protease mediated elution increases the recovery from cross-linked antibody-conjugated beads. J Proteome Res (2010) 0.96
Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry. J Proteome Res (2011) 0.96
A method to resolve the composition of heterogeneous affinity-purified protein complexes assembled around a common protein by chemical cross-linking, gel electrophoresis and mass spectrometry. Nat Protoc (2012) 0.95
Affinity purification strategy to capture human endogenous proteasome complexes diversity and to identify proteasome-interacting proteins. Mol Cell Proteomics (2009) 0.94
Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway. Mol Syst Biol (2009) 0.94
Construction and analysis of protein-protein interaction networks. Autom Exp (2010) 0.94
Proteome-wide identification of novel binding partners to the oncogenic fusion gene protein, NPM-ALK, using tandem affinity purification and mass spectrometry. Am J Pathol (2009) 0.94
Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. Methods (2013) 0.94
Dicer-dependent and -independent Argonaute2 protein interaction networks in mammalian cells. Mol Cell Proteomics (2012) 0.94
The SUMO-specific isopeptidase SENP2 associates dynamically with nuclear pore complexes through interactions with karyopherins and the Nup107-160 nucleoporin subcomplex. Mol Biol Cell (2011) 0.93
Toll-like receptor 9 protects non-immune cells from stress by modulating mitochondrial ATP synthesis through the inhibition of SERCA2. EMBO Rep (2014) 0.93
High-throughput analysis of peptide-binding modules. Proteomics (2012) 0.93
Characterization of molecules binding to the 70K N-terminal region of fibronectin by IFAST purification coupled with mass spectrometry. J Proteome Res (2013) 0.93
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. Curr Protoc Bioinformatics (2012) 0.92
Distinct roles of FKF1, Gigantea, and Zeitlupe proteins in the regulation of Constans stability in Arabidopsis photoperiodic flowering. Proc Natl Acad Sci U S A (2014) 0.92
Triple SILAC to determine stimulus specific interactions in the Wnt pathway. J Proteome Res (2011) 0.91
Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes. Anal Chem (2009) 0.91
Effective identification of Akt interacting proteins by two-step chemical crosslinking, co-immunoprecipitation and mass spectrometry. PLoS One (2013) 0.91
Quantitation of the dynamic profiles of the innate immune response using multiplex selected reaction monitoring-mass spectrometry. Mol Cell Proteomics (2013) 0.90
Madm (Mlf1 adapter molecule) cooperates with Bunched A to promote growth in Drosophila. J Biol (2010) 0.90
Quaternary diamines as mass spectrometry cleavable crosslinkers for protein interactions. J Am Soc Mass Spectrom (2011) 0.89
Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies. Anal Chim Acta (2008) 0.89
T cell Ig and mucin domain-containing protein 3 is recruited to the immune synapse, disrupts stable synapse formation, and associates with receptor phosphatases. J Immunol (2013) 0.89
Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics (2013) 0.88
Plant protein-protein interaction network and interactome. Curr Genomics (2010) 0.88
When one and one gives more than two: challenges and opportunities of integrative omics. Front Genet (2012) 0.88
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. BMC Syst Biol (2011) 0.88
Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions. Anal Chem (2012) 0.87
Extending the dynamic range of label-free mass spectrometric quantification of affinity purifications. Mol Cell Proteomics (2011) 0.87
Proteomic studies of Syk-interacting proteins using a novel amine-specific isotope tag and GFP nanotrap. J Am Soc Mass Spectrom (2011) 0.86
Unraveling the histone's potential: a proteomics perspective. Epigenetics (2008) 0.86
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
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
Arsenic degrades PML or PML-RARalpha through a SUMO-triggered RNF4/ubiquitin-mediated pathway. Nat Cell Biol (2008) 4.68
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
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
The mTOR/PI3K and MAPK pathways converge on eIF4B to control its phosphorylation and activity. EMBO J (2006) 3.57
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
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
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
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
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Nat Struct Mol Biol (2011) 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
A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet (2004) 2.54
PIMS modulates immune tolerance by negatively regulating Drosophila innate immune signaling. Cell Host Microbe (2008) 2.48
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet (2009) 2.44
The study of macromolecular complexes by quantitative proteomics. Nat Genet (2003) 2.44
NSs protein of rift valley fever virus induces the specific degradation of the double-stranded RNA-dependent protein kinase. J Virol (2009) 2.39
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS (2006) 2.38
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
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal (2010) 2.36
An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol Cell Proteomics (2008) 2.35
Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science (2012) 2.34
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell (2004) 2.34
Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell (2013) 2.33
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry. Cell (2011) 2.28
Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol (2009) 2.25
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics (2008) 2.23