Published in J Mass Spectrom on March 01, 2007
Cancer proteomics by quantitative shotgun proteomics. Mol Oncol (2007) 1.08
Differential expression of ribosomal proteins in a human metastasis model identified by coupling 2-D liquid chromatography and mass spectrometry. Cancer Genomics Proteomics (2007) 0.85
High resolution two-dimensional electrophoresis of proteins. J Biol Chem (1975) 133.45
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol (2001) 28.01
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem (2001) 6.90
Protein import into mitochondria. Annu Rev Biochem (1997) 6.82
Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics (2005) 6.28
Malignant MCF10CA1 cell lines derived from premalignant human breast epithelial MCF10AT cells. Breast Cancer Res Treat (2001) 3.77
Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci U S A (2002) 3.70
Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem (2004) 2.53
Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res (2004) 2.49
High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal Chem (2002) 1.88
Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics. Anal Chem (2005) 1.87
Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Anal Chem (2004) 1.66
Peptide mass fingerprinting. Methods (2005) 1.24
Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: a strategy for identification of candidate cancer biomarkers. Proteomics (2004) 1.15
Protein pI shifts due to posttranslational modifications in the separation and characterization of proteins. Anal Chem (2005) 1.14
The continuing evolution of shotgun proteomics. Drug Discov Today (2005) 1.12
High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. Anal Chem (2001) 1.11
Comparison of protein and peptide prefractionation methods for the shotgun proteomic analysis of Synechocystis sp. PCC 6803. Proteomics (2005) 1.06
Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. J Proteome Res (2004) 1.06
A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics (2004) 1.02
Separation, detection, and identification of peptides by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry at high and low pH. J Chromatogr A (2005) 1.02
Identification of metastasis-associated proteins in a human tumor metastasis model using the mass-mapping technique. Proteomics (2004) 1.00
Proteome analysis of gastric cancer metastasis by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-mass spectrometry for identification of metastasis-related proteins. J Proteome Res (2004) 0.97
Integration of multidimensional chromatographic protein separations with a combined "top-down" and "bottom-up" proteomic strategy. J Proteome Res (2006) 0.90
Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests. Proteomics (2004) 0.88
Photopolymerized monolithic capillary columns for rapid micro high-performance liquid chromatographic separation of proteins. J Chromatogr A (2004) 0.87
Development of a two-dimensional protein-peptide separation protocol for comprehensive proteome measurements. J Chromatogr B Analyt Technol Biomed Life Sci (2003) 0.87
Analysis of biological and synthetic ribonucleic acids by liquid chromatography-mass spectrometry using monolithic capillary columns. Anal Chem (2005) 0.86
Two-dimensional liquid chromatography protein expression mapping for differential proteomic analysis of normal and O157:H7 Escherichia coli. Biotechniques (2003) 0.85
Rapid profiling of induced proteins in bacteria using MALDI-TOF mass spectrometric detection of nonporous RP HPLC-separated whole cell lysates. Anal Chem (1999) 0.85
Recent advances in capillary separations for proteomics. Electrophoresis (2004) 0.85
Identification of low molecular weight proteins isolated by 2-D liquid separations. J Mass Spectrom (2004) 0.83
Differential expression of proteins in response to ceramide-mediated stress signal in colon cancer cells by 2-D gel electrophoresis and MALDI-TOF-MS. J Proteome Res (2005) 0.83
Separation and detection of phosphorylated and nonphosphorylated peptides in liquid chromatography-mass spectrometry using monolithic columns and acidic or alkaline mobile phases. Anal Chem (2005) 0.82
Peptide mapping by reversed-phase high-performance liquid chromatography employing silica rod monoliths. J Chromatogr A (2003) 0.80
Multidimensional proteomic analysis of photosynthetic membrane proteins by liquid extraction-ultracentrifugation-liquid chromatography-mass spectrometry. Proteomics (2004) 0.80
Simple 2D-HPLC using a monolithic silica column for peptide separation. J Sep Sci (2004) 0.78
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
TGF-beta switches from tumor suppressor to prometastatic factor in a model of breast cancer progression. J Clin Invest (2003) 3.01
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
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
Comparative serum glycoproteomics using lectin selected sialic acid glycoproteins with mass spectrometric analysis: application to pancreatic cancer serum. J Proteome Res (2006) 1.65
The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol (2013) 1.63
Bladder cancer associated glycoprotein signatures revealed by urinary proteomic profiling. J Proteome Res (2007) 1.62
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci U S A (2007) 1.60
Clioquinol and pyrrolidine dithiocarbamate complex with copper to form proteasome inhibitors and apoptosis inducers in human breast cancer cells. Breast Cancer Res (2005) 1.60
Prognostic significance of tissue transglutaminase in drug resistant and metastatic breast cancer. Clin Cancer Res (2004) 1.58
N-linked glycosylation profiling of pancreatic cancer serum using capillary liquid phase separation coupled with mass spectrometric analysis. J Proteome Res (2007) 1.51
Urinary glycoprotein biomarker discovery for bladder cancer detection using LC/MS-MS and label-free quantification. Clin Cancer Res (2011) 1.50
Dynamic stromal-epithelial interactions during progression of MCF10DCIS.com xenografts. Int J Cancer (2007) 1.50
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol (2006) 1.45
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
Monolithic materials: Promises, challenges, achievements. Anal Chem (2006) 1.36
Monolithic capillary-based ion-selective electrodes. Anal Chem (2005) 1.36
Glycoprotein microarrays with multi-lectin detection: unique lectin binding patterns as a tool for classifying normal, chronic pancreatitis and pancreatic cancer sera. J Proteome Res (2007) 1.32
Pancreatic cancer serum detection using a lectin/glyco-antibody array method. J Proteome Res (2009) 1.30
Plasma glycoprotein profiling for colorectal cancer biomarker identification by lectin glycoarray and lectin blot. J Proteome Res (2008) 1.29
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
Identification of cell surface glycoprotein markers for glioblastoma-derived stem-like cells using a lectin microarray and LC-MS/MS approach. J Proteome Res (2010) 1.23
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics (2009) 1.23
Membrane glycoproteins associated with breast tumor cell progression identified by a lectin affinity approach. J Proteome Res (2008) 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
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
Identification and confirmation of differentially expressed fucosylated glycoproteins in the serum of ovarian cancer patients using a lectin array and LC-MS/MS. J Proteome Res (2012) 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
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
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics (2005) 1.17
CD90 is identified as a candidate marker for cancer stem cells in primary high-grade gliomas using tissue microarrays. Mol Cell Proteomics (2011) 1.16
Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: a strategy for identification of candidate cancer biomarkers. Proteomics (2004) 1.15
Protein pI shifts due to posttranslational modifications in the separation and characterization of proteins. Anal Chem (2005) 1.14
Mass spectrometric assay for analysis of haptoglobin fucosylation in pancreatic cancer. J Proteome Res (2011) 1.14
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. PLoS One (2009) 1.14
Two-dimensional reversed-phase x ion-pair reversed-phase HPLC: an alternative approach to high-resolution peptide separation for shotgun proteome analysis. J Proteome Res (2007) 1.13
Identification of glycoprotein markers for pancreatic cancer CD24+CD44+ stem-like cells using nano-LC-MS/MS and tissue microarray. J Proteome Res (2012) 1.13
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13
Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. Mol Cell Proteomics (2009) 1.13
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol (2011) 1.12
Radiation produces differential changes in cytokine profiles in radiation lung fibrosis sensitive and resistant mice. J Hematol Oncol (2009) 1.11
p38γ mitogen-activated protein kinase contributes to oncogenic properties maintenance and resistance to poly (ADP-ribose)-polymerase-1 inhibition in breast cancer. Neoplasia (2011) 1.11
Assertive community treatment as part of integrated care versus standard care: a 12-month trial in patients with first- and multiple-episode schizophrenia spectrum disorders treated with quetiapine immediate release (ACCESS trial). J Clin Psychiatry (2010) 1.11
Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics (2010) 1.10
Cystatin m: a novel candidate tumor suppressor gene for breast cancer. Cancer Res (2004) 1.10
Mitogen activated protein kinase pathway is involved in RhoC GTPase induced motility, invasion and angiogenesis in inflammatory breast cancer. Clin Exp Metastasis (2002) 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
Comedo-ductal carcinoma in situ: A paradoxical role for programmed cell death. Cancer Biol Ther (2008) 1.08
Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res (2006) 1.07
Serum metabolomic analysis of pancreatic cancer--letter. Cancer Epidemiol Biomarkers Prev (2013) 1.07
Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress. J Proteomics (2012) 1.06
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
Identification and confirmation of biomarkers using an integrated platform for quantitative analysis of glycoproteins and their glycosylations. J Proteome Res (2010) 1.05
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics. BMC Bioinformatics (2007) 1.05
Impact of duration of untreated psychosis on pre-treatment, baseline, and outcome characteristics in an epidemiological first-episode psychosis cohort. J Psychiatr Res (2008) 1.05
Analysis of serum haptoglobin fucosylation in hepatocellular carcinoma and liver cirrhosis of different etiologies. J Proteome Res (2014) 1.05
Glycoprotein biomarker panel for pancreatic cancer discovered by quantitative proteomics analysis. J Proteome Res (2014) 1.04
Target proteomic profiling of frozen pancreatic CD24+ adenocarcinoma tissues by immuno-laser capture microdissection and nano-LC-MS/MS. J Proteome Res (2013) 1.03
A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics (2004) 1.02
Proteomic and phosphoproteomic alterations in benign, premalignant and tumor human breast epithelial cells and xenograft lesions: biomarkers of progression. Int J Cancer (2009) 1.02
Engagement of I-branching {beta}-1, 6-N-acetylglucosaminyltransferase 2 in breast cancer metastasis and TGF-{beta} signaling. Cancer Res (2011) 1.02
Early detection and biomarkers in pancreatic cancer. J Natl Compr Canc Netw (2007) 1.02
Assessing protein immunogenicity with a dendritic cell line-derived endolysosomal degradome. PLoS One (2011) 1.02
Separation, detection, and identification of peptides by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry at high and low pH. J Chromatogr A (2005) 1.02
Screening of glycosylation patterns in serum using natural glycoprotein microarrays and multi-lectin fluorescence detection. Anal Chem (2006) 1.01
Depression, anxiety, and disturbed sleep in glaucoma. J Neuropsychiatry Clin Neurosci (2013) 1.00
Glycoproteomic analysis of glioblastoma stem cell differentiation. J Proteome Res (2010) 1.00
Identification of metastasis-associated proteins in a human tumor metastasis model using the mass-mapping technique. Proteomics (2004) 1.00