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Volumn 17, Issue 3, 2010, Pages 277-286

Annotation of Non-synonymous single polymorphisms in human liver proteome by mass spectrometry

Author keywords

Liquid chromatography tandem mass spectrometry; Liver proteins; nsSNP; Peptide database; SIFT

Indexed keywords

PEPTIDE FRAGMENT; PROTEOME;

EID: 77949997448     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986610790780242     Document Type: Article
Times cited : (4)

References (41)
  • 4
    • 3242792729 scopus 로고    scopus 로고
    • Review: Structural bioinformatics and its impact to biomedical science
    • Chou, K. C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
    • (2004) Curr. Med. Chem , vol.11 , pp. 2105-2134
    • Chou, K.C.1
  • 5
    • 1642377868 scopus 로고    scopus 로고
    • Modelling extracellular domains of GABA-A receptors: Subtypes 1, 2, 3, and 5
    • Chou, K. C. Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Commun., 2004, 316, 636-642.
    • (2004) Biochem. Biophys. Res. Commun , vol.316 , pp. 636-642
    • Chou, K.C.1
  • 6
    • 11144275172 scopus 로고    scopus 로고
    • Molecular therapeutic target for type-2 diabetes
    • Chou, K. C. Molecular therapeutic target for type-2 diabetes. J. Proteome Res., 2004, 3, 1284-1288.
    • (2004) J. Proteome Res , vol.3 , pp. 1284-1288
    • Chou, K.C.1
  • 7
    • 39449105071 scopus 로고    scopus 로고
    • Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms
    • Chou, K. C.; Shen, H. B. Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Protocols, 2008, 3, 153-162.
    • (2008) Nat. Protocols , vol.3 , pp. 153-162
    • Chou, K.C.1    Shen, H.B.2
  • 8
    • 34548606295 scopus 로고    scopus 로고
    • Review: Recent progresses in protein subcellular location prediction
    • Chou, K. C.; Shen, H. B. Review: Recent progresses in protein subcellular location prediction. Analy. Biochem., 2007, 370, 1-16.
    • (2007) Analy. Biochem , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 9
    • 34447095147 scopus 로고    scopus 로고
    • MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM
    • Chou, K. C.; Shen, H. B. MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Comm., 2007, 360, 339-345.
    • (2007) Biochem. Biophys. Res. Comm , vol.360 , pp. 339-345
    • Chou, K.C.1    Shen, H.B.2
  • 10
    • 52149087297 scopus 로고    scopus 로고
    • Predicting membrane protein types by the LLDA algorithm. Protein Pept
    • Wang, T.; Yang, J.; Shen, H. B.; Chou, K. C. Predicting membrane protein types by the LLDA algorithm. Protein Pept. Lett., 2008, 15, 915-921.
    • (2008) Lett , vol.15 , pp. 915-921
    • Wang, T.1    Yang, J.2    Shen, H.B.3    Chou, K.C.4
  • 11
    • 34247544233 scopus 로고    scopus 로고
    • Signal-CF: A subsite-coupled and window-fusing approach for predicting signal peptides
    • Chou, K. C.; Shen, H. B. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem. Bio-phys. Res. Comm., 2007, 357, 633-640.
    • (2007) Biochem. Bio-phys. Res. Comm , vol.357 , pp. 633-640
    • Chou, K.C.1    Shen, H.B.2
  • 12
    • 34748902270 scopus 로고    scopus 로고
    • Signal-3L: A 3-layer approach for predicting signal peptide
    • Shen, H. B.; Chou, K. C. Signal-3L: a 3-layer approach for predicting signal peptide. Biochem. Biophys. Res. Comm., 2007, 363, 297-303.
    • (2007) Biochem. Biophys. Res. Comm , vol.363 , pp. 297-303
    • Shen, H.B.1    Chou, K.C.2
  • 13
    • 0030049315 scopus 로고    scopus 로고
    • Review: Prediction of HIV protease cleavage sites in proteins
    • Chou, K. C. Review: Prediction of HIV protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
    • (1996) Anal. Biochem , vol.233 , pp. 1-14
    • Chou, K.C.1
  • 14
    • 0027219970 scopus 로고
    • A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins
    • Chou, K. C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
    • (1993) J. Biol. Chem , vol.268 , pp. 16938-16948
    • Chou, K.C.1
  • 15
    • 0032997217 scopus 로고    scopus 로고
    • The essence of SNPs
    • Brookes, A.J. The essence of SNPs. Gene, 1999, 234, 177-186.
    • (1999) Gene , vol.234 , pp. 177-186
    • Brookes, A.J.1
  • 17
    • 0035065485 scopus 로고    scopus 로고
    • SNPs, protein structure, and disease
    • Wang, Z.; Moult, J. SNPs, protein structure, and disease. Human Mutation, 2001, 17, 263-270.
    • (2001) Human Mutation , vol.17 , pp. 263-270
    • Wang, Z.1    Moult, J.2
  • 18
    • 0034191958 scopus 로고    scopus 로고
    • Towards a structural basis of human non-synonymous single nucleotide polymorphisms
    • Sunyaev, S.; Ramensky, V.; Bork, P. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet, 2000, 16,198-200.
    • (2000) Trends Genet , vol.16 , pp. 198-200
    • Sunyaev, S.1    Ramensky, V.2    Bork, P.3
  • 19
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • Ng, P.C.; Henikoff, S. Predicting deleterious amino acid substitutions. Genome Res., 2001, 11, 863-874.
    • (2001) Genome Res , vol.11 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 20
    • 0032903821 scopus 로고    scopus 로고
    • Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat
    • Howell, W.M.; Jobs, M.; Gyllensten, U.; Brookes, A.J. Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat. Biotechnol., 1999, 17, 87-88.
    • (1999) Biotechnol , vol.17 , pp. 87-88
    • Howell, W.M.1    Jobs, M.2    Gyllensten, U.3    Brookes, A.J.4
  • 24
    • 0030914509 scopus 로고    scopus 로고
    • Mass spectrometric gene diagnosis of one-base substitution from polymerase chain reaction amplified human DNA. Rapid Commun
    • Tsuneyoshi, T.; Ishikawa, K.; Koga Naito, Y.; Baba, S.; Terunuma, H.; Arakawa, R.; Prockop, D.J. Mass spectrometric gene diagnosis of one-base substitution from polymerase chain reaction amplified human DNA. Rapid Commun. Mass Spectrom., 1997, 11, 719-722.
    • (1997) Mass Spectrom , vol.11 , pp. 719-722
    • Tsuneyoshi, T.1    Ishikawa, K.2    Koga Naito, Y.3    Baba, S.4    Terunuma, H.5    Arakawa, R.6    Prockop, D.J.7
  • 25
    • 0033032090 scopus 로고    scopus 로고
    • Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry
    • Griffin, T.J.; Hall, J.G.; Prudent, J.R.; Smith, L.M. Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry. Proc. Natl. Acad. Sci. USA, 1999, 96, 6301-6306.
    • (1999) Proc. Natl. Acad. Sci. Usa , vol.96 , pp. 6301-6306
    • Griffin, T.J.1    Hall, J.G.2    Prudent, J.R.3    Smith, L.M.4
  • 26
    • 12944281622 scopus 로고    scopus 로고
    • Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins
    • Savas, S.; Ahmad, F. M.; Shariff, M.; Kim, D.Y.; Ozcelik, H. Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins. Proteins, 2005, 58, 697-705.
    • (2005) Proteins , vol.58 , pp. 697-705
    • Savas, S.1    Ahmad, F.M.2    Shariff, M.3    Kim, D.Y.4    Ozcelik, H.5
  • 27
    • 33847232891 scopus 로고    scopus 로고
    • Mouse SNP Miner: An annotated database of mouse functional single nucleotide polymorphisms
    • Reuveni, E.; Ramensky, V. E.; Gross, C. Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms. BMC Genomics, 2007, 8, 24.
    • (2007) Bmc Genomics , vol.8 , pp. 24
    • Reuveni, E.1    Ramensky, V.E.2    Gross, C.3
  • 29
    • 41949118839 scopus 로고    scopus 로고
    • Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions
    • Teng, S.; Michonova-Alexova E, Alexov, E. Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Curr. Pharm. Biotechnol., 2008, 9(2): 123-133.
    • (2008) Curr. Pharm. Biotechnol , vol.9 , Issue.2 , pp. 123-133
    • Teng, S.1    Michonova-Alexova, E.2    Alexov, E.3
  • 30
    • 0035860293 scopus 로고    scopus 로고
    • PicSNP: A browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Bio-chem
    • Chang, H.; Fujita, T. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Bio-chem. Biophys. Res. Commun., 2001, 287, 288-291.
    • (2001) Biophys. Res. Commun , vol.287 , pp. 288-291
    • Chang, H.1    Fujita, T.2
  • 31
    • 0036119504 scopus 로고    scopus 로고
    • Accounting for human polymorphisms predicted to affect protein function
    • Ng, P.C.; Henikoff, S. Accounting for human polymorphisms predicted to affect protein function. Genome Res., 2002, 12, 436-446.
    • (2002) Genome Res , vol.12 , pp. 436-446
    • Ng, P.C.1    Henikoff, S.2
  • 33
    • 1642554457 scopus 로고    scopus 로고
    • Identification and characterization of mouse TRMU gene encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase
    • Yan, Q.; Guan, M.X. Identification and characterization of mouse TRMU gene encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase. Biochim. Biophys. Acta, 2004, 1676, 119-126.
    • (2004) Biochim. Biophys. Acta , vol.1676 , pp. 119-126
    • Yan, Q.1    Guan, M.X.2
  • 34
    • 18544364500 scopus 로고    scopus 로고
    • Screening for deleterious nonsynonymous single-nucleotide polymorphisms in genes involved in steroid hormone metabolism and response. Cancer Epidemiol
    • Johnson, M.M.; Houck, J.; Chen, C. Screening for deleterious nonsynonymous single-nucleotide polymorphisms in genes involved in steroid hormone metabolism and response. Cancer Epidemiol. Biomarkers Prev., 2005, 14, 1326-1329.
    • (2005) Biomarkers Prev , vol.14 , pp. 1326-1329
    • Johnson, M.M.1    Houck, J.2    Chen, C.3
  • 36
    • 24944544077 scopus 로고    scopus 로고
    • Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. Mol
    • Roth, M.J.; Forbes, A.J.; Boyne, M.T.; Kim, Y.B.; Robinson, D.E.; Kelleher, N.L. Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. Mol. Cell Proteomics., 2005, 4, 1002-1008.
    • (2005) Cell Proteomics , vol.4 , pp. 1002-1008
    • Roth, M.J.1    Forbes, A.J.2    Boyne, M.T.3    Kim, Y.B.4    Robinson, D.E.5    Kelleher, N.L.6
  • 37
    • 2442636680 scopus 로고    scopus 로고
    • Molecular-level description of proteins from saccharomyces cerevisiae using quadrupole FT hybrid mass spec-trometry for top down proteomics
    • Meng, F; Du, Y.; Miller, L.M.; Patrie, S.M.; Robinson, D.E.; Kelleher NL. Molecular-level description of proteins from saccharomyces cerevisiae using quadrupole FT hybrid mass spec-trometry for top down proteomics. Anal. Chem., 2004, 76, 2852-2858.
    • (2004) Anal Chem , vol.76 , pp. 2852-2858
    • Meng, F.1    Du, Y.2    Miller, L.M.3    Patrie, S.M.4    Robinson, D.E.5    Kelleher, N.L.6
  • 38
    • 34249807325 scopus 로고    scopus 로고
    • A mass spectrometry-friendly database for cSNP identification
    • Schandorff, S.; Olsen, J.V.; Bunkenborg, J. A mass spectrometry-friendly database for cSNP identification. Nat. Methods, 2007, 4, 465-466.
    • (2007) Nat. Methods , vol.4 , pp. 465-466
    • Schandorff, S.1    Olsen, J.V.2    Bunkenborg, J.3
  • 41
    • 0003385172 scopus 로고
    • Selective constraint in protein polymorphism: Study of the effectively neutral mutation model by using an improved pseudosampling method
    • Kimura, M. and Takahata, N. Selective constraint in protein polymorphism: study of the effectively neutral mutation model by using an improved pseudosampling method. Proc. Natl. Acad. Sci. USA, 1983, 80, 1048-1052.
    • (1983) Proc. Natl. Acad. Sci. Usa , vol.80 , pp. 1048-1052
    • Kimura, M.1    Takahata, N.2


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