Published in Anal Chem on April 01, 2002
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci U S A (2006) 4.44
Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 2.73
Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci U S A (2002) 2.27
Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol Syst Biol (2007) 1.73
iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res (2007) 1.71
15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res (2007) 1.58
Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol. J Proteome Res (2007) 1.55
Recent highlights in antimalarial drug resistance and chemotherapy research. Trends Parasitol (2008) 1.52
Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics (2006) 1.49
Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol (2006) 1.47
Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop. Genes Dev (2007) 1.43
Quantitative proteomics by metabolic labeling of model organisms. Mol Cell Proteomics (2009) 1.42
ZoomQuant: an application for the quantitation of stable isotope labeled peptides. J Am Soc Mass Spectrom (2005) 1.41
Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res (2007) 1.39
Differential protein expression by Porphyromonas gingivalis in response to secreted epithelial cell components. Proteomics (2005) 1.39
Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res (2008) 1.39
Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans. J Bacteriol (2006) 1.38
Quantitative proteomics of intracellular Porphyromonas gingivalis. Proteomics (2007) 1.33
Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics. Analyst (2006) 1.29
Identification of novel chondroitin proteoglycans in Caenorhabditis elegans: embryonic cell division depends on CPG-1 and CPG-2. J Cell Biol (2006) 1.29
A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS. J Proteome Res (2007) 1.29
Proteomics of Porphyromonas gingivalis within a model oral microbial community. BMC Microbiol (2009) 1.28
Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol (2015) 1.26
Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions. Proteomics (2008) 1.20
Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: non-label methods comparison, q-values and LOWESS curve fitting. Int J Mass Spectrom (2007) 1.20
Search engine processor: Filtering and organizing peptide spectrum matches. Proteomics (2012) 1.15
CAND1 controls in vivo dynamics of the cullin 1-RING ubiquitin ligase repertoire. Nat Commun (2013) 1.14
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13
Quantitative shotgun proteomics using a uniform ¹⁵N-labeled standard to monitor proteome dynamics in time course experiments reveals new insights into the heat stress response of Chlamydomonas reinhardtii. Mol Cell Proteomics (2011) 1.12
Mass spectrometry-based approaches toward absolute quantitative proteomics. Curr Genomics (2008) 1.10
Analyzing shotgun proteomic data with PatternLab for proteomics. Curr Protoc Bioinformatics (2010) 1.10
Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis. BMC Microbiol (2009) 1.09
Protein abundance ratios for global studies of prokaryotes. Proteomics (2007) 1.09
Cancer proteomics by quantitative shotgun proteomics. Mol Oncol (2007) 1.08
Comparative transcriptional and translational analysis of leptospiral outer membrane protein expression in response to temperature. PLoS Negl Trop Dis (2009) 1.08
Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One (2012) 1.07
Comparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures. J Am Soc Mass Spectrom (2009) 1.01
Combining low and high mass ion accumulation for enhancing shotgun proteome analysis by accurate mass measurement. J Am Soc Mass Spectrom (2006) 1.01
Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant". J Am Soc Mass Spectrom (2005) 1.01
Metalloendoprotease cleavage triggers gelsolin amyloidogenesis. EMBO J (2005) 1.00
Proteomic analysis of Bifidobacterium longum subsp. infantis reveals the metabolic insight on consumption of prebiotics and host glycans. PLoS One (2013) 0.97
Identification of quantitative trait loci underlying proteome variation in human lymphoblastoid cells. Mol Cell Proteomics (2010) 0.97
Mass spectrometry-based proteomics and its application to studies of Porphyromonas gingivalis invasion and pathogenicity. Infect Disord Drug Targets (2006) 0.94
Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution. Proc Natl Acad Sci U S A (2009) 0.94
Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry. J Proteomics (2010) 0.92
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database. BMC Microbiol (2009) 0.91
Verification of single-peptide protein identifications by the application of complementary database search algorithms. J Biomol Tech (2006) 0.91
A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development. Proteome Sci (2010) 0.91
UNiquant, a program for quantitative proteomics analysis using stable isotope labeling. J Proteome Res (2011) 0.90
Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides. Anal Chem (2009) 0.90
Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy. J Bacteriol (2010) 0.89
Microbial proteomics: a mass spectrometry primer for biologists. Microb Cell Fact (2007) 0.88
A label-free quantitative shotgun proteomics analysis of rice grain development. Proteome Sci (2011) 0.87
Tools for interpreting large-scale protein profiling in microbiology. J Dent Res (2008) 0.87
DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. Nucleic Acids Res (2005) 0.87
RAPID AND AUTOMATED PROCESSING OF MALDI-FTICR/MS DATA FOR N-METABOLIC LABELING IN A SHOTGUN PROTEOMICS ANALYSIS. Int J Mass Spectrom (2009) 0.86
Comparative transcriptomic and proteomic profiling of industrial wine yeast strains. Appl Environ Microbiol (2010) 0.85
Science, marketing and wishful thinking in quantitative proteomics. Proteomics (2008) 0.85
Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. Curr Protoc Bioinformatics (2005) 0.84
Characterizing the altered cellular proteome induced by the stress-independent activation of heat shock factor 1. ACS Chem Biol (2014) 0.84
Global survey of protein expression during gonadal sex determination in mice. Mol Cell Proteomics (2009) 0.83
Identification of a novel proliferation-related protein, WHSC1 4a, in human gliomas. Neuro Oncol (2008) 0.83
Quantitative proteomics using reductive dimethylation for stable isotope labeling. J Vis Exp (2014) 0.83
The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J Am Chem Soc (2013) 0.82
Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-Orbitrap Velos mass spectrometry, and pathway analysis. J Proteome Res (2012) 0.81
PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. J Proteome Res (2014) 0.81
Molecular targets for 17α-ethynyl-5-androstene-3β,7β,17β-triol, an anti-inflammatory agent derived from the human metabolome. PLoS One (2012) 0.81
Keck Foundation Biotechnology Resource Laboratory, Yale University. Yale J Biol Med (2007) 0.80
Seasonal liver protein differences in a hibernator revealed by quantitative proteomics using whole animal isotopic labeling. Comp Biochem Physiol Part D Genomics Proteomics (2011) 0.80
Neuroproteomics as a promising tool in Parkinson's disease research. J Neural Transm (Vienna) (2008) 0.79
Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol (2015) 0.79
Development of a 45kpsi ultrahigh pressure liquid chromatography instrument for gradient separations of peptides using long microcapillary columns and sub-2μm particles. J Chromatogr A (2016) 0.78
From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics. J Am Soc Mass Spectrom (2015) 0.78
Proteomic Characterization of Cerebrospinal Fluid from Ataxia-Telangiectasia (A-T) Patients Using a LC/MS-Based Label-Free Protein Quantification Technology. Int J Proteomics (2011) 0.78
Proteomic analysis of signaling network regulation in renal cell carcinomas with differential hypoxia-inducible factor-2α expression. PLoS One (2013) 0.78
RABA (reductive alkylation by acetone): a novel stable isotope labeling approach for quantitative proteomics. J Am Soc Mass Spectrom (2009) 0.77
Infrared multiphoton dissociation for quantitative shotgun proteomics. Anal Chem (2012) 0.77
Quantitative proteomics employing primary amine affinity tags. J Biomol Tech (2003) 0.76
Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case. Proteomics (2015) 0.76
Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics. Curr Protoc Bioinformatics (2016) 0.75
Understanding cell signaling in cancer stem cells for targeted therapy - can phosphoproteomics help to reveal the secrets? Cell Commun Signal (2017) 0.75
A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme. Front Oncol (2016) 0.75
Identifying Predictors of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-Based Proteomics Technology. PLoS One (2015) 0.75
PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data. Mol Cell Proteomics (2016) 0.75
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
Wnt proteins are lipid-modified and can act as stem cell growth factors. Nature (2003) 12.54
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2003) 12.31
A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
A role for the P-body component GW182 in microRNA function. Nat Cell Biol (2005) 7.54
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol (2006) 6.85
A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol (2003) 6.32
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell (2002) 5.91
A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev (2004) 5.23
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature (2005) 5.15
Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell (2009) 5.05
Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. Cell (2006) 5.01
DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med (2011) 4.98
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science (2004) 4.97
The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell (2004) 4.91
The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol (2006) 4.89
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom (2004) 4.76
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods (2004) 4.62
Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative regulation of focal adhesion maturation. Nat Cell Biol (2011) 4.59
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell (2009) 4.57
Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature (2008) 4.52
Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell (2006) 4.50
Global analysis of protein palmitoylation in yeast. Cell (2006) 4.43
PRAK is essential for ras-induced senescence and tumor suppression. Cell (2007) 4.30
The biological impact of mass-spectrometry-based proteomics. Nature (2007) 4.24
Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell (2007) 4.22
Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell (2009) 4.22
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting. Am J Obstet Gynecol (2011) 4.18
Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network. Dev Cell (2007) 4.17
The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem (2003) 4.13
Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem (2002) 3.86
Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry. Science (2008) 3.77
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci U S A (2002) 3.70
Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science (2003) 3.64
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods (2004) 3.62
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
Molecular architecture of the human pre-mRNA 3' processing complex. Mol Cell (2009) 3.52
Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science (2007) 3.46
Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface. Mol Cell (2010) 3.44
Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell (2009) 3.43
A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods (2008) 3.35
A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. J Cell Biol (2005) 3.18
DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med (2012) 3.18
Chemical and biological approaches synergize to ameliorate protein-folding diseases. Cell (2008) 3.11
Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proc Natl Acad Sci U S A (2007) 3.08
Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science (2006) 3.05
A streamlined platform for high-content functional proteomics of primary human specimens. Nat Methods (2005) 3.00
Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol (2004) 2.98
Architecture of the budding yeast kinetochore reveals a conserved molecular core. J Cell Biol (2003) 2.92
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem (2003) 2.91
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem (2003) 2.89
Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes. Curr Biol (2005) 2.86
TOR complex 2 integrates cell movement during chemotaxis and signal relay in Dictyostelium. Mol Biol Cell (2005) 2.76
GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem (2003) 2.74
Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 2.73
Automatic quality assessment of peptide tandem mass spectra. Bioinformatics (2004) 2.70
Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nat Chem Biol (2009) 2.70
Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity. Dev Cell (2005) 2.65
The application of mass spectrometry to membrane proteomics. Nat Biotechnol (2003) 2.61
Global analysis of protein sumoylation in Saccharomyces cerevisiae. J Biol Chem (2004) 2.60
LRRTM2 interacts with Neurexin1 and regulates excitatory synapse formation. Neuron (2009) 2.60
Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Mol Cell Biol (2004) 2.55
Code developments to improve the efficiency of automated MS/MS spectra interpretation. J Proteome Res (2003) 2.53
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 2.53
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
Digestion and depletion of abundant proteins improves proteomic coverage. Nat Methods (2012) 2.48
Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem (2003) 2.48
Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol (2005) 2.40
Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem (2004) 2.40
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38
Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinformatics (2007) 2.37
Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science (2009) 2.37
ZW10 links mitotic checkpoint signaling to the structural kinetochore. J Cell Biol (2005) 2.36
Attenuation of a phosphorylation-dependent activator by an HDAC-PP1 complex. Nat Struct Biol (2003) 2.32
Mass spectrometry for proteomics. Curr Opin Chem Biol (2008) 2.31
Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain. Nat Cell Biol (2004) 2.30
A hormone-dependent module regulating energy balance. Cell (2011) 2.30
PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant J (2009) 2.29
Molecular analysis of kinetochore architecture in fission yeast. EMBO J (2005) 2.29
Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci U S A (2002) 2.27
Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA. Cell (2002) 2.23
Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem (2003) 2.20
One-step affinity purification of the yeast ribosome and its associated proteins and mRNAs. RNA (2002) 2.19
Sirt1 mediates neuroprotection from mutant huntingtin by activation of the TORC1 and CREB transcriptional pathway. Nat Med (2011) 2.17
Adaptation of energy metabolism in breast cancer brain metastases. Cancer Res (2007) 2.17
The human kinetochore Ska1 complex facilitates microtubule depolymerization-coupled motility. Dev Cell (2009) 2.14
PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics (2008) 2.13
TFG-1 function in protein secretion and oncogenesis. Nat Cell Biol (2011) 2.13