Published in Proteomics on December 01, 2008
Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics (2014) 5.09
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84
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L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity. Cell (2016) 2.28
Spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome. J Cell Biol (2011) 2.23
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol Cell Proteomics (2013) 1.60
Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics (2012) 1.55
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva. J Proteome Res (2009) 1.42
Single muscle fiber proteomics reveals unexpected mitochondrial specialization. EMBO Rep (2015) 1.37
Proteomic changes resulting from gene copy number variations in cancer cells. PLoS Genet (2010) 1.32
miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun (2015) 1.18
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res (2011) 1.14
Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3. PLoS One (2012) 1.13
The human leukocyte antigen-presented ligandome of B lymphocytes. Mol Cell Proteomics (2013) 1.13
Expanding the dipeptidyl peptidase 4-regulated peptidome via an optimized peptidomics platform. J Am Chem Soc (2010) 1.12
Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J Proteome Res (2009) 1.11
Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast). Mol Cell Proteomics (2014) 1.06
Enhanced mass spectrometric mapping of the human GalNAc-type O-glycoproteome with SimpleCells. Mol Cell Proteomics (2013) 1.04
Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors. Mol Cell Proteomics (2015) 0.99
Proteome sequencing goes deep. Curr Opin Chem Biol (2014) 0.94
Spatial distribution of cellular function: the partitioning of proteins between mitochondria and the nucleus in MCF7 breast cancer cells. J Proteome Res (2012) 0.93
Sub-proteomic fractionation, iTRAQ, and OFFGEL-LC-MS/MS approaches to cardiac proteomics. J Proteomics (2010) 0.90
Stabilization of p21 (Cip1/WAF1) following Tip60-dependent acetylation is required for p21-mediated DNA damage response. Cell Death Differ (2012) 0.89
Systematic comparison of fractionation methods for in-depth analysis of plasma proteomes. J Proteome Res (2012) 0.88
Optimization of iTRAQ labelling coupled to OFFGEL fractionation as a proteomic workflow to the analysis of microsomal proteins of Medicago truncatula roots. Proteome Sci (2012) 0.88
Characterization of the E. coli proteome and its modifications during growth and ethanol stress. Front Microbiol (2015) 0.88
Label-free quantitative proteomics and N-glycoproteomics analysis of KRAS-activated human bronchial epithelial cells. Mol Cell Proteomics (2012) 0.87
Sample preparation techniques for the untargeted LC-MS-based discovery of peptides in complex biological matrices. J Biomed Biotechnol (2011) 0.87
Protein composition of bronchoalveolar lavage fluid and airway surface liquid from newborn pigs. Am J Physiol Lung Cell Mol Physiol (2013) 0.86
Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. J Proteome Res (2012) 0.85
Comparison of strong cation exchange and SDS-PAGE fractionation for analysis of multiprotein complexes. J Proteome Res (2010) 0.85
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 approaches to understanding the role of the cytoskeleton in host-defense mechanisms. Expert Rev Proteomics (2011) 0.81
Proteomic comparison of mcf-7 tumoursphere and monolayer cultures. PLoS One (2012) 0.80
Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times. J Proteome Res (2013) 0.79
Proteomics, metabolomics, and protein interactomics in the characterization of the molecular features of major depressive disorder. Dialogues Clin Neurosci (2014) 0.78
Changes in the Plasma Proteome of Manduca sexta Larvae in Relation to the Transcriptome Variations after an Immune Challenge: Evidence for High Molecular Weight Immune Complex Formation. Mol Cell Proteomics (2016) 0.78
Combining isoelectric point-based fractionation, liquid chromatography and mass spectrometry to improve peptide detection and protein identification. J Am Soc Mass Spectrom (2010) 0.77
Comparing cellular proteomes by mass spectrometry. Genome Biol (2009) 0.75
Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis. Clin Proteomics (2011) 0.75
MS-analysis of SILAC-labeled MYC-driven B lymphoma cells overexpressing miR-17-19b. Data Brief (2016) 0.75
IQcat: multiplexed protein quantification by isoelectric QconCAT. Proteomics (2012) 0.75
In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins. Oncotarget (2016) 0.75
Dataset of proteins mapped on HepG2 cells and those differentially abundant after expression of the dengue non-structural 1 protein. Data Brief (2016) 0.75
Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing. BMC Bioinformatics (2010) 0.75
Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics. Mol Cell Proteomics (2017) 0.75
Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology. Proteomes (2016) 0.75
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
Mass spectrometry-based proteomics. Nature (2003) 28.94
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science (2009) 20.49
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88
In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc (2006) 16.56
Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res (2011) 14.82
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem (2003) 13.58
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67
Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 10.28
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Proteomic characterization of the human centrosome by protein correlation profiling. Nature (2003) 8.74
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52
Nucleolar proteome dynamics. Nature (2005) 7.32
Directed proteomic analysis of the human nucleolus. Curr Biol (2002) 7.04
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell (2007) 6.62
Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature (2002) 6.26
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6. Nature (2005) 5.72
Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 5.22
A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc (2006) 5.21
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04
SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell (2008) 5.02
Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A (2003) 4.87
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84
Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics (2004) 4.79
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol (2007) 4.66
A mammalian organelle map by protein correlation profiling. Cell (2006) 4.54
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell (2010) 4.31
The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol (2004) 4.24
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Paraspeckles: a novel nuclear domain. Curr Biol (2002) 4.19
Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity (2010) 4.03
Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathway. Genes Dev (2002) 3.80
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol (2006) 3.79
Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics (2008) 3.78
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology. Cell (2005) 3.77
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics (2011) 3.75
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell (2010) 3.60
Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol Cell Proteomics (2007) 3.60
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics (2012) 3.57
Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res (2009) 3.56
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr Biol (2007) 3.55
A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol (2003) 3.54
A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell (2013) 3.53
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res (2011) 3.53
System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50
Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol Syst Biol (2005) 3.48
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A (2004) 3.43
Mass spectrometric-based approaches in quantitative proteomics. Methods (2003) 3.38
Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science (2005) 3.37
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature (2007) 3.32
Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell (2010) 3.25
Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem (2011) 3.19
Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming. Cell (2010) 3.08
ERCC1/XPF removes the 3' overhang from uncapped telomeres and represses formation of telomeric DNA-containing double minute chromosomes. Mol Cell (2003) 3.01
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
Regulation of ubiquitin-binding proteins by monoubiquitination. Nat Cell Biol (2006) 2.99
Decoding human cytomegalovirus. Science (2012) 2.98
Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods (2010) 2.95
Is proteomics the new genomics? Cell (2007) 2.92
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature (2006) 2.78
System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics (2011) 2.77
On the proper use of mass accuracy in proteomics. Mol Cell Proteomics (2006) 2.76
From genomics to proteomics. Nature (2003) 2.70
Mass spectrometry-based proteomics in cell biology. J Cell Biol (2010) 2.66
Distinct and overlapping sets of SUMO-1 and SUMO-2 target proteins revealed by quantitative proteomics. Mol Cell Proteomics (2006) 2.64
PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res (2010) 2.61
RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. Cell (2004) 2.57
Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol Cell Proteomics (2006) 2.57
Metabolic priming by a secreted fungal effector. Nature (2011) 2.56
System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal (2011) 2.54
Global and site-specific quantitative phosphoproteomics: principles and applications. Annu Rev Pharmacol Toxicol (2009) 2.53
β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. Nat Cell Biol (2013) 2.52
Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res (2003) 2.51
Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response. Mol Cell (2012) 2.51
Large-scale proteomics analysis of the human kinome. Mol Cell Proteomics (2009) 2.49
Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat Methods (2008) 2.44
In-depth analysis of the membrane and cytosolic proteome of red blood cells. Blood (2006) 2.44
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res (2010) 2.40