A nonparametric model for quality control of database search results in shotgun proteomics.

PubWeight™: 0.84‹?›

🔗 View Article (PMC 2267700)

Published in BMC Bioinformatics on January 21, 2008

Authors

Jiyang Zhang1, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, Fuchu He

Author Affiliations

1: College of Mechanical & Electronic Engineering and Automatization, National University of Defense Technology, Changsha, 410073, China. zhangjy@hupo.org.cn

Articles cited by this

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 45.51

Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30

Mass spectrometry-based proteomics. Nature (2003) 28.94

Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol (1999) 12.42

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2003) 12.31

A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol (2006) 12.13

Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res (2003) 11.96

Mass spectrometry and protein analysis. Science (2006) 8.05

Proteomics to study genes and genomes. Nature (2000) 7.48

Nucleolar proteome dynamics. Nature (2005) 7.32

Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods (2005) 6.73

The need for a public proteomics repository. Nat Biotechnol (2004) 4.60

Computational cluster validation in post-genomic data analysis. Bioinformatics (2005) 4.46

Qscore: an algorithm for evaluating SEQUEST database search results. J Am Soc Mass Spectrom (2002) 4.31

Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol Cell Proteomics (2006) 4.25

Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res (2005) 4.13

The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol (2006) 3.79

Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods (2004) 3.62

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem (2003) 3.50

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34

A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem (2003) 2.91

Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today (2004) 2.82

Prediction of low-energy collision-induced dissociation spectra of peptides. Anal Chem (2004) 2.80

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem (2004) 2.53

Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J Proteome Res (2005) 2.27

Proteomics: the first decade and beyond. Nat Genet (2003) 2.17

A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res (2003) 2.16

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics (2005) 2.15

Large-scale and high-confidence proteomic analysis of human seminal plasma. Genome Biol (2006) 1.84

Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. J Proteome Res (2006) 1.82

Randomized sequence databases for tandem mass spectrometry peptide and protein identification. OMICS (2005) 1.74

DBParser: web-based software for shotgun proteomic data analyses. J Proteome Res (2004) 1.69

Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. J Proteome Res (2007) 1.60

Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J Proteome Res (2004) 1.56

Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal Chem (2004) 1.50

Challenges and opportunities in proteomics data analysis. Mol Cell Proteomics (2006) 1.49

Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal Chem (2004) 1.48

Standard mixtures for proteome studies. OMICS (2004) 1.43

Improved validation of peptide MS/MS assignments using spectral intensity prediction. Mol Cell Proteomics (2006) 1.28

Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol Cell Proteomics (2005) 1.08

A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics (2004) 1.08

Valid data from large-scale proteomics studies. Nat Methods (2005) 0.99

A new strategy to filter out false positive identifications of peptides in SEQUEST database search results. Proteomics (2007) 0.95

A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis. Proteomics (2002) 0.87

Analysis of human liver proteome using replicate shotgun strategy. Proteomics (2007) 0.86

AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results. Mol Cell Proteomics (2004) 0.84

Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics. Anal Chem (2004) 0.83

RScore: a peptide randomicity score for evaluating tandem mass spectra. Rapid Commun Mass Spectrom (2004) 0.79

Articles by these authors

Regulation of cellular metabolism by protein lysine acetylation. Science (2010) 10.55

Prostate-specific deletion of the murine Pten tumor suppressor gene leads to metastatic prostate cancer. Cancer Cell (2003) 8.11

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20

Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84

Cre/loxP-mediated inactivation of the murine Pten tumor suppressor gene. Genesis (2002) 4.23

Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21

Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. Nat Genet (2010) 4.01

Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res (2011) 3.05

miR-214 targets ATF4 to inhibit bone formation. Nat Med (2012) 3.01

PTEN negatively regulates neural stem cell self-renewal by modulating G0-G1 cell cycle entry. Proc Natl Acad Sci U S A (2005) 2.93

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol (2011) 2.87

Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol (2012) 2.82

Apatinib for chemotherapy-refractory advanced metastatic gastric cancer: results from a randomized, placebo-controlled, parallel-arm, phase II trial. J Clin Oncol (2013) 2.69

The PSA(-/lo) prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration. Cell Stem Cell (2012) 2.69

Genetic characterization of Nipah virus, Bangladesh, 2004. Emerg Infect Dis (2005) 2.62

A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nat Genet (2010) 2.62

Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A (2008) 2.60

A delivery system targeting bone formation surfaces to facilitate RNAi-based anabolic therapy. Nat Med (2012) 2.53

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45

Conditional loss of PTEN leads to precocious development and neoplasia in the mammary gland. Development (2002) 2.42

T-cell and natural killer-cell large granular lymphocyte leukemia neoplasias. Leuk Lymphoma (2011) 2.37

The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34

Multiple genes for essential-hypertension susceptibility on chromosome 1q. Am J Hum Genet (2006) 2.34

NKX3.1 stabilizes p53, inhibits AKT activation, and blocks prostate cancer initiation caused by PTEN loss. Cancer Cell (2006) 2.29

Association of estrogen receptor alpha polymorphisms with susceptibility to chronic hepatitis B virus infection. Hepatology (2004) 2.12

Oxidative stress and covalent modification of protein with bioactive aldehydes. J Biol Chem (2008) 2.09

PTEN dosage is essential for neurofibroma development and malignant transformation. Proc Natl Acad Sci U S A (2009) 2.07

Ulinastatin is a novel candidate drug for sepsis and secondary acute lung injury, evidence from an optimized CLP rat model. Int Immunopharmacol (2013) 2.06

A critical role of erythropoietin receptor in neurogenesis and post-stroke recovery. J Neurosci (2006) 2.04

Variability of antibiotic concentrations in critically ill patients receiving continuous renal replacement therapy: a multicentre pharmacokinetic study. Crit Care Med (2012) 2.04

Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res (2011) 1.94

Elevated phosphatidylinositol 3,4,5-trisphosphate in glia triggers cell-autonomous membrane wrapping and myelination. J Neurosci (2010) 1.93

Purple acid phosphatases of Arabidopsis thaliana. Comparative analysis and differential regulation by phosphate deprivation. J Biol Chem (2002) 1.93

Characterization and expression of three novel differentiation-related genes belong to the human NDRG gene family. Mol Cell Biochem (2002) 1.89

Ultrasound-mediated tumor imaging and nanotherapy using drug loaded, block copolymer stabilized perfluorocarbon nanoemulsions. J Control Release (2011) 1.89

Deletion of the neuron-specific protein delta-catenin leads to severe cognitive and synaptic dysfunction. Curr Biol (2004) 1.80

Pten deletion in adult neural stem/progenitor cells enhances constitutive neurogenesis. J Neurosci (2009) 1.80

Maternal embryonic leucine zipper kinase (MELK) regulates multipotent neural progenitor proliferation. J Cell Biol (2005) 1.74

Comparisons of image quality and radiation dose between iterative reconstruction and filtered back projection reconstruction algorithms in 256-MDCT coronary angiography. AJR Am J Roentgenol (2012) 1.73

3D noncontrast MR angiography of the distal lower extremities using flow-sensitive dephasing (FSD)-prepared balanced SSFP. Magn Reson Med (2009) 1.72

8q24 and prostate cancer: association with advanced disease and meta-analysis. Eur J Hum Genet (2008) 1.72

Direct, nonoxidative conversion of methane to ethylene, aromatics, and hydrogen. Science (2014) 1.71

iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res (2007) 1.71

Polymorphisms in DNA base excision repair genes ADPRT and XRCC1 and risk of lung cancer. Cancer Res (2005) 1.69

L-fucose utilization provides Campylobacter jejuni with a competitive advantage. Proc Natl Acad Sci U S A (2011) 1.68

GJB2 mutation spectrum in 2,063 Chinese patients with nonsyndromic hearing impairment. J Transl Med (2009) 1.66

Radiation dose reduction in computed tomography: techniques and future perspective. Imaging Med (2009) 1.65

Identification of genetic variants in base excision repair pathway and their associations with risk of esophageal squamous cell carcinoma. Cancer Res (2004) 1.64

Genetic background controls tumor development in PTEN-deficient mice. Cancer Res (2006) 1.63

Telbivudine or lamivudine use in late pregnancy safely reduces perinatal transmission of hepatitis B virus in real-life practice. Hepatology (2014) 1.62

Contrast-enhanced whole-heart coronary magnetic resonance angiography at 3.0-T: a comparative study with X-ray angiography in a single center. J Am Coll Cardiol (2009) 1.61

Electromagnetic imaging methods for nondestructive evaluation applications. Sensors (Basel) (2011) 1.59

SUMO1 modification of PTEN regulates tumorigenesis by controlling its association with the plasma membrane. Nat Commun (2012) 1.58

Essential role of AKT-1/protein kinase B alpha in PTEN-controlled tumorigenesis. Mol Cell Biol (2002) 1.57

Proteome analysis of hepatocellular carcinoma by two-dimensional difference gel electrophoresis: novel protein markers in hepatocellular carcinoma tissues. Mol Cell Proteomics (2007) 1.57

Improvement of resistive switching characteristics in ZrO2 film by embedding a thin TiOx layer. Nanotechnology (2011) 1.55

Development of two avidity-based assays to detect recent HIV type 1 seroconversion using a multisubtype gp41 recombinant protein. AIDS Res Hum Retroviruses (2010) 1.53

Discovery of marinopyrrole A (maritoclax) as a selective Mcl-1 antagonist that overcomes ABT-737 resistance by binding to and targeting Mcl-1 for proteasomal degradation. J Biol Chem (2012) 1.53

Architecture of an RNA polymerase II transcription pre-initiation complex. Science (2013) 1.52

Targeting WW domains linker of HECT-type ubiquitin ligase Smurf1 for activation by CKIP-1. Nat Cell Biol (2008) 1.51

Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl (2009) 1.51

Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol (2011) 1.51

Percent fat mass is inversely associated with bone mass and hip geometry in rural Chinese adolescents. J Bone Miner Res (2010) 1.47

Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography-stable isotope labeling and tandem mass spectrometry. Proteomics (2007) 1.47

Podocalyxin variants and risk of prostate cancer and tumor aggressiveness. Hum Mol Genet (2006) 1.46

An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells. Nat Commun (2011) 1.45

Molecular profiling of LGL leukemia reveals role of sphingolipid signaling in survival of cytotoxic lymphocytes. Blood (2008) 1.45

LDA--a java-based linkage disequilibrium analyzer. Bioinformatics (2003) 1.44

Identification of natural coumarin compounds that rescue defective DeltaF508-CFTR chloride channel gating. Clin Exp Pharmacol Physiol (2008) 1.43

A mechanism-based inactivator for histone demethylase LSD1. J Am Chem Soc (2006) 1.43

KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis. Nat Cell Biol (2009) 1.43

[Ln2(C2O4)2(pyzc)2(H2O)2]n[Ln = Pr (1), Er (2)]: novel two-dimensional lanthanide coordination polymers with 2-pyrazinecarboxylate and oxalate. Inorg Chem (2006) 1.41

Assembly information services in the European Nucleotide Archive. Nucleic Acids Res (2013) 1.40

A cascade of protein kinase C isozymes promotes cytoskeletal polarization in T cells. Nat Immunol (2011) 1.39

c-MYC-regulated miR-23a/24-2/27a cluster promotes mammary carcinoma cell invasion and hepatic metastasis by targeting Sprouty2. J Biol Chem (2013) 1.37

Laminar and compartmental regulation of dendritic growth in mature cortex. Nat Neurosci (2009) 1.37

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol (2013) 1.36

Image quality optimization and evaluation of linearly mixed images in dual-source, dual-energy CT. Med Phys (2009) 1.36

lncRNA H19/miR-675 axis represses prostate cancer metastasis by targeting TGFBI. FEBS J (2014) 1.36

PTEN deletion in Bergmann glia leads to premature differentiation and affects laminar organization. Development (2005) 1.35

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet (2013) 1.34

The common rs9939609 variant of the fat mass and obesity-associated gene is associated with obesity risk in children and adolescents of Beijing, China. BMC Med Genet (2010) 1.31

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics (2008) 1.31

NOD2 regulates hematopoietic cell function during graft-versus-host disease. J Exp Med (2009) 1.30

Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana. J Genet Genomics (2009) 1.29

Metabolism of dietary soy isoflavones to equol by human intestinal microflora--implications for health. Mol Nutr Food Res (2007) 1.28

Broadening of neutralization activity to directly block a dominant antibody-driven SARS-coronavirus evolution pathway. PLoS Pathog (2008) 1.27

The beginning of the rpoB gene in addition to the rifampin resistance determination region might be needed for identifying rifampin/rifabutin cross-resistance in multidrug-resistant Mycobacterium tuberculosis isolates from Southern China. J Clin Microbiol (2011) 1.26

Substantial reduction in risk of lung adenocarcinoma associated with genetic polymorphism in CYP2A13, the most active cytochrome P450 for the metabolic activation of tobacco-specific carcinogen NNK. Cancer Res (2003) 1.25

Delta-catenin regulates spine and synapse morphogenesis and function in hippocampal neurons during development. J Neurosci (2009) 1.24

Sodium selenate mitigates tau pathology, neurodegeneration, and functional deficits in Alzheimer's disease models. Proc Natl Acad Sci U S A (2010) 1.24

Toward an understanding of the protein interaction network of the human liver. Mol Syst Biol (2011) 1.24

Proteomic mapping of 4-hydroxynonenal protein modification sites by solid-phase hydrazide chemistry and mass spectrometry. Anal Chem (2007) 1.23