Published in J Proteome Res on March 02, 2012
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics (2014) 5.09
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods (2015) 1.77
SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. J Proteomics (2013) 1.27
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20
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
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98
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
Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. FEBS Lett (2012) 0.86
From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. Proteomics (2014) 0.81
The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae. Mol Biosyst (2014) 0.81
TRAF1 Coordinates Polyubiquitin Signaling to Enhance Epstein-Barr Virus LMP1-Mediated Growth and Survival Pathway Activation. PLoS Pathog (2015) 0.81
Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (2016) 0.78
APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res (2016) 0.77
Immunoprecipitation and mass spectrometry defines an extensive RBM45 protein-protein interaction network. Brain Res (2016) 0.76
SIRT2 regulates nuclear envelope reassembly via ANKLE2 deacetylation. J Cell Sci (2016) 0.75
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. BMC Bioinformatics (2013) 0.75
Data Independent Acquisition analysis in ProHits 4.0. J Proteomics (2016) 0.75
Proteomic network analysis of human uterine smooth muscle in pregnancy, labor, and preterm labor. Integr Mol Med (2015) 0.75
msVolcano: A flexible web application for visualizing quantitative proteomics data. Proteomics (2016) 0.75
The CLASP2 Protein Interaction Network in Adipocytes Links CLIP2 to AGAP3, CLASP2 to G2L1, MARK2, and SOGA1, and Identifies SOGA1 as a Microtubule-Associated Protein. Mol Cell Proteomics (2017) 0.75
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
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
Mass spectrometry-based proteomics. Nature (2003) 28.94
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Global quantification of mammalian gene expression control. Nature (2011) 22.36
Defining the human deubiquitinating enzyme interaction landscape. Cell (2009) 11.39
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16
Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics (2005) 6.37
A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95
Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol (2007) 4.70
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol (2003) 3.54
Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol (2008) 3.53
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics (2006) 3.35
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23
Analysis of the human endogenous coregulator complexome. Cell (2011) 2.97
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
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
The study of macromolecular complexes by quantitative proteomics. Nat Genet (2003) 2.44
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res (2007) 2.09
Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor. Nat Biotechnol (2011) 1.90
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci U S A (2007) 1.60
Affinity-purification mass spectrometry (AP-MS) of serine/threonine phosphatases. Methods (2007) 1.51
Mapping multiprotein complexes by affinity purification and mass spectrometry. Curr Opin Biotechnol (2008) 1.36
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol Cell Proteomics (2009) 1.28
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol (2011) 1.12
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. Mol Syst Biol (2010) 0.99
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A (2009) 3.82
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50
Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics (2008) 3.12
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
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
Experimental protein mixture for validating tandem mass spectral analysis. OMICS (2002) 2.54
NSs protein of rift valley fever virus induces the specific degradation of the double-stranded RNA-dependent protein kinase. J Virol (2009) 2.39
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal (2010) 2.36
False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res (2007) 2.36
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. J Proteome Res (2007) 2.33
ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol (2010) 2.22
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res (2007) 2.09
Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. J Proteome Res (2008) 1.81
Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J Proteome Res (2006) 1.69
Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations. Nat Cell Biol (2011) 1.69
Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nat Struct Mol Biol (2013) 1.67
The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol (2013) 1.63
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci U S A (2007) 1.60
SAM68 regulates neuronal activity-dependent alternative splicing of neurexin-1. Cell (2011) 1.60
Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. EMBO J (2009) 1.51
Quantitative interaction proteomics using mass spectrometry. Nat Methods (2009) 1.47
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol (2006) 1.45
Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics (2013) 1.39
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J Proteome Res (2012) 1.39
Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol (2004) 1.38
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics (2011) 1.24
Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. Proteomics (2011) 1.24
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics (2009) 1.23
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20
Combining results of multiple search engines in proteomics. Mol Cell Proteomics (2013) 1.20
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res (2011) 1.19
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics (2005) 1.17
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. J Proteome Res (2008) 1.17
Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics (2007) 1.17
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. PLoS One (2009) 1.14
Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. Mol Cell Proteomics (2009) 1.13
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol (2011) 1.12
Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics (2010) 1.10
"Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response. PLoS One (2010) 1.10
Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics (2007) 1.09
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. BMC Bioinformatics (2010) 1.05
A novel capture compound for the identification and analysis of cyclic di-GMP binding proteins. J Proteomics (2012) 1.01
Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. Mol Syst Biol (2010) 0.99
Global analysis of protein palmitoylation in African trypanosomes. Eukaryot Cell (2010) 0.97
Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res (2009) 0.95
Proteomic study of the mucin granulae in an intestinal goblet cell model. J Proteome Res (2012) 0.95
A dual role for receptor-interacting protein kinase 2 (RIP2) kinase activity in nucleotide-binding oligomerization domain 2 (NOD2)-dependent autophagy. J Biol Chem (2012) 0.94
Investigation of neutral loss during collision-induced dissociation of peptide ions. Anal Chem (2005) 0.94
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. BMC Bioinformatics (2012) 0.93
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. Curr Protoc Bioinformatics (2012) 0.92
SUMOylation pathway in Trypanosoma cruzi: functional characterization and proteomic analysis of target proteins. Mol Cell Proteomics (2011) 0.92
Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites. J Proteome Res (2014) 0.91
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. J Proteome Res (2014) 0.91
Reconstructing targetable pathways in lung cancer by integrating diverse omics data. Nat Commun (2013) 0.90
LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics (2013) 0.88
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics (2010) 0.88
The nucleotide synthesis enzyme CAD inhibits NOD2 antibacterial function in human intestinal epithelial cells. Gastroenterology (2012) 0.88
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. BMC Bioinformatics (2010) 0.86
Lipid raft proteins and their identification in T lymphocytes. Subcell Biochem (2004) 0.85
An experimental strategy for the identification of AMPylation targets from complex protein samples. Proteomics (2014) 0.83
Improved sequence tag generation method for peptide identification in tandem mass spectrometry. J Proteome Res (2008) 0.83
Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics. J Proteome Res (2013) 0.82
Prestroke proteomic changes in cerebral microvessels in stroke-prone, transgenic[hCETP]-Hyperlipidemic, Dahl salt-sensitive hypertensive rats. Mol Med (2011) 0.82
Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. J Mass Spectrom (2007) 0.78
Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma. PLoS One (2011) 0.78
Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. Methods Mol Biol (2008) 0.77
Sparsely correlated hidden Markov models with application to genome-wide location studies. Bioinformatics (2013) 0.77
Correction to "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells". J Proteome Res (2016) 0.77
Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer. Mol Cell Proteomics (2013) 0.76
Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro. Sci Rep (2017) 0.75
Identification of Novel Host Interactors of Effectors Secreted by Salmonella and Citrobacter. mSystems (2016) 0.75
Antibody Binding Alters the Characteristics and Contents of Extracellular Vesicles Released by Histoplasma capsulatum. mSphere (2016) 0.75