Published in Mol Syst Biol on January 01, 2012
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Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics (2014) 1.33
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Proteomic sample preparation from formalin fixed and paraffin embedded tissue. J Vis Exp (2013) 1.00
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Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics. Mol Cell Proteomics (2014) 0.91
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Diagnosing inflammation and infection in the urinary system via proteomics. J Transl Med (2015) 0.81
Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). Mol Cell Proteomics (2014) 0.80
Membrane protein profiling of human colon reveals distinct regional differences. Mol Cell Proteomics (2014) 0.79
Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling. Mol Cell Proteomics (2014) 0.79
A Novel Phosphopeptide Microarray Based Interactome Map in Breast Cancer Cells Reveals Phosphoprotein-GRB2 Cell Signaling Networks. PLoS One (2013) 0.78
Quantitative analysis of the Escherichia coli proteome. Data Brief (2014) 0.78
Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine. PLoS One (2015) 0.77
Large scale systematic proteomic quantification from non-metastatic to metastatic colorectal cancer. Sci Rep (2015) 0.77
A sequence upstream of canonical PDZ-binding motif within CFTR COOH-terminus enhances NHERF1 interaction. Am J Physiol Lung Cell Mol Physiol (2016) 0.75
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Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ (2016) 0.75
Insulin/IGF1-PI3K-dependent nucleolar localization of a glycolytic enzyme--phosphoglycerate mutase 2, is necessary for proper structure of nucleolus and RNA synthesis. Oncotarget (2015) 0.75
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Maximizing in vivo target clearance by design of pH-dependent target binding antibodies with altered affinity to FcRn. MAbs (2017) 0.75
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Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ (2017) 0.75
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A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
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Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci U S A (2003) 4.47
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Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J Proteome Res (2010) 1.47
Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal Chem (2012) 1.45
Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method. Anal Biochem (2010) 1.44
Sucrase-isomaltase: a marker of foetal and malignant epithelial cells of the human colon. Int J Cancer (1983) 1.36
High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J Proteome Res (2011) 1.35
A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol Cell Proteomics (2011) 1.31
A quantitative proteomic approach of the different stages of colorectal cancer establishes OLFM4 as a new nonmetastatic tumor marker. Mol Cell Proteomics (2011) 1.27
Gene expression profiling of colorectal cancer and metastases divides tumours according to their clinicopathological stage. J Pathol (2004) 1.26
Gene expression profiles of primary colorectal carcinomas, liver metastases, and carcinomatoses. Mol Cancer (2007) 1.23
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Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol Cell Proteomics (2010) 1.16
Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target. Mol Cell Proteomics (2011) 1.14
Genome-wide screening of genes showing altered expression in liver metastases of human colorectal cancers by cDNA microarray. Neoplasia (2001) 1.13
Absolute quantification and differential expression of drug transporters, cytochrome P450 enzymes, and UDP-glucuronosyltransferases in cultured primary human hepatocytes. Drug Metab Dispos (2011) 1.10
Morphometric analysis of the membranes and organelles of small intestinal enterocytes. I. Fasted hamster. J Ultrastruct Res (1981) 1.07
Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. J Proteome Res (2012) 1.06
Proteomics of colorectal cancer: overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers. J Proteomics (2010) 1.04
Synchronous global assessment of gene and protein expression in colorectal cancer progression. Genomics (2005) 1.04
Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer. J Pathol (2012) 1.03
Identification of new accessible tumor antigens in human colon cancer by ex vivo protein biotinylation and comparative mass spectrometry analysis. Int J Cancer (2008) 1.03
Comparative profiling of primary colorectal carcinomas and liver metastases identifies LEF1 as a prognostic biomarker. PLoS One (2011) 1.03
An "Omics" based survey of human colon cancer. Mutat Res (2010) 1.00
Genome wide expression profiling identifies genes associated with colorectal liver metastasis. Oncol Rep (2007) 0.97
An informatics-assisted label-free approach for personalized tissue membrane proteomics: case study on colorectal cancer. Mol Cell Proteomics (2011) 0.94
PTRF/cavin-1 and MIF proteins are identified as non-small cell lung cancer biomarkers by label-free proteomics. PLoS One (2012) 0.91
Analysis of proteomic changes induced upon cellular differentiation of the human intestinal cell line Caco-2. Dev Growth Differ (2011) 0.91
Comparing the scoring mechanisms of p16INK4a immunohistochemistry based on independent nucleic stains and independent cytoplasmic stains in distinguishing between endocervical and endometrial adenocarcinomas in a tissue microarray study. Arch Gynecol Obstet (2009) 0.91
Corticostatic peptides cause nifedipine-sensitive volume reduction in jejunal villus enterocytes. Proc Natl Acad Sci U S A (1991) 0.89
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Proteomic analysis of advanced colorectal cancer by laser capture microdissection and two-dimensional difference gel electrophoresis. J Proteomics (2011) 0.87
Tools for phospho- and glycoproteomics of plasma membranes. Amino Acids (2011) 0.78
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
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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
Recurrent R-spondin fusions in colon cancer. Nature (2012) 5.10
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
Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet (2012) 4.70
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
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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
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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
Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics (2008) 2.76
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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