메뉴 건너뛰기




Volumn 14, Issue 23-24, 2014, Pages 2360-2675

Proteogenomics in microbiology: Taking the right turn at the junction of genomics and proteomics

Author keywords

Genome annotation; Microbiology; MS MS; Synonymous proteogenomics

Indexed keywords

GENOMIC DNA; SIGNAL PEPTIDE;

EID: 84913559600     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400168     Document Type: Review
Times cited : (26)

References (167)
  • 1
    • 77957220211 scopus 로고    scopus 로고
    • Two-dimensional gel electrophoresis in proteomics: past, present and future
    • Rabilloud, T., Chevallet, M., Luche, S., Lelong, C., Two-dimensional gel electrophoresis in proteomics: past, present and future. J. Proteomics 2010, 73, 2064-2077.
    • (2010) J. Proteomics , vol.73 , pp. 2064-2077
    • Rabilloud, T.1    Chevallet, M.2    Luche, S.3    Lelong, C.4
  • 2
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I., Vitek, O., Aebersold, R., Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4, 787-797.
    • (2007) Nat. Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 3
    • 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, 3202-3210.
    • (1995) Anal. Chem. , vol.67 , pp. 3202-3210
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 4
    • 0030298218 scopus 로고    scopus 로고
    • Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides
    • Yates, J., Eng, J., Clauser, K., Burlingame, A., Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides. J. Am. Soc. Mass Spectrom. 1996, 7, 1089-1098.
    • (1996) J. Am. Soc. Mass Spectrom. , vol.7 , pp. 1089-1098
    • Yates, J.1    Eng, J.2    Clauser, K.3    Burlingame, A.4
  • 5
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J. C., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 7
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 8
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotech. 2008, 26, 1367-1372.
    • (2008) Nat. Biotech. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 11
    • 84885072320 scopus 로고    scopus 로고
    • Proteogenomics for environmental microbiology
    • Armengaud, J., Marie Hartmann, E., Bland, C., Proteogenomics for environmental microbiology. Proteomics 2013, 13, 2731-2742.
    • (2013) Proteomics , vol.13 , pp. 2731-2742
    • Armengaud, J.1    Marie Hartmann, E.2    Bland, C.3
  • 13
    • 84856692718 scopus 로고    scopus 로고
    • De novo sequencing and homology searching
    • O111.014902.
    • Ma, B., Johnson, R., De novo sequencing and homology searching. Mol. Cell. Proteomics 2012, 11, O111.014902.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Ma, B.1    Johnson, R.2
  • 14
    • 35848949043 scopus 로고    scopus 로고
    • Decoding protein modifications using top-down mass spectrometry
    • Siuti, N., Kelleher, N. L., Decoding protein modifications using top-down mass spectrometry. Nat. Methods 2007, 4, 817-821.
    • (2007) Nat. Methods , vol.4 , pp. 817-821
    • Siuti, N.1    Kelleher, N.L.2
  • 15
    • 60749119754 scopus 로고    scopus 로고
    • Systems biology: functional analysis of natural microbial consortia using community proteomics
    • VerBerkmoes, N. C., Denef, V. J., Hettich, R. L., Banfield, J. F., Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat. Rev. Microbiol. 2009, 7, 196-205.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 196-205
    • VerBerkmoes, N.C.1    Denef, V.J.2    Hettich, R.L.3    Banfield, J.F.4
  • 16
    • 84877338299 scopus 로고    scopus 로고
    • Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities
    • Hettich, R. L., Pan, C., Chourey, K., Giannone, R. J., Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal. Chem. 2013, 85, 4203-4214.
    • (2013) Anal. Chem. , vol.85 , pp. 4203-4214
    • Hettich, R.L.1    Pan, C.2    Chourey, K.3    Giannone, R.J.4
  • 17
    • 80052036518 scopus 로고    scopus 로고
    • Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella typhimurium
    • Ansong, C., Tolic, N., Purvine, S., Porwollik, S. et al., Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella typhimurium. BMC Genomics 2011, 12, 433.
    • (2011) BMC Genomics , vol.12 , pp. 433
    • Ansong, C.1    Tolic, N.2    Purvine, S.3    Porwollik, S.4
  • 18
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-the next generation
    • Metzker, M. L., Sequencing technologies-the next generation. Nat. Rev. Genet. 2010, 11, 31-46.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 19
    • 84890558766 scopus 로고    scopus 로고
    • Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions
    • Fricke, W. F., Rasko, D. A., Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat. Rev. Genet. 2014, 15, 49-55.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 49-55
    • Fricke, W.F.1    Rasko, D.A.2
  • 20
    • 0035408587 scopus 로고    scopus 로고
    • Genome annotation: from sequence to biology
    • Stein, L., Genome annotation: from sequence to biology. Nat. Rev. Genet. 2001, 2, 493-503.
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 493-503
    • Stein, L.1
  • 21
    • 77954157143 scopus 로고    scopus 로고
    • Genome (re-)annotation and open-source annotation pipelines
    • Siezen, R. J., Van Hijum, S. A. F. T., Genome (re-)annotation and open-source annotation pipelines. Microbial Biotechnol. 2010, 3, 362-369.
    • (2010) Microbial Biotechnol. , vol.3 , pp. 362-369
    • Siezen, R.J.1    Van Hijum, S.A.F.T.2
  • 22
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J. et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4
  • 23
    • 84861898310 scopus 로고    scopus 로고
    • IMG: the integrated microbial genomes database and comparative analysis system
    • Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K. et al., IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012, 40, D115-D122.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D115-D122
    • Markowitz, V.M.1    Chen, I.-M.A.2    Palaniappan, K.3    Chu, K.4
  • 24
    • 40549120596 scopus 로고    scopus 로고
    • The RAST server: rapid annotations using subsystems technology
    • Aziz, R., Bartels, D., Best, A., DeJongh, M. et al., The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008, 9, 75.
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.1    Bartels, D.2    Best, A.3    DeJongh, M.4
  • 25
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L., Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23, 673-679.
    • (2007) Bioinformatics , vol.23 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.A.2    Powers, E.C.3    Salzberg, S.L.4
  • 26
    • 23144452801 scopus 로고    scopus 로고
    • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
    • Besemer, J., Borodovsky, M., GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005, 33, W451-W454.
    • (2005) Nucleic Acids Res. , vol.33 , pp. W451-W454
    • Besemer, J.1    Borodovsky, M.2
  • 27
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn, R. D., Clements, J., Eddy, S. R., HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011, 39, W29-W37.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 28
    • 84874663959 scopus 로고    scopus 로고
    • A large-scale evaluation of computational protein function prediction
    • Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M. et al., A large-scale evaluation of computational protein function prediction. Nat. Methods 2013, 10, 221-227.
    • (2013) Nat. Methods , vol.10 , pp. 221-227
    • Radivojac, P.1    Clark, W.T.2    Oron, T.R.3    Schnoes, A.M.4
  • 29
    • 48249147316 scopus 로고    scopus 로고
    • High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
    • de Souza, G., Malen, H., Softeland, T., Saelensminde, G. et al., High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example. BMC Genomics 2008, 9, 316.
    • (2008) BMC Genomics , vol.9 , pp. 316
    • de Souza, G.1    Malen, H.2    Softeland, T.3    Saelensminde, G.4
  • 31
    • 0036253914 scopus 로고    scopus 로고
    • An accurate mass tag strategy for quantitative and high-throughput proteome measurements
    • Smith, R. D., Anderson, G. A., Lipton, M. S., Pasa-Tolic, L. et al., An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2002, 2, 513-523.
    • (2002) Proteomics , vol.2 , pp. 513-523
    • Smith, R.D.1    Anderson, G.A.2    Lipton, M.S.3    Pasa-Tolic, L.4
  • 32
    • 0035987510 scopus 로고    scopus 로고
    • The proteome of the bacterium Mycoplasma pneumoniae: comparing predicted open reading frames to identified gene products
    • Ueberle, B., Frank, R., Herrmann, R., The proteome of the bacterium Mycoplasma pneumoniae: comparing predicted open reading frames to identified gene products. Proteomics 2002, 2, 754-764.
    • (2002) Proteomics , vol.2 , pp. 754-764
    • Ueberle, B.1    Frank, R.2    Herrmann, R.3
  • 33
    • 0037143692 scopus 로고    scopus 로고
    • Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags
    • Lipton, M. S., Paša-Tolić, L., Anderson, G. A., Anderson, D. J. et al., Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. 2002, 99, 11049-11054.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 11049-11054
    • Lipton, M.S.1    Paša-Tolić, L.2    Anderson, G.A.3    Anderson, D.J.4
  • 34
    • 0034868629 scopus 로고    scopus 로고
    • Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics
    • Jungblut, P. R., Müller, E.-C., Mattow, J., Kaufmann, S. H. E., Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect. Immun. 2001, 69, 5905-5907.
    • (2001) Infect. Immun. , vol.69 , pp. 5905-5907
    • Jungblut, P.R.1    Müller, E.-C.2    Mattow, J.3    Kaufmann, S.H.E.4
  • 35
    • 28944435815 scopus 로고    scopus 로고
    • Large-scale prokaryotic gene prediction and comparison to genome annotation
    • Nielsen, P., Krogh, A., Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 2005, 21, 4322-4329.
    • (2005) Bioinformatics , vol.21 , pp. 4322-4329
    • Nielsen, P.1    Krogh, A.2
  • 36
    • 67651091927 scopus 로고    scopus 로고
    • Evaluation of three automated genome annotations for Halorhabdus utahensis
    • Bakke, P., Carney, N., DeLoache, W., Gearing, M. et al., Evaluation of three automated genome annotations for Halorhabdus utahensis. PLoS ONE 2009, 4, e6291.
    • (2009) PLoS ONE , vol.4 , pp. e6291
    • Bakke, P.1    Carney, N.2    DeLoache, W.3    Gearing, M.4
  • 37
    • 84894619287 scopus 로고    scopus 로고
    • HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics
    • Branca, R. M. M., Orre, L. M., Johansson, H. J., Granholm, V. et al., HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat. Methods 2014, 11, 59-62.
    • (2014) Nat. Methods , vol.11 , pp. 59-62
    • Branca, R.M.M.1    Orre, L.M.2    Johansson, H.J.3    Granholm, V.4
  • 39
    • 58549101102 scopus 로고    scopus 로고
    • Discovery and revision of Arabidopsis genes by proteogenomics
    • Castellana, N. E., Payne, S. H., Shen, Z., Stanke, M. et al., Discovery and revision of Arabidopsis genes by proteogenomics. Proc. Natl. Acad. Sci. 2008, 105, 21034-21038.
    • (2008) Proc. Natl. Acad. Sci. , vol.105 , pp. 21034-21038
    • Castellana, N.E.1    Payne, S.H.2    Shen, Z.3    Stanke, M.4
  • 40
    • 60849113118 scopus 로고    scopus 로고
    • Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
    • Wright, J., Sugden, D., Francis-McIntyre, S., Riba-Garcia, I. et al., Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics 2009, 10, 61.
    • (2009) BMC Genomics , vol.10 , pp. 61
    • Wright, J.1    Sugden, D.2    Francis-McIntyre, S.3    Riba-Garcia, I.4
  • 41
    • 84855533919 scopus 로고    scopus 로고
    • Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry
    • Prasad, T. S. K., Harsha, H. C., Keerthikumar, S., Sekhar, N. R. et al., Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. J. Proteome Res. 2011, 11, 247-260.
    • (2011) J. Proteome Res. , vol.11 , pp. 247-260
    • Prasad, T.S.K.1    Harsha, H.C.2    Keerthikumar, S.3    Sekhar, N.R.4
  • 42
    • 84904999159 scopus 로고    scopus 로고
    • Neglected tropical diseases and omics science: proteogenomics analysis of the promastigote stage of Leishmania major parasite
    • Pawar, H., Renuse, S., Khobragade, S. N., Chavan, S. et al., Neglected tropical diseases and omics science: proteogenomics analysis of the promastigote stage of Leishmania major parasite. OMICS 2014, 18, 499-512.
    • (2014) OMICS , vol.18 , pp. 499-512
    • Pawar, H.1    Renuse, S.2    Khobragade, S.N.3    Chavan, S.4
  • 43
    • 84903795994 scopus 로고    scopus 로고
    • Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry
    • Nagarajha Selvan, L., Kaviyil, J., Nirujogi, R., Muthusamy, B. et al., Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clin. Proteomics 2014, 11, 5.
    • (2014) Clin. Proteomics , vol.11 , pp. 5
    • Nagarajha Selvan, L.1    Kaviyil, J.2    Nirujogi, R.3    Muthusamy, B.4
  • 44
    • 44649172475 scopus 로고    scopus 로고
    • How much non-coding DNA do eukaryotes require?
    • Ahnert, S. E., Fink, T. M. A., Zinovyev, A., How much non-coding DNA do eukaryotes require? J. Theor. Biol. 2008, 252, 587-592.
    • (2008) J. Theor. Biol. , vol.252 , pp. 587-592
    • Ahnert, S.E.1    Fink, T.M.A.2    Zinovyev, A.3
  • 45
    • 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, 2124-2135.
    • (2010) J. Proteomics , vol.73 , pp. 2124-2135
    • Castellana, N.1    Bafna, V.2
  • 46
    • 0035150398 scopus 로고    scopus 로고
    • Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
    • Mann, M., Pandey, A., Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem. Sci. 2001, 26, 54-61.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 54-61
    • Mann, M.1    Pandey, A.2
  • 47
    • 77957221582 scopus 로고    scopus 로고
    • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
    • Nesvizhskii, A. I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 2010, 73, 2092-2123.
    • (2010) J. Proteomics , vol.73 , pp. 2092-2123
    • Nesvizhskii, A.I.1
  • 48
    • 84887111113 scopus 로고    scopus 로고
    • Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments
    • Krug, K., Carpy, A., Behrends, G., Matic, K. et al., Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments. Mol. Cell. Proteomics 2013, 12, 3420-3430.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3420-3430
    • Krug, K.1    Carpy, A.2    Behrends, G.3    Matic, K.4
  • 49
    • 84868310579 scopus 로고    scopus 로고
    • Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies
    • Blakeley, P., Overton, I. M., Hubbard, S. J., Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J. Proteome Res. 2012, 11, 5221-5234.
    • (2012) J. Proteome Res. , vol.11 , pp. 5221-5234
    • Blakeley, P.1    Overton, I.M.2    Hubbard, S.J.3
  • 50
    • 0942287072 scopus 로고    scopus 로고
    • Proteogenomic mapping as a complementary method to perform genome annotation
    • Jaffe, J. D., Berg, H. C., Church, G. M., Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 2004, 4, 59-77.
    • (2004) Proteomics , vol.4 , pp. 59-77
    • Jaffe, J.D.1    Berg, H.C.2    Church, G.M.3
  • 51
    • 4444350869 scopus 로고    scopus 로고
    • The complete genome and proteome of Mycoplasma mobile
    • Jaffe, J. D., Stange-Thomann, N., Smith, C., DeCaprio, D. et al., The complete genome and proteome of Mycoplasma mobile. Genome Res. 2004, 14, 1447-1461.
    • (2004) Genome Res. , vol.14 , pp. 1447-1461
    • Jaffe, J.D.1    Stange-Thomann, N.2    Smith, C.3    DeCaprio, D.4
  • 52
    • 63549124859 scopus 로고    scopus 로고
    • Alliance of proteomics and genomics to unravel the specificities of sahara bacterium Deinococcus deserti
    • de Groot, A., Dulermo, R., Ortet, P., Blanchard, L. et al., Alliance of proteomics and genomics to unravel the specificities of sahara bacterium Deinococcus deserti. PLoS Genet. 2009, 5, e1000434.
    • (2009) PLoS Genet. , vol.5 , pp. e1000434
    • de Groot, A.1    Dulermo, R.2    Ortet, P.3    Blanchard, L.4
  • 53
    • 79960911372 scopus 로고    scopus 로고
    • Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity
    • Deshpande, N. P., Kaakoush, N. O., Mitchell, H., Janitz, K. et al., Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity. PLoS ONE 2011, 6, e22170.
    • (2011) PLoS ONE , vol.6 , pp. e22170
    • Deshpande, N.P.1    Kaakoush, N.O.2    Mitchell, H.3    Janitz, K.4
  • 55
    • 67650763466 scopus 로고    scopus 로고
    • Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea
    • Zivanovic, Y., Armengaud, J., Lagorce, A., Leplat, C. et al., Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol. 2009, 10, R70.
    • (2009) Genome Biol. , vol.10 , pp. R70
    • Zivanovic, Y.1    Armengaud, J.2    Lagorce, A.3    Leplat, C.4
  • 56
    • 84876869596 scopus 로고    scopus 로고
    • The genome organization of Thermotoga maritima reflects is lifestyle
    • Latif, H., Lerman, J. A., Portnoy, V. A., Tarasova, Y. et al., The genome organization of Thermotoga maritima reflects is lifestyle. PLoS Genet. 2013, 9, e1003485.
    • (2013) PLoS Genet. , vol.9 , pp. e1003485
    • Latif, H.1    Lerman, J.A.2    Portnoy, V.A.3    Tarasova, Y.4
  • 58
    • 78651088622 scopus 로고    scopus 로고
    • Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database
    • M110.002527.
    • de Souza, G. A., Arntzen, M. Ø., Fortuin, S., Schürch, A. C. et al., Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol. Cell. Proteomics 2011, 10, M110.002527.
    • (2011) Mol. Cell. Proteomics , vol.10
    • de Souza, G.A.1    Arntzen, M.Ø.2    Fortuin, S.3    Schürch, A.C.4
  • 59
    • 84856759434 scopus 로고    scopus 로고
    • Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria
    • M111.013110.
    • Christie-Oleza, J. A., Piña-Villalonga, J. M., Bosch, R., Nogales, B., Armengaud, J., Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol. Cell. Proteomics 2012, 11, M111.013110.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Christie-Oleza, J.A.1    Piña-Villalonga, J.M.2    Bosch, R.3    Nogales, B.4    Armengaud, J.5
  • 60
    • 43749090090 scopus 로고    scopus 로고
    • Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes
    • Gupta, N., Benhamida, J., Bhargava, V., Goodman, D. et al., Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008, 18, 1133-1142.
    • (2008) Genome Res. , vol.18 , pp. 1133-1142
    • Gupta, N.1    Benhamida, J.2    Bhargava, V.3    Goodman, D.4
  • 61
    • 70349912263 scopus 로고    scopus 로고
    • False discovery rates of protein identifications: a strike against the two-peptide rule
    • Gupta, N., Pevzner, P. A., False discovery rates of protein identifications: a strike against the two-peptide rule. J. Proteome Res. 2009, 8, 4173-4181.
    • (2009) J. Proteome Res. , vol.8 , pp. 4173-4181
    • Gupta, N.1    Pevzner, P.A.2
  • 62
    • 77949576079 scopus 로고    scopus 로고
    • MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
    • de Souza, G. A., Arntzen, M. Ø., Wiker, H. G., MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes. Bioinformatics 2010, 26, 698-699.
    • (2010) Bioinformatics , vol.26 , pp. 698-699
    • de Souza, G.A.1    Arntzen, M.Ø.2    Wiker, H.G.3
  • 63
    • 84860316503 scopus 로고    scopus 로고
    • A proteogenomic approach to map the proteome of an unsequenced pathogen-Leishmania donovani
    • Pawar, H., Sahasrabuddhe, N. A., Renuse, S., Keerthikumar, S. et al., A proteogenomic approach to map the proteome of an unsequenced pathogen-Leishmania donovani. Proteomics 2012, 12, 832-844.
    • (2012) Proteomics , vol.12 , pp. 832-844
    • Pawar, H.1    Sahasrabuddhe, N.A.2    Renuse, S.3    Keerthikumar, S.4
  • 64
    • 77955212650 scopus 로고    scopus 로고
    • A proteogenomic update to Yersinia: enhancing genome annotation
    • Payne, S., Huang, S.-T., Pieper, R., A proteogenomic update to Yersinia: enhancing genome annotation. BMC Genomics 2010, 11, 460.
    • (2010) BMC Genomics , vol.11 , pp. 460
    • Payne, S.1    Huang, S.-T.2    Pieper, R.3
  • 65
    • 84857006793 scopus 로고    scopus 로고
    • High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade
    • Christie-Oleza, J., Miotello, G., Armengaud, J., High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC Genomics 2012, 13, 73.
    • (2012) BMC Genomics , vol.13 , pp. 73
    • Christie-Oleza, J.1    Miotello, G.2    Armengaud, J.3
  • 66
    • 61449116914 scopus 로고    scopus 로고
    • Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol
    • Gallien, S., Perrodou, E., Carapito, C., Deshayes, C. et al., Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res. 2009, 19, 128-135.
    • (2009) Genome Res. , vol.19 , pp. 128-135
    • Gallien, S.1    Perrodou, E.2    Carapito, C.3    Deshayes, C.4
  • 67
    • 76649085822 scopus 로고    scopus 로고
    • Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons
    • Baudet, M., Ortet, P., Gaillard, J.-C., Fernandez, B. et al., Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol. Cell. Proteomics 2010, 9, 415-426.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 415-426
    • Baudet, M.1    Ortet, P.2    Gaillard, J.-C.3    Fernandez, B.4
  • 68
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M., Snyder, M., RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 69
    • 70449370314 scopus 로고    scopus 로고
    • The transcription unit architecture of the Escherichia coli genome
    • Cho, B.-K., Zengler, K., Qiu, Y., Park, Y. S. et al., The transcription unit architecture of the Escherichia coli genome. Nat. Biotech. 2009, 27, 1043-1049.
    • (2009) Nat. Biotech. , vol.27 , pp. 1043-1049
    • Cho, B.-K.1    Zengler, K.2    Qiu, Y.3    Park, Y.S.4
  • 70
    • 84887407404 scopus 로고    scopus 로고
    • Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
    • Omasits, U., Quebatte, M., Stekhoven, D. J., Fortes, C. et al., Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Res. 2013, 23, 1916-1927.
    • (2013) Genome Res. , vol.23 , pp. 1916-1927
    • Omasits, U.1    Quebatte, M.2    Stekhoven, D.J.3    Fortes, C.4
  • 71
    • 84858988418 scopus 로고    scopus 로고
    • Comparative omics-driven genome annotation refinement: application across Yersiniae
    • Schrimpe-Rutledge, A. C., Jones, M. B., Chauhan, S., Purvine, S. O. et al., Comparative omics-driven genome annotation refinement: application across Yersiniae. PLoS ONE 2012, 7, e33903.
    • (2012) PLoS ONE , vol.7 , pp. e33903
    • Schrimpe-Rutledge, A.C.1    Jones, M.B.2    Chauhan, S.3    Purvine, S.O.4
  • 72
    • 84902988221 scopus 로고    scopus 로고
    • RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti
    • de Groot, A., Roche, D., Fernandez, B., Ludanyi, M. et al., RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. Genome Biol. Evol. 2014, 6, 932-948.
    • (2014) Genome Biol. Evol. , vol.6 , pp. 932-948
    • de Groot, A.1    Roche, D.2    Fernandez, B.3    Ludanyi, M.4
  • 73
    • 84885353313 scopus 로고    scopus 로고
    • Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach
    • Marcellin, E., Licona-Cassani, C., Mercer, T., Palfreyman, R., Nielsen, L., Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. BMC Genomics 2013, 14, 699.
    • (2013) BMC Genomics , vol.14 , pp. 699
    • Marcellin, E.1    Licona-Cassani, C.2    Mercer, T.3    Palfreyman, R.4    Nielsen, L.5
  • 74
    • 84867574100 scopus 로고    scopus 로고
    • Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production
    • Licona-Cassani, C., Marcellin, E., Quek, L.-E., Jacob, S., Nielsen, L., Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. A. van Leeuw. 2012, 102, 493-502.
    • (2012) A. van Leeuw. , vol.102 , pp. 493-502
    • Licona-Cassani, C.1    Marcellin, E.2    Quek, L.-E.3    Jacob, S.4    Nielsen, L.5
  • 75
  • 76
    • 0034060929 scopus 로고    scopus 로고
    • Powers and pitfalls in sequence analysis: the 70% hurdle
    • Bork, P., Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res. 2000, 10, 398-400.
    • (2000) Genome Res. , vol.10 , pp. 398-400
    • Bork, P.1
  • 77
    • 0035161543 scopus 로고    scopus 로고
    • Genomes OnLine Database (GOLD): a monitor of genome projects world-wide
    • Bernal, A., Ear, U., Kyrpides, N., Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 2001, 29, 126-127.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 126-127
    • Bernal, A.1    Ear, U.2    Kyrpides, N.3
  • 78
    • 28844492648 scopus 로고    scopus 로고
    • Protein surface analysis for function annotation in high-throughput structural genomics pipeline
    • Binkowski, T. A., Joachimiak, A., Liang, J., Protein surface analysis for function annotation in high-throughput structural genomics pipeline. Protein Sci. 2005, 14, 2972-2981.
    • (2005) Protein Sci. , vol.14 , pp. 2972-2981
    • Binkowski, T.A.1    Joachimiak, A.2    Liang, J.3
  • 79
    • 0037407924 scopus 로고    scopus 로고
    • Predicting gene function by conserved co-expression
    • van Noort, V., Snel, B., Huynen, M. A., Predicting gene function by conserved co-expression. Trends Genet. 2003, 19, 238-242.
    • (2003) Trends Genet. , vol.19 , pp. 238-242
    • van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 81
    • 84863400707 scopus 로고    scopus 로고
    • Activity-based protein profiling: an enabling technology in chemical biology research
    • Li, N., Overkleeft, H. S., Florea, B. I., Activity-based protein profiling: an enabling technology in chemical biology research. Curr. Opin. Chem. Biol. 2012, 16, 227-233.
    • (2012) Curr. Opin. Chem. Biol. , vol.16 , pp. 227-233
    • Li, N.1    Overkleeft, H.S.2    Florea, B.I.3
  • 82
    • 35848965006 scopus 로고    scopus 로고
    • Activity-based protein profiling for the functional annotation of enzymes
    • Barglow, K. T., Cravatt, B. F., Activity-based protein profiling for the functional annotation of enzymes. Nat. Methods 2007, 4, 822-827.
    • (2007) Nat. Methods , vol.4 , pp. 822-827
    • Barglow, K.T.1    Cravatt, B.F.2
  • 83
    • 50649112213 scopus 로고    scopus 로고
    • Activity-based protein profiling: from enzyme chemistry to proteomic chemistry
    • Cravatt, B. F., Wright, A. T., Kozarich, J. W., Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 2008, 77, 383-414.
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 383-414
    • Cravatt, B.F.1    Wright, A.T.2    Kozarich, J.W.3
  • 84
    • 83055180536 scopus 로고    scopus 로고
    • Functional imaging of proteases: recent advances in the design and application of substrate-based and activity-based probes
    • Edgington, L. E., Verdoes, M., Bogyo, M., Functional imaging of proteases: recent advances in the design and application of substrate-based and activity-based probes. Curr. Opin. Chem. Biol. 2011, 15, 798-805.
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 798-805
    • Edgington, L.E.1    Verdoes, M.2    Bogyo, M.3
  • 85
    • 33846807650 scopus 로고    scopus 로고
    • Tagging and detection strategies for activity-based proteomics
    • Sadaghiani, A. M., Verhelst, S. H. L., Bogyo, M., Tagging and detection strategies for activity-based proteomics. Curr. Opin. Chem. Biol. 2007, 11, 20-28.
    • (2007) Curr. Opin. Chem. Biol. , vol.11 , pp. 20-28
    • Sadaghiani, A.M.1    Verhelst, S.H.L.2    Bogyo, M.3
  • 86
    • 84883479874 scopus 로고    scopus 로고
    • Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses
    • Puri, A. W., Bogyo, M., Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses. Biochemistry 2013, 52, 5985-5996.
    • (2013) Biochemistry , vol.52 , pp. 5985-5996
    • Puri, A.W.1    Bogyo, M.2
  • 87
    • 33748595526 scopus 로고    scopus 로고
    • Mechanism-based profiling of enzyme families
    • Evans, M. J., Cravatt, B. F., Mechanism-based profiling of enzyme families. Chem. Rev. 2006, 106, 3279-3301.
    • (2006) Chem. Rev. , vol.106 , pp. 3279-3301
    • Evans, M.J.1    Cravatt, B.F.2
  • 88
    • 77951216021 scopus 로고    scopus 로고
    • Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study
    • Simon, G. M., Cravatt, B. F., Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study. J. Biol. Chem. 2010, 285, 11051-11055.
    • (2010) J. Biol. Chem. , vol.285 , pp. 11051-11055
    • Simon, G.M.1    Cravatt, B.F.2
  • 89
    • 79952064512 scopus 로고    scopus 로고
    • Autoproteolytic activation of bacterial toxins
    • Shen, A., Autoproteolytic activation of bacterial toxins. Toxins 2010, 2, 963-977.
    • (2010) Toxins , vol.2 , pp. 963-977
    • Shen, A.1
  • 90
    • 81255127216 scopus 로고    scopus 로고
    • Regulated proteolysis in Gram-negative bacteria-how and when?
    • Gur, E., Biran, D., Ron, E. Z., Regulated proteolysis in Gram-negative bacteria-how and when? Nat. Rev. Microbiol. 2011, 9, 839-848.
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 839-848
    • Gur, E.1    Biran, D.2    Ron, E.Z.3
  • 91
    • 53549118638 scopus 로고    scopus 로고
    • β-Lactams as selective chemical probes for the in vivo labeling of bacterial enzymes involved in cell wall biosynthesis, antibiotic resistance, and virulence
    • Staub, I., Sieber, S. A., β-Lactams as selective chemical probes for the in vivo labeling of bacterial enzymes involved in cell wall biosynthesis, antibiotic resistance, and virulence. J. Am. Chem. Soc. 2008, 130, 13400-13409.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 13400-13409
    • Staub, I.1    Sieber, S.A.2
  • 92
    • 70149092317 scopus 로고    scopus 로고
    • β-Lactam probes as selective chemical-proteomic tools for the identification and functional characterization of resistance associated enzymes in MRSA
    • Staub, I., Sieber, S. A., β-Lactam probes as selective chemical-proteomic tools for the identification and functional characterization of resistance associated enzymes in MRSA. J. Am. Chem. Soc. 2009, 131, 6271-6276.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 6271-6276
    • Staub, I.1    Sieber, S.A.2
  • 93
    • 84875182792 scopus 로고    scopus 로고
    • Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria
    • Deng, X., Weerapana, E., Ulanovskaya, O., Sun, F. et al., Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe 2013, 13, 358-370.
    • (2013) Cell Host Microbe , vol.13 , pp. 358-370
    • Deng, X.1    Weerapana, E.2    Ulanovskaya, O.3    Sun, F.4
  • 94
    • 84867169460 scopus 로고    scopus 로고
    • Oxidative modification of proteins: an emerging mechanism of cell signaling
    • Wall, S. B., Oh, J.-Y., Diers, A. R., Landar, A., Oxidative modification of proteins: an emerging mechanism of cell signaling. Front. Physiol. 2012, 3, 1-9.
    • (2012) Front. Physiol. , vol.3 , pp. 1-9
    • Wall, S.B.1    Oh, J.-Y.2    Diers, A.R.3    Landar, A.4
  • 95
    • 84872908803 scopus 로고    scopus 로고
    • Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis
    • Ansong, C., Ortega, C., Payne, Samuel H., Haft, Daniel H. et al., Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Chem. Biol. 2013, 20, 123-133.
    • (2013) Chem. Biol. , vol.20 , pp. 123-133
    • Ansong, C.1    Ortega, C.2    Payne, S.H.3    Haft, D.H.4
  • 96
    • 84857502685 scopus 로고    scopus 로고
    • Statistics of N-terminal alignment as a guide for refining prokaryotic gene annotation
    • Sato, N., Tajima, N., Statistics of N-terminal alignment as a guide for refining prokaryotic gene annotation. Genomics 2012, 99, 138-143.
    • (2012) Genomics , vol.99 , pp. 138-143
    • Sato, N.1    Tajima, N.2
  • 97
    • 33646898143 scopus 로고    scopus 로고
    • Proteome analysis of an aerobic hyperthermophilic Crenarchaeon, Aeropyrum pernix K1
    • Yamazaki, S., Yamazaki, J., Nishijima, K., Otsuka, R. et al., Proteome analysis of an aerobic hyperthermophilic Crenarchaeon, Aeropyrum pernix K1. Mol. Cell. Proteomics 2006, 5, 811-823.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 811-823
    • Yamazaki, S.1    Yamazaki, J.2    Nishijima, K.3    Otsuka, R.4
  • 98
    • 84899708164 scopus 로고    scopus 로고
    • N-terminal-oriented proteogenomics of the marine bacterium Roseobacter denitrificans OCh114 using TMPP labeling and diagonal chromatography
    • Bland, C., Hartmann, E. M., Christie-Oleza, J. A., Fernandez, B., Armengaud, J., N-terminal-oriented proteogenomics of the marine bacterium Roseobacter denitrificans OCh114 using TMPP labeling and diagonal chromatography. Mol. Cell. Proteomics 2014, 13, 1369-1381.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 1369-1381
    • Bland, C.1    Hartmann, E.M.2    Christie-Oleza, J.A.3    Fernandez, B.4    Armengaud, J.5
  • 99
    • 34548452940 scopus 로고    scopus 로고
    • Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
    • Gupta, N., Tanner, S., Jaitly, N., Adkins, J. N. et al., Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007, 17, 1362-1377.
    • (2007) Genome Res. , vol.17 , pp. 1362-1377
    • Gupta, N.1    Tanner, S.2    Jaitly, N.3    Adkins, J.N.4
  • 100
    • 34250886391 scopus 로고    scopus 로고
    • Large-scale identification of N-terminal peptides in the halophilic Archaea Halobacterium salinarum and Natronomonas pharaonis
    • Aivaliotis, M., Gevaert, K., Falb, M., Tebbe, A. et al., Large-scale identification of N-terminal peptides in the halophilic Archaea Halobacterium salinarum and Natronomonas pharaonis. J. Proteome Res. 2007, 6, 2195-2204.
    • (2007) J. Proteome Res. , vol.6 , pp. 2195-2204
    • Aivaliotis, M.1    Gevaert, K.2    Falb, M.3    Tebbe, A.4
  • 101
    • 84879343630 scopus 로고    scopus 로고
    • An improved stable isotope n-terminal labeling approach with light/heavy tmpp to automate proteogenomics data validation: dN-TOP
    • Bertaccini, D., Vaca, S., Carapito, C., Arsène-Ploetze, F. et al., An improved stable isotope n-terminal labeling approach with light/heavy tmpp to automate proteogenomics data validation: dN-TOP. J. Proteome Res. 2013, 12, 3063-3070.
    • (2013) J. Proteome Res. , vol.12 , pp. 3063-3070
    • Bertaccini, D.1    Vaca, S.2    Carapito, C.3    Arsène-Ploetze, F.4
  • 102
    • 84893870655 scopus 로고    scopus 로고
    • Magnetic immunoaffinity enrichment for selective capture and ms/ms analysis of n-terminal-TMPP-labeled peptides
    • Bland, C., Bellanger, L., Armengaud, J., Magnetic immunoaffinity enrichment for selective capture and ms/ms analysis of n-terminal-TMPP-labeled peptides. J. Proteome Res. 2013, 13, 668-680.
    • (2013) J. Proteome Res. , vol.13 , pp. 668-680
    • Bland, C.1    Bellanger, L.2    Armengaud, J.3
  • 103
    • 66349116973 scopus 로고    scopus 로고
    • A perfect genome annotation is within reach with the proteomics and genomics alliance
    • Armengaud, J., A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr. Opin. Microbiol. 2009, 12, 292-300.
    • (2009) Curr. Opin. Microbiol. , vol.12 , pp. 292-300
    • Armengaud, J.1
  • 104
    • 40549086253 scopus 로고    scopus 로고
    • Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS
    • Nakazawa, T., Yamaguchi, M., Okamura, T.-a., Ando, E. et al., Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS. Proteomics 2008, 8, 673-685.
    • (2008) Proteomics , vol.8 , pp. 673-685
    • Nakazawa, T.1    Yamaguchi, M.2    Okamura, T.-A.3    Ando, E.4
  • 105
    • 84890577781 scopus 로고    scopus 로고
    • Proteolytic post-translational modification of proteins: proteomic tools and methodology
    • Rogers, L. D., Overall, C. M., Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol. Cell. Proteomics 2013, 12, 3532-3542.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3532-3542
    • Rogers, L.D.1    Overall, C.M.2
  • 106
    • 80053415277 scopus 로고    scopus 로고
    • Protein alpha-N-acetylation studied by N-terminomics
    • Van Damme, P., Arnesen, T., Gevaert, K., Protein alpha-N-acetylation studied by N-terminomics. FEBS J. 2011, 278, 3822-3834.
    • (2011) FEBS J. , vol.278 , pp. 3822-3834
    • Van Damme, P.1    Arnesen, T.2    Gevaert, K.3
  • 108
    • 33847208190 scopus 로고    scopus 로고
    • Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis
    • Rison, S. C. G., Mattow, J., Jungblut, P. R., Stoker, N. G., Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis. Microbiology 2007, 153, 521-528.
    • (2007) Microbiology , vol.153 , pp. 521-528
    • Rison, S.C.G.1    Mattow, J.2    Jungblut, P.R.3    Stoker, N.G.4
  • 109
    • 27244439061 scopus 로고    scopus 로고
    • Deciphering the model pathogenic fungus Cryptococcus neoformans
    • Idnurm, A., Bahn, Y.-S., Nielsen, K., Lin, X. et al., Deciphering the model pathogenic fungus Cryptococcus neoformans. Nat. Rev. Microbiol. 2005, 3, 753-764.
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 753-764
    • Idnurm, A.1    Bahn, Y.-S.2    Nielsen, K.3    Lin, X.4
  • 110
    • 80053604348 scopus 로고    scopus 로고
    • Selecting protein N-terminal peptides by combined fractional diagonal chromatography
    • Staes, A., Impens, F., Van Damme, P., Ruttens, B. et al., Selecting protein N-terminal peptides by combined fractional diagonal chromatography. Nat. Protocols 2011, 6, 1130-1141.
    • (2011) Nat. Protocols , vol.6 , pp. 1130-1141
    • Staes, A.1    Impens, F.2    Van Damme, P.3    Ruttens, B.4
  • 111
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotech. 2003, 21, 566-569.
    • (2003) Nat. Biotech. , vol.21 , pp. 566-569
    • Gevaert, K.1    Goethals, M.2    Martens, L.3    Van Damme, J.4
  • 112
    • 79961232419 scopus 로고    scopus 로고
    • Bioinformatics snalysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation
    • Helsens, K., Van Damme, P., Degroeve, S., Martens, L. et al., Bioinformatics snalysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. J. Proteome Res. 2011, 10, 3578-3589.
    • (2011) J. Proteome Res. , vol.10 , pp. 3578-3589
    • Helsens, K.1    Van Damme, P.2    Degroeve, S.3    Martens, L.4
  • 114
    • 84872160508 scopus 로고    scopus 로고
    • Unexpected diversity of signal peptides in prokaryotes
    • Payne, S. H., Bonissone, S., Wu, S., Brown, R. N. et al., Unexpected diversity of signal peptides in prokaryotes. mBio 2012, 3, e00339-12.
    • (2012) mBio , vol.3
    • Payne, S.H.1    Bonissone, S.2    Wu, S.3    Brown, R.N.4
  • 115
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • Petersen, T. N., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8, 785-786.
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 116
    • 34547584314 scopus 로고    scopus 로고
    • Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server
    • Käll, L., Krogh, A., Sonnhammer, E. L. L., Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res. 2007, 35, W429-W432.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W429-W432
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 117
    • 69949116837 scopus 로고    scopus 로고
    • Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods
    • Leversen, N. A., de Souza, G. A., Målen, H., Prasad, S. et al., Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods. Microbiology 2009, 155, 2375-2383.
    • (2009) Microbiology , vol.155 , pp. 2375-2383
    • Leversen, N.A.1    de Souza, G.A.2    Målen, H.3    Prasad, S.4
  • 118
    • 84860575662 scopus 로고    scopus 로고
    • Proteogenomic analysis of bacteria and archaea: a 46 organism case study
    • Venter, E., Smith, R. D., Payne, S. H., Proteogenomic analysis of bacteria and archaea: a 46 organism case study. PLoS ONE 2011, 6, e27587.
    • (2011) PLoS ONE , vol.6 , pp. e27587
    • Venter, E.1    Smith, R.D.2    Payne, S.H.3
  • 120
    • 84894232328 scopus 로고    scopus 로고
    • Top-down characterization of the post-translationally modified intact periplasmic proteome from the bacterium Novosphingobium aromaticivorans
    • Wu, S., Brown, R. N., Payne, S. H., Meng, D. et al., Top-down characterization of the post-translationally modified intact periplasmic proteome from the bacterium Novosphingobium aromaticivorans. Int. J. Proteomics 2013, 2013, 10.
    • (2013) Int. J. Proteomics , vol.2013 , pp. 10
    • Wu, S.1    Brown, R.N.2    Payne, S.H.3    Meng, D.4
  • 121
    • 77952040946 scopus 로고    scopus 로고
    • Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community
    • Erickson, B. K., Mueller, R. S., VerBerkmoes, N. C., Shah, M. et al., Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. J. Proteome Res. 2010, 9, 2148-2159.
    • (2010) J. Proteome Res. , vol.9 , pp. 2148-2159
    • Erickson, B.K.1    Mueller, R.S.2    VerBerkmoes, N.C.3    Shah, M.4
  • 122
    • 84878953727 scopus 로고    scopus 로고
    • Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
    • Müller, S. A., Findeiß, S., Pernitzsch, S. R., Wissenbach, D. K. et al., Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J. Proteomics 2013, 86, 27-42.
    • (2013) J. Proteomics , vol.86 , pp. 27-42
    • Müller, S.A.1    Findeiß, S.2    Pernitzsch, S.R.3    Wissenbach, D.K.4
  • 123
    • 84892876508 scopus 로고    scopus 로고
    • Beyond gene expression: the impact of protein post-translational modifications in bacteria
    • Cain, J. A., Solis, N., Cordwell, S. J., Beyond gene expression: the impact of protein post-translational modifications in bacteria. J. Proteomics 2014, 97, 265-286.
    • (2014) J. Proteomics , vol.97 , pp. 265-286
    • Cain, J.A.1    Solis, N.2    Cordwell, S.J.3
  • 124
    • 70350247861 scopus 로고    scopus 로고
    • Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques
    • Zhao, Y., Jensen, O. N., Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 2009, 9, 4632-4641.
    • (2009) Proteomics , vol.9 , pp. 4632-4641
    • Zhao, Y.1    Jensen, O.N.2
  • 125
    • 79959424627 scopus 로고    scopus 로고
    • Quantitative, high-resolution proteomics for data-driven systems biology
    • Cox, J., Mann, M., Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 2011, 80, 273-299.
    • (2011) Annu. Rev. Biochem. , vol.80 , pp. 273-299
    • Cox, J.1    Mann, M.2
  • 127
    • 84890644637 scopus 로고    scopus 로고
    • Status of large-scale analysis of post-translational modifications by mass spectrometry
    • Olsen, J. V., Mann, M., Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol. Cell. Proteomics 2013, 12, 3444-3452.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3444-3452
    • Olsen, J.V.1    Mann, M.2
  • 128
    • 49849098210 scopus 로고    scopus 로고
    • Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins
    • Gaucher, S. P., Redding, A. M., Mukhopadhyay, A., Keasling, J. D., Singh, A. K., Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins. J. Proteome Res. 2008, 7, 2320-2331.
    • (2008) J. Proteome Res. , vol.7 , pp. 2320-2331
    • Gaucher, S.P.1    Redding, A.M.2    Mukhopadhyay, A.3    Keasling, J.D.4    Singh, A.K.5
  • 129
    • 74249106136 scopus 로고    scopus 로고
    • What does the future hold for top down mass spectrometry?
    • Garcia, B., What does the future hold for top down mass spectrometry? J. Am. Soc. Mass Spectrom. 2010, 21, 193-202.
    • (2010) J. Am. Soc. Mass Spectrom. , vol.21 , pp. 193-202
    • Garcia, B.1
  • 131
    • 33847393182 scopus 로고    scopus 로고
    • Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry
    • Sharma, S., Simpson, D. C., Tolić, N., Jaitly, N. et al., Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. J. Proteome Res. 2006, 6, 602-610.
    • (2006) J. Proteome Res. , vol.6 , pp. 602-610
    • Sharma, S.1    Simpson, D.C.2    Tolić, N.3    Jaitly, N.4
  • 132
    • 31644435925 scopus 로고    scopus 로고
    • Top down mass spectrometry of <60-kda proteins from Methanosarcina acetivorans using quadrupole ftms with automated octopole collisionally activated dissociation
    • Patrie, S. M., Ferguson, J. T., Robinson, D. E., Whipple, D. et al., Top down mass spectrometry of <60-kda proteins from Methanosarcina acetivorans using quadrupole ftms with automated octopole collisionally activated dissociation. Mol. Cell. Proteomics 2006, 5, 14-25.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 14-25
    • Patrie, S.M.1    Ferguson, J.T.2    Robinson, D.E.3    Whipple, D.4
  • 133
    • 76849109997 scopus 로고    scopus 로고
    • Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa
    • Vellaichamy, A., Tran, J. C., Catherman, A. D., Lee, J. E. et al., Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa. Anal. Chem. 2010, 82, 1234-1244.
    • (2010) Anal. Chem. , vol.82 , pp. 1234-1244
    • Vellaichamy, A.1    Tran, J.C.2    Catherman, A.D.3    Lee, J.E.4
  • 134
    • 84862596522 scopus 로고    scopus 로고
    • Impact of phosphoproteomics on studies of bacterial physiology
    • Mijakovic, I., Macek, B., Impact of phosphoproteomics on studies of bacterial physiology. FEMS Microbiol. Rev. 2012, 36, 877-892.
    • (2012) FEMS Microbiol. Rev. , vol.36 , pp. 877-892
    • Mijakovic, I.1    Macek, B.2
  • 135
    • 84879536162 scopus 로고    scopus 로고
    • The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence
    • Hansen, A.-M., Chaerkady, R., Sharma, J., Díaz-Mejía, J. J. et al., The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathog. 2013, 9, e1003403.
    • (2013) PLoS Pathog. , vol.9 , pp. e1003403
    • Hansen, A.-M.1    Chaerkady, R.2    Sharma, J.3    Díaz-Mejía, J.J.4
  • 136
    • 84255170511 scopus 로고    scopus 로고
    • Bacterial phosphoproteomic analysis reveals the correlation between protein phosphorylation and bacterial pathogenicity
    • Ge, R., Shan, W., Bacterial phosphoproteomic analysis reveals the correlation between protein phosphorylation and bacterial pathogenicity. Genomics Proteomics Bioinformatics 2011, 9, 119-127.
    • (2011) Genomics Proteomics Bioinformatics , vol.9 , pp. 119-127
    • Ge, R.1    Shan, W.2
  • 137
    • 84893721888 scopus 로고    scopus 로고
    • The phosphoproteome and its physiological dynamics in Staphylococcus aureus
    • Bäsell, K., Otto, A., Junker, S., Zühlke, D. et al., The phosphoproteome and its physiological dynamics in Staphylococcus aureus. Int. J. Med. Microbiol. 2014, 304, 121-132.
    • (2014) Int. J. Med. Microbiol. , vol.304 , pp. 121-132
    • Bäsell, K.1    Otto, A.2    Junker, S.3    Zühlke, D.4
  • 138
    • 84905281353 scopus 로고    scopus 로고
    • Quantitative phosphoproteome analysis of Bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC
    • Ravikumar, V., Shi, L., Krug, K., Derouiche, A. et al., Quantitative phosphoproteome analysis of Bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC. Mol. Cell. Proteomics 2014, 13, 1965-1978.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 1965-1978
    • Ravikumar, V.1    Shi, L.2    Krug, K.3    Derouiche, A.4
  • 139
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    • Kim, S., Gupta, N., Pevzner, P. A., Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 2008, 7, 3354-3363.
    • (2008) J. Proteome Res. , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 140
    • 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, 207-214.
    • (2007) Nat. Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 141
    • 34547556725 scopus 로고    scopus 로고
    • Introduction to computational proteomics
    • Colinge, J., Bennett, K. L., Introduction to computational proteomics. PLoS Comput. Biol. 2007, 3, e114.
    • (2007) PLoS Comput. Biol. , vol.3 , pp. e114
    • Colinge, J.1    Bennett, K.L.2
  • 142
    • 84869211929 scopus 로고    scopus 로고
    • Inference and validation of protein identifications
    • Claassen, M., Inference and validation of protein identifications. Mol. Cell. Proteomics 2012, 11, 1097-1104.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1097-1104
    • Claassen, M.1
  • 143
    • 84886054819 scopus 로고    scopus 로고
    • Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite, an automated multi-algorithmic pipeline
    • Kumar, D., Yadav, A. K., Kadimi, P. K., Nagaraj, S. H. et al., Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite, an automated multi-algorithmic pipeline. Mol. Cell. Proteomics 2013, 12, 3388-3397.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3388-3397
    • Kumar, D.1    Yadav, A.K.2    Kadimi, P.K.3    Nagaraj, S.H.4
  • 144
    • 77951987273 scopus 로고    scopus 로고
    • Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
    • Lamontagne, J., Beland, M., Forest, A., Cote-Martin, A. et al., Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome. BMC Genomics 2010, 11, 300.
    • (2010) BMC Genomics , vol.11 , pp. 300
    • Lamontagne, J.1    Beland, M.2    Forest, A.3    Cote-Martin, A.4
  • 145
    • 84892863715 scopus 로고    scopus 로고
    • Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani
    • Nirujogi, R. S., Pawar, H., Renuse, S., Kumar, P. et al., Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. J. Proteomics 2014, 97, 48-61.
    • (2014) J. Proteomics , vol.97 , pp. 48-61
    • Nirujogi, R.S.1    Pawar, H.2    Renuse, S.3    Kumar, P.4
  • 146
    • 67650750887 scopus 로고    scopus 로고
    • Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry
    • de Souza, G. A., Søfteland, T., Koehler, C. J., Thiede, B., Wiker, H. G., Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry. Proteomics 2009, 9, 3233-3243.
    • (2009) Proteomics , vol.9 , pp. 3233-3243
    • de Souza, G.A.1    Søfteland, T.2    Koehler, C.J.3    Thiede, B.4    Wiker, H.G.5
  • 147
    • 23744515352 scopus 로고    scopus 로고
    • Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias
    • Wang, R., Prince, J. T., Marcotte, E. M., Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005, 15, 1118-1126.
    • (2005) Genome Res. , vol.15 , pp. 1118-1126
    • Wang, R.1    Prince, J.T.2    Marcotte, E.M.3
  • 148
    • 83055173265 scopus 로고    scopus 로고
    • Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry
    • M111.011627.
    • Kelkar, D. S., Kumar, D., Kumar, P., Balakrishnan, L. et al., Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol. Cell. Proteomics 2011, 10, M111.011627.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Kelkar, D.S.1    Kumar, D.2    Kumar, P.3    Balakrishnan, L.4
  • 149
    • 0037015610 scopus 로고    scopus 로고
    • Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry
    • Lasonder, E., Ishihama, Y., Andersen, J. S., Vermunt, A. M. W. et al., Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 2002, 419, 537-542.
    • (2002) Nature , vol.419 , pp. 537-542
    • Lasonder, E.1    Ishihama, Y.2    Andersen, J.S.3    Vermunt, A.M.W.4
  • 150
    • 33750967613 scopus 로고    scopus 로고
    • Expressed peptide tags: an additional layer of data for genome annotation
    • Savidor, A., Donahoo, R. S., Hurtado-Gonzales, O., VerBerkmoes, N. C. et al., Expressed peptide tags: an additional layer of data for genome annotation. J. Proteome Res. 2006, 5, 3048-3058.
    • (2006) J. Proteome Res. , vol.5 , pp. 3048-3058
    • Savidor, A.1    Donahoo, R.S.2    Hurtado-Gonzales, O.3    VerBerkmoes, N.C.4
  • 151
    • 80055020945 scopus 로고    scopus 로고
    • A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF
    • Zhao, L., Liu, L., Leng, W., Wei, C., Jin, Q., A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF. BMC Genomics 2011, 12, 528.
    • (2011) BMC Genomics , vol.12 , pp. 528
    • Zhao, L.1    Liu, L.2    Leng, W.3    Wei, C.4    Jin, Q.5
  • 152
    • 80755189686 scopus 로고    scopus 로고
    • Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome
    • Okamoto, A., Yamada, K., Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome. BMC Microbiol. 2011, 11, 249.
    • (2011) BMC Microbiol. , vol.11 , pp. 249
    • Okamoto, A.1    Yamada, K.2
  • 153
    • 58149328654 scopus 로고    scopus 로고
    • Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach
    • Rodriguez-Ortega, M., Luque, I., Tarradas, C., Barcena, J., Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach. BMC Genomics 2008, 9, 588.
    • (2008) BMC Genomics , vol.9 , pp. 588
    • Rodriguez-Ortega, M.1    Luque, I.2    Tarradas, C.3    Barcena, J.4
  • 154
    • 36549015654 scopus 로고    scopus 로고
    • Mass spectrometry-based prokaryote gene annotation
    • Ishino, Y., Okada, H., Ikeuchi, M., Taniguchi, H., Mass spectrometry-based prokaryote gene annotation. Proteomics 2007, 7, 4053-4065.
    • (2007) Proteomics , vol.7 , pp. 4053-4065
    • Ishino, Y.1    Okada, H.2    Ikeuchi, M.3    Taniguchi, H.4
  • 155
    • 84894110748 scopus 로고    scopus 로고
    • customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search
    • Wang, X., Zhang, B., customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search. Bioinformatics 2013, 29, 3235-3237.
    • (2013) Bioinformatics , vol.29 , pp. 3235-3237
    • Wang, X.1    Zhang, B.2
  • 157
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S., Shu, H., Frank, A., Wang, L.-C. et al., InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
    • (2005) Anal. Chem. , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4
  • 158
    • 84870751362 scopus 로고    scopus 로고
    • iPiG: integrating peptide spectrum matches into genome browser visualizations
    • Kuhring, M., Renard, B. Y., iPiG: integrating peptide spectrum matches into genome browser visualizations. PLoS ONE 2012, 7, e50246.
    • (2012) PLoS ONE , vol.7 , pp. e50246
    • Kuhring, M.1    Renard, B.Y.2
  • 159
    • 58049218989 scopus 로고    scopus 로고
    • MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
    • Brouwer, R. W. W., van Hijum, S. A. F. T., Kuipers, O. P., MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinformatics 2009, 25, 139-140.
    • (2009) Bioinformatics , vol.25 , pp. 139-140
    • Brouwer, R.W.W.1    van Hijum, S.A.F.T.2    Kuipers, O.P.3
  • 160
    • 84891792626 scopus 로고    scopus 로고
    • Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing
    • Pang, C. N. I., Tay, A. P., Aya, C., Twine, N. A. et al., Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing. J. Proteome Res. 2013, 13, 84-98.
    • (2013) J. Proteome Res. , vol.13 , pp. 84-98
    • Pang, C.N.I.1    Tay, A.P.2    Aya, C.3    Twine, N.A.4
  • 161
    • 52049102297 scopus 로고    scopus 로고
    • PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences
    • Ferro, M., Tardif, M., Reguer, E., Cahuzac, R. et al., PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J. Proteome Res. 2008, 7, 1873-1883.
    • (2008) J. Proteome Res. , vol.7 , pp. 1873-1883
    • Ferro, M.1    Tardif, M.2    Reguer, E.3    Cahuzac, R.4
  • 163
    • 84900804573 scopus 로고    scopus 로고
    • PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
    • Tovchigrechko, A., Venepally, P., Payne, S. H., PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. Bioinformatics 2014, 30, 1469-1470.
    • (2014) Bioinformatics , vol.30 , pp. 1469-1470
    • Tovchigrechko, A.1    Venepally, P.2    Payne, S.H.3
  • 165
    • 84897873840 scopus 로고    scopus 로고
    • Protter: interactive protein feature visualization and integration with experimental proteomic data
    • Omasits, U., Ahrens, C. H., Müller, S., Wollscheid, B., Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics 2013, 30, 884-886.
    • (2013) Bioinformatics , vol.30 , pp. 884-886
    • Omasits, U.1    Ahrens, C.H.2    Müller, S.3    Wollscheid, B.4
  • 166
    • 84862227658 scopus 로고    scopus 로고
    • TopFIND 2.0-linking protein termini with proteolytic processing and modifications altering protein function
    • Lange, P. F., Huesgen, P. F., Overall, C. M., TopFIND 2.0-linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res. 2012, 40, D351-D361.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D351-D361
    • Lange, P.F.1    Huesgen, P.F.2    Overall, C.M.3
  • 167
    • 84859323308 scopus 로고    scopus 로고
    • VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
    • Peterson, E., McCue, L. A., Schrimpe-Rutledge, A., Jensen, J. et al., VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics 2012, 13, 131.
    • (2012) BMC Genomics , vol.13 , pp. 131
    • Peterson, E.1    McCue, L.A.2    Schrimpe-Rutledge, A.3    Jensen, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.