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Volumn 34, Issue 2, 2015, Pages 133-147

Software eyes for protein post-translational modifications

Author keywords

Computational proteomics; Post translational modification; Software; Tandem mass spectrometry

Indexed keywords

COMPUTER SOFTWARE; COVALENT BONDS; MASS SPECTROMETRY; PROTEOMICS; SEARCH ENGINES; SULFUR COMPOUNDS;

EID: 84923088385     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.21425     Document Type: Article
Times cited : (48)

References (95)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M. 2003. Mass spectrometry-based proteomics. Nature 422:198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 77149158441 scopus 로고    scopus 로고
    • Unrestricted identification of modified proteins using MS/MS
    • Ahrné E, Müller M, Lisacek F. 2010. Unrestricted identification of modified proteins using MS/MS. Proteomics 10:671-686.
    • (2010) Proteomics , vol.10 , pp. 671-686
    • Ahrné, E.1    Müller, M.2    Lisacek, F.3
  • 3
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: History, character, and diagnostic prospects
    • Anderson NL, Anderson NG. 2002. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 1:845-867.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 6
    • 55249092493 scopus 로고    scopus 로고
    • SeMoP: A new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data
    • Baumgartner C, Rejtar T, Kullolli M, Akella LM, Karger BL. 2008. SeMoP: A new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data. J Proteome Res 7:4199-4208.
    • (2008) J Proteome Res , vol.7 , pp. 4199-4208
    • Baumgartner, C.1    Rejtar, T.2    Kullolli, M.3    Akella, L.M.4    Karger, B.L.5
  • 8
    • 33749853607 scopus 로고    scopus 로고
    • A probabilitybased approach for high-throughput protein phosphorylation analysis and site localization
    • Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP. 2006. A probabilitybased approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24:1285-1292.
    • (2006) Nat Biotechnol , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villén, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 9
    • 33847234661 scopus 로고    scopus 로고
    • Lookup peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry
    • Bern M, Cai Y, Goldberg D. 2007. Lookup peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Anal Chem 79:1393-1400.
    • (2007) Anal Chem , vol.79 , pp. 1393-1400
    • Bern, M.1    Cai, Y.2    Goldberg, D.3
  • 10
    • 79953711171 scopus 로고    scopus 로고
    • Comment on "Unbiased statistical analysis for multistage proteomic search strategies"
    • Bern M, Kil YJ. 2011. Comment on "Unbiased statistical analysis for multistage proteomic search strategies". J Proteome Res 10:2123-2127.
    • (2011) J Proteome Res , vol.10 , pp. 2123-2127
    • Bern, M.1    Kil, Y.J.2
  • 12
    • 5644247544 scopus 로고    scopus 로고
    • Strategies for shotgun identification of posttranslational modifications by mass spectrometry
    • Cantin GT, Yates JR III. 2004. Strategies for shotgun identification of posttranslational modifications by mass spectrometry. J Chromatogr A 1053:7-14.
    • (2004) J Chromatogr A , vol.1053 , pp. 7-14
    • Cantin, G.T.1    Yates, J.R.2
  • 13
    • 66749092934 scopus 로고    scopus 로고
    • Systematic LC-MS analysis of labile post-translational modifications in complex mixtures
    • Carapito C, Klemm C, Aebersold R, Domon B. 2009. Systematic LC-MS analysis of labile post-translational modifications in complex mixtures. J Proteome Res 8:2608-2614.
    • (2009) J Proteome Res , vol.8 , pp. 2608-2614
    • Carapito, C.1    Klemm, C.2    Aebersold, R.3    Domon, B.4
  • 15
    • 77954583307 scopus 로고    scopus 로고
    • Identification of tandem mass spectra of mixtures of isomeric peptides
    • Chen X, Drogaris P, Bern M. 2010. Identification of tandem mass spectra of mixtures of isomeric peptides. J Proteome Res 9:3270-3279.
    • (2010) J Proteome Res , vol.9 , pp. 3270-3279
    • Chen, X.1    Drogaris, P.2    Bern, M.3
  • 16
    • 73649112404 scopus 로고    scopus 로고
    • New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra
    • Choi S, Jeong J, Na S, Lee HS, Kim HY, Lee KJ, Paek E. 2010. New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra. J Proteome Res 9:626-635.
    • (2010) J Proteome Res , vol.9 , pp. 626-635
    • Choi, S.1    Jeong, J.2    Na, S.3    Lee, H.S.4    Kim, H.Y.5    Lee, K.J.6    Paek, E.7
  • 17
    • 76649135167 scopus 로고    scopus 로고
    • Finding chimeras: A bioinformatics strategy for identification of cross-linked peptides
    • Chu F, Baker PR, Burlingame AL, Chalkley RJ. 2010. Finding chimeras: A bioinformatics strategy for identification of cross-linked peptides. Mol Cell Proteomics 9:25-31.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 25-31
    • Chu, F.1    Baker, P.R.2    Burlingame, A.L.3    Chalkley, R.J.4
  • 18
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: Towards high-throughput tandem mass spectrometry data identification
    • Colinge J, Masselot A, Giron M, Dessingy T, Magnin J. 2003. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 3:1454-1463.
    • (2003) Proteomics , vol.3 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 20
    • 0141955057 scopus 로고    scopus 로고
    • A method for reducing the time required to match protein sequences with tandem mass spectra
    • Craig R, Beavis RC. 2003. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 17:2310-2316.
    • (2003) Rapid Commun Mass Spectrom , vol.17 , pp. 2310-2316
    • Craig, R.1    Beavis, R.C.2
  • 21
    • 33747170146 scopus 로고    scopus 로고
    • Using annotated peptide mass spectrum libraries for protein identification
    • Craig R, Cortens JC, Fenyo D, Beavis RC. 2006. Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res 5:1843-1849.
    • (2006) J Proteome Res , vol.5 , pp. 1843-1849
    • Craig, R.1    Cortens, J.C.2    Fenyo, D.3    Beavis, R.C.4
  • 22
    • 0036807449 scopus 로고    scopus 로고
    • Error tolerant searching of uninterpreted tandem mass spectrometry data
    • Creasy DM, Cottrell JS. 2002. Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2:1426-1434.
    • (2002) Proteomics , vol.2 , pp. 1426-1434
    • Creasy, D.M.1    Cottrell, J.S.2
  • 27
    • 71049141077 scopus 로고    scopus 로고
    • A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry
    • DiMaggio PA Jr, Young NL, Baliban RC, Garcia BA, Floudas CA. 2009. A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry. Mol Cell Proteomics 8:2527-2543.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2527-2543
    • DiMaggio, P.A.1    Young, N.L.2    Baliban, R.C.3    Garcia, B.A.4    Floudas, C.A.5
  • 28
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng JK, McCormack AL, Yates JR. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976-989.
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 29
    • 80555146717 scopus 로고    scopus 로고
    • A face in the crowd: Recognizing peptides through database search
    • 009522
    • Eng JK, Searle BC, Clauser KR, Tabb DL. 2011. A face in the crowd: Recognizing peptides through database search. Mol Cell Proteomics 10:R111.009522.
    • (2011) Mol Cell Proteomics , vol.10 , pp. R111
    • Eng, J.K.1    Searle, B.C.2    Clauser, K.R.3    Tabb, D.L.4
  • 30
    • 76149098839 scopus 로고    scopus 로고
    • Unbiased statistical analysis for multistage proteomic search strategies
    • Everett LJ, Bierl C, Master SR. 2010. Unbiased statistical analysis for multistage proteomic search strategies. J Proteome Res 9:700-707.
    • (2010) J Proteome Res , vol.9 , pp. 700-707
    • Everett, L.J.1    Bierl, C.2    Master, S.R.3
  • 31
    • 58149391408 scopus 로고    scopus 로고
    • A spectral clustering approach to MS/MS identification of post-translational modifications
    • Falkner JA, Falkner JW, Yocum AK, Andrews PC. 2008. A spectral clustering approach to MS/MS identification of post-translational modifications. J Proteome Res 7:4614-4622.
    • (2008) J Proteome Res , vol.7 , pp. 4614-4622
    • Falkner, J.A.1    Falkner, J.W.2    Yocum, A.K.3    Andrews, P.C.4
  • 32
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: De novo peptide sequencing via probabilistic network modeling
    • Frank A, Pevzner P. 2005. PepNovo: De novo peptide sequencing via probabilistic network modeling. Anal Chem 77:964-973.
    • (2005) Anal Chem , vol.77 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 33
    • 23944455372 scopus 로고    scopus 로고
    • Peptide sequence tags for fast database search in mass-spectrometry
    • Frank A, Tanner S, Bafna V, Pevzner P. 2005. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res 4:1287-1295.
    • (2005) J Proteome Res , vol.4 , pp. 1287-1295
    • Frank, A.1    Tanner, S.2    Bafna, V.3    Pevzner, P.4
  • 34
    • 33747626954 scopus 로고    scopus 로고
    • Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
    • Frewen BE, Merrihew GE,Wu CC, Noble WS, MacCoss MJ. 2006. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem 78:5678-5684.
    • (2006) Anal Chem , vol.78 , pp. 5678-5684
    • Frewen, B.E.1    Merrihew, G.E.2    Wu, C.C.3    Noble, W.S.4    MacCoss, M.J.5
  • 35
    • 79955762105 scopus 로고    scopus 로고
    • DeltAMT: A statistical algorithm for fast detection of protein modifications from LC-MS/MS data
    • 000455
    • Fu Y, Xiu LY, Jia W, Ye D, Sun RX, Qian XH, He SM. 2011. DeltAMT: A statistical algorithm for fast detection of protein modifications from LC-MS/MS data. Mol Cell Proteomics 10:M110.000455.
    • (2011) Mol Cell Proteomics , vol.10 , pp. M110
    • Fu, Y.1    Xiu, L.Y.2    Jia, W.3    Ye, D.4    Sun, R.X.5    Qian, X.H.6    He, S.M.7
  • 38
    • 0036882287 scopus 로고    scopus 로고
    • Protein disulfide bond determination by mass spectrometry
    • Gorman JJ, Wallis TP, Pitt JJ. 2002. Protein disulfide bond determination by mass spectrometry. Mass Spectrom Rev 21:183-216.
    • (2002) Mass Spectrom Rev , vol.21 , pp. 183-216
    • Gorman, J.J.1    Wallis, T.P.2    Pitt, J.J.3
  • 39
    • 79960010160 scopus 로고    scopus 로고
    • PeaksPTM: Mass spectrometrybased identification of peptides with unspecified modifications
    • Han X, He L, Xin L, Shan B, Ma B. 2011. PeaksPTM: Mass spectrometrybased identification of peptides with unspecified modifications. J Proteome Res 10:2930-2936.
    • (2011) J Proteome Res , vol.10 , pp. 2930-2936
    • Han, X.1    He, L.2    Xin, L.3    Shan, B.4    Ma, B.5
  • 40
    • 22544465253 scopus 로고    scopus 로고
    • SPIDER: Software for protein identification from sequence tags with de novo sequencing error
    • Han Y, Ma B, Zhang K. 2005. SPIDER: Software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol 3:697-716.
    • (2005) J Bioinform Comput Biol , vol.3 , pp. 697-716
    • Han, Y.1    Ma, B.2    Zhang, K.3
  • 41
    • 33847242627 scopus 로고    scopus 로고
    • Large-scale unrestricted identification of posttranslation modifications using tandem mass spectrometry
    • Havilio M, Wool A. 2007. Large-scale unrestricted identification of posttranslation modifications using tandem mass spectrometry. Anal Chem 79:1362-1368.
    • (2007) Anal Chem , vol.79 , pp. 1362-1368
    • Havilio, M.1    Wool, A.2
  • 42
    • 84879362013 scopus 로고    scopus 로고
    • De nono sequencing with limited number of posttranslational modifications per peptide
    • He L, Han X, Ma B. 2013. De nono sequencing with limited number of posttranslational modifications per peptide. J Bioinform Comput Biol 11:1350007.
    • (2013) J Bioinform Comput Biol , vol.11 , pp. 1350007
    • He, L.1    Han, X.2    Ma, B.3
  • 43
    • 0038047148 scopus 로고    scopus 로고
    • Popitam: Towards new heuristic strategies to improve protein identification from tandem mass spectrometry data
    • Hernandez P, Gras R, Frey J, Appel RD. 2003. Popitam: Towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics 3:870-878.
    • (2003) Proteomics , vol.3 , pp. 870-878
    • Hernandez, P.1    Gras, R.2    Frey, J.3    Appel, R.D.4
  • 44
    • 83055168555 scopus 로고    scopus 로고
    • Building and searching tandem mass spectral libraries for peptide identification
    • 008565
    • Lam H. 2011. Building and searching tandem mass spectral libraries for peptide identification. Mol Cell Proteomics 10:R111.008565.
    • (2011) Mol Cell Proteomics , vol.10 , pp. R111
    • Lam, H.1
  • 45
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. 2007. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7:655-667.
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6    Aebersold, R.7
  • 47
    • 34248588175 scopus 로고    scopus 로고
    • A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation
    • Lioe H, O'Hair RA. 2007. A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation. J Am Soc Mass Spectrom 18:1109-1123.
    • (2007) J Am Soc Mass Spectrom , vol.18 , pp. 1109-1123
    • Lioe, H.1    O'Hair, R.A.2
  • 48
    • 33847194634 scopus 로고    scopus 로고
    • Automatic validation of phosphopeptide identifications from tandem mass spectra
    • Lu B, Ruse C, Xu T, Park SK, Yates J III. 2007. Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal Chem 79:1301-1310.
    • (2007) Anal Chem , vol.79 , pp. 1301-1310
    • Lu, B.1    Ruse, C.2    Xu, T.3    Park, S.K.4    Yates, J.5
  • 51
    • 0037338365 scopus 로고    scopus 로고
    • Proteomic analysis of post-translational modifications
    • Mann M, Jensen ON. 2003. Proteomic analysis of post-translational modifications. Nat Biotechnol 21:255-261.
    • (2003) Nat Biotechnol , vol.21 , pp. 255-261
    • Mann, M.1    Jensen, O.N.2
  • 52
    • 0028575316 scopus 로고
    • Error-tolerant identification of peptides in sequence databases by peptide sequence tags
    • Mann M, Wilm M. 1994. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66:4390-4399.
    • (1994) Anal Chem , vol.66 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 53
    • 18344364099 scopus 로고    scopus 로고
    • Understanding alternative splicing: Towards a cellular code
    • Matlin AJ, Clark F, Smith CW. 2005. Understanding alternative splicing: Towards a cellular code. Nat Rev Mol Cell Biol 6:386-398.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 386-398
    • Matlin, A.J.1    Clark, F.2    Smith, C.W.3
  • 54
    • 29144535689 scopus 로고    scopus 로고
    • VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins
    • Matthiesen R, Trelle MB, Højrup P, Bunkenborg J, Jensen ON. 2005. VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J Proteome Res 4:2338-2347.
    • (2005) J Proteome Res , vol.4 , pp. 2338-2347
    • Matthiesen, R.1    Trelle, M.B.2    Højrup, P.3    Bunkenborg, J.4    Jensen, O.N.5
  • 55
    • 33847782587 scopus 로고    scopus 로고
    • Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry
    • Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. 2007. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci USA 104:2199-2204.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 2199-2204
    • Molina, H.1    Horn, D.M.2    Tang, N.3    Mathivanan, S.4    Pandey, A.5
  • 56
    • 34447097453 scopus 로고    scopus 로고
    • Analysis of protein glycosylation by mass spectrometry
    • Morelle W, Michalski JC. 2007. Analysis of protein glycosylation by mass spectrometry. Nat Protoc 2:1585-1602.
    • (2007) Nat Protoc , vol.2 , pp. 1585-1602
    • Morelle, W.1    Michalski, J.C.2
  • 57
    • 84859877187 scopus 로고    scopus 로고
    • Fast multi-blind modification search through tandem mass spectrometry
    • 010199
    • Na S, Bandeira N, Paek E. 2012. Fast multi-blind modification search through tandem mass spectrometry. Mol Cell Proteomics 11: M111.010199.
    • (2012) Mol Cell Proteomics , vol.11 , pp. M111
    • Na, S.1    Bandeira, N.2    Paek, E.3
  • 58
    • 58149307960 scopus 로고    scopus 로고
    • Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach
    • Na S, Jeong J, Park H, Lee KJ, Paek E. 2008. Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach. Mol Cell Proteomics 7:2452-2463.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 2452-2463
    • Na, S.1    Jeong, J.2    Park, H.3    Lee, K.J.4    Paek, E.5
  • 59
    • 70349974843 scopus 로고    scopus 로고
    • Prediction of novel modifications by unrestrictive search of tandem mass spectra
    • Na S, Paek E. 2009. Prediction of novel modifications by unrestrictive search of tandem mass spectra. J Proteome Res 8:4418-4427.
    • (2009) J Proteome Res , vol.8 , pp. 4418-4427
    • Na, S.1    Paek, E.2
  • 60
    • 33846010726 scopus 로고    scopus 로고
    • Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics
    • Nielsen ML, Savitski MM, Zubarev RA. 2006. Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics. Mol Cell Proteomics 5:2384-2391.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 2384-2391
    • Nielsen, M.L.1    Savitski, M.M.2    Zubarev, R.A.3
  • 61
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. 2006. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127:635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5    Mortensen, P.6    Mann, M.7
  • 62
    • 21844457685 scopus 로고    scopus 로고
    • Fragmentation pathways of protonated peptides
    • Paizs B, Suhai S. 2005. Fragmentation pathways of protonated peptides. Mass Spectrom Rev 24:508-548.
    • (2005) Mass Spectrom Rev , vol.24 , pp. 508-548
    • Paizs, B.1    Suhai, S.2
  • 63
    • 77952027769 scopus 로고    scopus 로고
    • xComb: A crosslinked peptide database approach to protein-protein interaction analysis
    • Panchaud A, Singh P, Shaffer SA, Goodlett DR. 2010. xComb: A crosslinked peptide database approach to protein-protein interaction analysis. J Proteome Res 9:2508-2515.
    • (2010) J Proteome Res , vol.9 , pp. 2508-2515
    • Panchaud, A.1    Singh, P.2    Shaffer, S.A.3    Goodlett, D.R.4
  • 64
    • 53049084796 scopus 로고    scopus 로고
    • Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis
    • Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. 2008. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res 7:3373-3381.
    • (2008) J Proteome Res , vol.7 , pp. 3373-3381
    • Payne, S.H.1    Yau, M.2    Smolka, M.B.3    Tanner, S.4    Zhou, H.5    Bafna, V.6
  • 65
    • 33745360876 scopus 로고    scopus 로고
    • Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software
    • Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R. 2006. Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nat Methods 3:533-539.
    • (2006) Nat Methods , vol.3 , pp. 533-539
    • Pedrioli, P.G.1    Raught, B.2    Zhang, X.D.3    Rogers, R.4    Aitchison, J.5    Matunis, M.6    Aebersold, R.7
  • 66
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 67
    • 0035107717 scopus 로고    scopus 로고
    • Efficiency of database search for identification of mutated and modified proteins via mass spectrometry
    • Pevzner PA, Mulyukov Z, Dancik V, Tang CL. 2001. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res 11:290-299.
    • (2001) Genome Res , vol.11 , pp. 290-299
    • Pevzner, P.A.1    Mulyukov, Z.2    Dancik, V.3    Tang, C.L.4
  • 71
    • 33646903914 scopus 로고    scopus 로고
    • ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures
    • Savitski MM, Nielsen ML, Zubarev RA. 2006. ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol Cell Proteomics 5:935-948.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 935-948
    • Savitski, M.M.1    Nielsen, M.L.2    Zubarev, R.A.3
  • 73
    • 39749099462 scopus 로고    scopus 로고
    • Strategy for comprehensive identification of post-translational modifications in cellular proteins, including low abundant modifications: Application to glyceraldehyde-3-phosphate dehydrogenase
    • Seo J, Jeong J, Kim YM, Hwang N, Paek E, Lee KJ. 2008. Strategy for comprehensive identification of post-translational modifications in cellular proteins, including low abundant modifications: Application to glyceraldehyde-3-phosphate dehydrogenase. J Proteome Res 7:587-602.
    • (2008) J Proteome Res , vol.7 , pp. 587-602
    • Seo, J.1    Jeong, J.2    Kim, Y.M.3    Hwang, N.4    Paek, E.5    Lee, K.J.6
  • 74
    • 0036842559 scopus 로고    scopus 로고
    • Formation and transfer of disulphide bonds in living cells
    • Sevier CS, Kaiser CA. 2002. Formation and transfer of disulphide bonds in living cells. Nat Rev Mol Cell Biol 3:836-847.
    • (2002) Nat Rev Mol Cell Biol , vol.3 , pp. 836-847
    • Sevier, C.S.1    Kaiser, C.A.2
  • 75
    • 34848889259 scopus 로고    scopus 로고
    • The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra
    • Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA. 2007. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 6:1638-1655.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1638-1655
    • Shilov, I.V.1    Seymour, S.L.2    Patel, A.A.3    Loboda, A.4    Tang, W.H.5    Keating, S.P.6    Hunter, C.L.7    Nuwaysir, L.M.8    Schaeffer, D.A.9
  • 77
    • 4444335470 scopus 로고    scopus 로고
    • The ABC's (and XYZ's) of peptide sequencing
    • Steen H, Mann M. 2004. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5:699-711.
    • (2004) Nat Rev Mol Cell Biol , vol.5 , pp. 699-711
    • Steen, H.1    Mann, M.2
  • 78
    • 56149086397 scopus 로고    scopus 로고
    • Decision tree-driven tandem mass spectrometry for shotgun proteomics
    • Swaney DL, McAlister GC, Coon JJ. 2008. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 5:959-964.
    • (2008) Nat Methods , vol.5 , pp. 959-964
    • Swaney, D.L.1    McAlister, G.C.2    Coon, J.J.3
  • 79
    • 3042789073 scopus 로고    scopus 로고
    • Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
    • Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. 2004. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101:9528-9533.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9528-9533
    • Syka, J.E.1    Coon, J.J.2    Schroeder, M.J.3    Shabanowitz, J.4    Hunt, D.F.5
  • 80
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Tabb DL, Fernando CG, Chambers MC. 2007. MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 6:654-661.
    • (2007) J Proteome Res , vol.6 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 81
    • 34548449808 scopus 로고    scopus 로고
    • Verification of automated peptide identifications from proteomic tandem mass spectra
    • Tabb DL, Friedman DB, Ham AJ. 2006. Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc 1:2213-2222.
    • (2006) Nat Protoc , vol.1 , pp. 2213-2222
    • Tabb, D.L.1    Friedman, D.B.2    Ham, A.J.3
  • 82
    • 0345600791 scopus 로고    scopus 로고
    • GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model
    • Tabb DL, Saraf A, Yates JR III. 2003. GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem 75:6415-6421.
    • (2003) Anal Chem , vol.75 , pp. 6415-6421
    • Tabb, D.L.1    Saraf, A.2    Yates, J.R.3
  • 85
    • 33750101570 scopus 로고    scopus 로고
    • Unrestrictive identification of posttranslational modifications through peptide mass spectrometry
    • Tanner S, Pevzner PA, Bafna V. 2006. Unrestrictive identification of posttranslational modifications through peptide mass spectrometry. Nat Protoc 1:67-72.
    • (2006) Nat Protoc , vol.1 , pp. 67-72
    • Tanner, S.1    Pevzner, P.A.2    Bafna, V.3
  • 86
  • 87
    • 0035356977 scopus 로고    scopus 로고
    • Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry
    • Taylor JA, Johnson RS. 2001. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem 73:2594-2604.
    • (2001) Anal Chem , vol.73 , pp. 2594-2604
    • Taylor, J.A.1    Johnson, R.S.2
  • 88
    • 40249116258 scopus 로고    scopus 로고
    • Fragmentation of peptide disulfides under conditions of negative ion mass spectrometry: Studies of oxidized glutathione and contryphan
    • Thakur SS, Balaram P. 2008. Fragmentation of peptide disulfides under conditions of negative ion mass spectrometry: Studies of oxidized glutathione and contryphan. J Am Soc Mass Spectrom 19:358-366.
    • (2008) J Am Soc Mass Spectrom , vol.19 , pp. 358-366
    • Thakur, S.S.1    Balaram, P.2
  • 89
    • 77949752005 scopus 로고    scopus 로고
    • Data maximization by multipass analysis of protein mass spectra
    • Tharakan R, Edwards N, Graham DR. 2010. Data maximization by multipass analysis of protein mass spectra. Proteomics 10:1160-1171.
    • (2010) Proteomics , vol.10 , pp. 1160-1171
    • Tharakan, R.1    Edwards, N.2    Graham, D.R.3
  • 90
    • 0019881763 scopus 로고
    • Disulphide bridges in globular proteins
    • Thornton JM. 1981. Disulphide bridges in globular proteins. J Mol Biol 151:261-287.
    • (1981) J Mol Biol , vol.151 , pp. 261-287
    • Thornton, J.M.1
  • 91
    • 28644447919 scopus 로고    scopus 로고
    • Identification of post-translational modifications by blind search of mass spectra
    • Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. 2005. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol 23:1562-1567.
    • (2005) Nat Biotechnol , vol.23 , pp. 1562-1567
    • Tsur, D.1    Tanner, S.2    Zandi, E.3    Bafna, V.4    Pevzner, P.A.5
  • 92
    • 28044433451 scopus 로고    scopus 로고
    • Protein posttranslational modifications: The chemistry of proteome diversifications
    • Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr. 2005. Protein posttranslational modifications: The chemistry of proteome diversifications. Angew Chem Int Ed Engl 44:7342-7372.
    • (2005) Angew Chem Int Ed Engl , vol.44 , pp. 7342-7372
    • Walsh, C.T.1    Garneau-Tsodikova, S.2    Gatto, G.J.3
  • 93
    • 33750142707 scopus 로고    scopus 로고
    • Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility?
    • Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. 2006. Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility? J Proteome Res 5:2554-2566.
    • (2006) J Proteome Res , vol.5 , pp. 2554-2566
    • Wilmarth, P.A.1    Tanner, S.2    Dasari, S.3    Nagalla, S.R.4    Riviere, M.A.5    Bafna, V.6    Pevzner, P.A.7    David, L.L.8
  • 94
    • 77954191980 scopus 로고    scopus 로고
    • Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
    • Ye D, Fu Y, Sun RX, Wang HP, Yuan ZF, Chi H, He SM. 2010. Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics 26:i399-i406.
    • (2010) Bioinformatics , vol.26 , pp. i399-i406
    • Ye, D.1    Fu, Y.2    Sun, R.X.3    Wang, H.P.4    Yuan, Z.F.5    Chi, H.6    He, S.M.7
  • 95
    • 0000944563 scopus 로고    scopus 로고
    • Electron capture dissociation of multiply charged protein cations. A nonergodic process
    • Zubarev RA, Kelleher NL, McLafferty FW. 1998. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J Am Chem Soc 120:3265-3266.
    • (1998) J Am Chem Soc , vol.120 , pp. 3265-3266
    • Zubarev, R.A.1    Kelleher, N.L.2    McLafferty, F.W.3


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