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Volumn 14, Issue 7, 2015, Pages 2784-2791

NextSearch: A Search Engine for Mass Spectrometry Data against a Compact Nucleotide Exon Graph

Author keywords

alternative splicing; exon graph; junction variation; proteogenomics

Indexed keywords

NUCLEOTIDE; TRANSCRIPTOME;

EID: 84947217723     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00047     Document Type: Article
Times cited : (11)

References (25)
  • 1
    • 84859898660 scopus 로고    scopus 로고
    • A beginners guide to eukaryotic genome annotation
    • Yandell, M.; Ence, D. A beginners guide to eukaryotic genome annotation Nat. Rev. Genet 2012, 13 (5) 329-342
    • (2012) Nat. Rev. Genet , vol.13 , Issue.5 , pp. 329-342
    • Yandell, M.1    Ence, D.2
  • 3
    • 77957237701 scopus 로고    scopus 로고
    • Proteogenomics to discover the full coding content of genomes: A computational perspective
    • Castellana, N.; Bafna, V. Proteogenomics to discover the full coding content of genomes: A computational perspective J. Proteomics 2010, 73 (11) 2124-2135
    • (2010) J. Proteomics , vol.73 , Issue.11 , pp. 2124-2135
    • Castellana, N.1    Bafna, V.2
  • 4
    • 84902106514 scopus 로고    scopus 로고
    • Integrating Genomic, Transcriptomic, and Interactome Data to Improve Peptide and Protein Identification in Shotgun Proteomics
    • Wang, X. J.; Zhang, B. Integrating Genomic, Transcriptomic, and Interactome Data to Improve Peptide and Protein Identification in Shotgun Proteomics J. Proteome Res. 2014, 13 (6) 2715-2723
    • (2014) J. Proteome Res. , vol.13 , Issue.6 , pp. 2715-2723
    • Wang, X.J.1    Zhang, B.2
  • 6
    • 0034652301 scopus 로고    scopus 로고
    • Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry
    • Gatlin, C. L.; Eng, J. K.; Cross, S. T.; Detter, J. C.; Yates, J. R. Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry Anal. Chem. 2000, 72 (4) 757-763
    • (2000) Anal. Chem. , vol.72 , Issue.4 , pp. 757-763
    • Gatlin, C.L.1    Eng, J.K.2    Cross, S.T.3    Detter, J.C.4    Yates, J.R.5
  • 7
    • 0029645432 scopus 로고
    • Mining Genomes - Correlating Tandem Mass-Spectra of Modified and Unmodified Peptides to Sequences in Nucleotide Databases
    • Yates, J. R.; Eng, J. K.; Mccormack, A. L. Mining Genomes-Correlating Tandem Mass-Spectra of Modified and Unmodified Peptides to Sequences in Nucleotide Databases Anal. Chem. 1995, 67 (18) 3202-3210
    • (1995) Anal. Chem. , vol.67 , Issue.18 , pp. 3202-3210
    • Yates, J.R.1    Eng, J.K.2    Mccormack, A.L.3
  • 8
    • 0035346719 scopus 로고    scopus 로고
    • Interrogating the human genome using uninterpreted mass spectrometry data
    • Choudhary, J. S.; Blackstock, W. P.; Creasy, D. M.; Cottrell, J. S. Interrogating the human genome using uninterpreted mass spectrometry data Proteomics 2001, 1 (5) 651-667
    • (2001) Proteomics , vol.1 , Issue.5 , pp. 651-667
    • Choudhary, J.S.1    Blackstock, W.P.2    Creasy, D.M.3    Cottrell, J.S.4
  • 14
    • 84881094423 scopus 로고    scopus 로고
    • Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq
    • Sheynkman, G. M.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq Mol. Cell Proteomics 2013, 12 (8) 2341-2353
    • (2013) Mol. Cell Proteomics , vol.12 , Issue.8 , pp. 2341-2353
    • Sheynkman, G.M.1    Shortreed, M.R.2    Frey, B.L.3    Smith, L.M.4
  • 15
    • 84863011504 scopus 로고    scopus 로고
    • Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data
    • Wang, X. J.; Slebos, R. J. C.; Wang, D.; Halvey, P. J.; Tabb, D. L.; Liebler, D. C.; Zhang, B. Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data J. Proteome Res. 2012, 11 (2) 1009-1017
    • (2012) J. Proteome Res. , vol.11 , Issue.2 , pp. 1009-1017
    • Wang, X.J.1    Slebos, R.J.C.2    Wang, D.3    Halvey, P.J.4    Tabb, D.L.5    Liebler, D.C.6    Zhang, B.7
  • 16
    • 84857938446 scopus 로고    scopus 로고
    • Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins
    • Geiger, T.; Wehner, A.; Schaab, C.; Cox, J.; Mann, M., Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins. Mol. Cell Proteomics 2012, 11 (3).
    • (2012) Mol. Cell Proteomics , vol.11 , Issue.3
    • Geiger, T.1    Wehner, A.2    Schaab, C.3    Cox, J.4    Mann, M.5
  • 17
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4 (3) 207-214
    • (2007) Nat. Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 18
    • 84908540871 scopus 로고    scopus 로고
    • Proteogenomics: Concepts, applications and computational strategies
    • Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11 (11) 1114-1125
    • (2014) Nat. Methods , vol.11 , Issue.11 , pp. 1114-1125
    • Nesvizhskii, A.I.1
  • 19
    • 84923247212 scopus 로고    scopus 로고
    • MS-GF plus makes progress towards a universal database search tool for proteomics
    • Kim, S.; Pevzner, P. A., MS-GF plus makes progress towards a universal database search tool for proteomics. Nat. Commun. 2014, 5.
    • (2014) Nat. Commun. , vol.5
    • Kim, S.1    Pevzner, P.A.2
  • 22
    • 84859877187 scopus 로고    scopus 로고
    • Fast Multi-blind Modification Search through Tandem Mass Spectrometry
    • Na, S.; Bandeira, N.; Paek, E., Fast Multi-blind Modification Search through Tandem Mass Spectrometry. Mol. Cell Proteomics 2012, 11 (4).
    • (2012) Mol. Cell Proteomics , vol.11 , Issue.4
    • Na, S.1    Bandeira, N.2    Paek, E.3
  • 24
    • 0016518897 scopus 로고
    • Efficient String Matching - Aid to Bibliographic Search
    • Aho, A. V.; Corasick, M. J. Efficient String Matching-Aid to Bibliographic Search Commun. Acm 1975, 18 (6) 333-340
    • (1975) Commun. Acm , vol.18 , Issue.6 , pp. 333-340
    • Aho, A.V.1    Corasick, M.J.2
  • 25
    • 37549003336 scopus 로고    scopus 로고
    • Mapreduce: Simplified data processing on large clusters
    • Dean, J.; Ghemawat, S. Mapreduce: Simplified data processing on large clusters Commun. Acm 2008, 51 (1) 107-113
    • (2008) Commun. Acm , vol.51 , Issue.1 , pp. 107-113
    • Dean, J.1    Ghemawat, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.