Published in Proteomics on August 01, 2005
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Human protein reference database--2006 update. Nucleic Acids Res (2006) 12.16
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res (2006) 4.19
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
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Recent de novo origin of human protein-coding genes. Genome Res (2009) 2.36
Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? J Proteome Res (2006) 2.17
Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid-chromatography-multiple- reaction-monitoring mass spectrometry. Clin Chem (2010) 2.11
Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med (2012) 2.06
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Building consensus spectral libraries for peptide identification in proteomics. Nat Methods (2008) 1.96
The blood peptidome: a higher dimension of information content for cancer biomarker discovery. Nat Rev Cancer (2006) 1.79
Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol Cell Proteomics (2010) 1.71
A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med (2013) 1.69
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52
The grand challenge to decipher the cancer proteome. Nat Rev Cancer (2010) 1.49
The PeptideAtlas Project. Methods Mol Biol (2010) 1.46
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol (2006) 1.45
Perspectives of targeted mass spectrometry for protein biomarker verification. Curr Opin Chem Biol (2009) 1.45
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol (2006) 1.43
Comparative human salivary and plasma proteomes. J Dent Res (2010) 1.41
Advances in proteomic workflows for systems biology. Curr Opin Biotechnol (2007) 1.26
An initial characterization of the serum phosphoproteome. J Proteome Res (2009) 1.26
A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin Appl (2011) 1.25
Analysis of the zebrafish proteome during embryonic development. Mol Cell Proteomics (2008) 1.09
Multiple-reaction monitoring-mass spectrometric assays can accurately measure the relative protein abundance in complex mixtures. Clin Chem (2012) 1.05
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res (2008) 1.03
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HIP2: an online database of human plasma proteins from healthy individuals. BMC Med Genomics (2008) 0.93
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'Omics' approaches to understanding interstitial cystitis/painful bladder syndrome/bladder pain syndrome. Int Neurourol J (2012) 0.90
Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma. Mol Cell Proteomics (2014) 0.87
Replacing immunoassays with tryptic digestion-peptide immunoaffinity enrichment and LC-MS/MS. Bioanalysis (2012) 0.83
Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. BMC Urol (2016) 0.78
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Data management and data integration in the HUPO plasma proteome project. Methods Mol Biol (2011) 0.77
MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration. Proteome Sci (2012) 0.76
Quantitative proteomic profiling identifies protein correlates to EGFR kinase inhibition. Mol Cancer Ther (2012) 0.76
A comparison of E15.5 fetus and newborn rat serum proteomes. Proteome Sci (2012) 0.75
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
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Selective killing of oncogenically transformed cells through a ROS-mediated mechanism by beta-phenylethyl isothiocyanate. Cancer Cell (2006) 10.10
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis. Nature (2011) 8.62
Mass spectrometry and protein analysis. Science (2006) 8.05
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol (2004) 7.69
Systems biology and new technologies enable predictive and preventative medicine. Science (2004) 7.59
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol (2003) 6.86
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol (2008) 6.38
Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics (2005) 6.28
Gemcitabine plus nab-paclitaxel is an active regimen in patients with advanced pancreatic cancer: a phase I/II trial. J Clin Oncol (2011) 6.16
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med (2007) 6.01
The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A (2002) 5.98
A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell (2002) 5.70
An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron (2007) 5.35
Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods (2012) 4.93
Targeting autophagy augments the anticancer activity of the histone deacetylase inhibitor SAHA to overcome Bcr-Abl-mediated drug resistance. Blood (2007) 4.91
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics (2007) 4.72
Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol (2007) 4.70
Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol (2005) 4.63
High-level coexpression of JAG1 and NOTCH1 is observed in human breast cancer and is associated with poor overall survival. Cancer Res (2005) 4.61
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
Immuno gold nanocages with tailored optical properties for targeted photothermal destruction of cancer cells. Nano Lett (2007) 4.37
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods (2009) 4.17
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics (2004) 4.15
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature (2009) 4.07
Rewiring of genetic networks in response to DNA damage. Science (2010) 4.03
Identification of cross-linked peptides from large sequence databases. Nat Methods (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Gold nanocages: bioconjugation and their potential use as optical imaging contrast agents. Nano Lett (2005) 3.96
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
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
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
Long-term entecavir therapy results in the reversal of fibrosis/cirrhosis and continued histological improvement in patients with chronic hepatitis B. Hepatology (2010) 3.57
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol (2010) 3.51
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50
Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol (2006) 3.49
Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res (2007) 3.48
Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods (2007) 3.46
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics (2010) 3.44
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A (2012) 3.42
Trial of celecoxib in amyotrophic lateral sclerosis. Ann Neurol (2006) 3.39
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics (2006) 3.35
Increased regulatory T cells correlate with CD8 T-cell impairment and poor survival in hepatocellular carcinoma patients. Gastroenterology (2007) 3.34
A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev (2009) 3.31
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics (2008) 3.29
Orm family proteins mediate sphingolipid homeostasis. Nature (2010) 3.29
Weekly nab-paclitaxel in combination with carboplatin versus solvent-based paclitaxel plus carboplatin as first-line therapy in patients with advanced non-small-cell lung cancer: final results of a phase III trial. J Clin Oncol (2012) 3.28
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell (2012) 3.26