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Volumn 34, Issue 1, 2015, Pages 43-63

Lessons in de novo peptide sequencing by tandem mass spectrometry

Author keywords

CID; De novo sequencing; Fragmentation; HCD; Peptides

Indexed keywords

ACTIVATION ANALYSIS; BIOLOGY; DATA ACQUISITION; MASS SPECTROMETRY; PEPTIDES; PROTEINS; SPECTROMETRY;

EID: 84922182266     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.21406     Document Type: Review
Times cited : (162)

References (104)
  • 1
    • 84990709433 scopus 로고
    • Collision-induced dissociation of peptide ions. 2. Remote charge-site fragmentation in a tandem, hybrid mass spectrometer
    • Alexander A.J. , Thibault P., Boyd R.K.. 1989. Collision-induced dissociation of peptide ions. 2. Remote charge-site fragmentation in a tandem, hybrid mass spectrometerRapid Commun Mass Spectrom3:30-34
    • (1989) Rapid Commun Mass Spectrom , vol.3 , pp. 30-34
    • Alexander, A.J.1    Thibault, P.2    Boyd, R.K.3
  • 2
    • 10044225829 scopus 로고    scopus 로고
    • Models of fragmentations induced by electron attachment to protonated peptides
    • Bakken V, Helgaker T, Uggerud E. 2004. Models of fragmentations induced by electron attachment to protonated peptides. Eur J Mass Spectrom 10:625-638.
    • (2004) Eur J Mass Spectrom , vol.10 , pp. 625-638
    • Bakken, V.1    Helgaker, T.2    Uggerud, E.3
  • 3
    • 0035870165 scopus 로고    scopus 로고
    • Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis
    • BaldwinM.A., Burlingame A.L.. 2001. Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysisAnal Chem73:1707-1720.
    • (2001) Anal Chem , vol.73 , pp. 1707-1720
    • Baldwin, M.A.1    Burlingame, A.L.2
  • 4
    • 0035870165 scopus 로고    scopus 로고
    • Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis
    • Baldwin MA, Medzihradszky KF, Lock CM, Fisher B, Settineri TA, Burlingame AL. 2001. Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis. Anal Chem 73:1707-1720.
    • (2001) Anal Chem , vol.73 , pp. 1707-1720
    • Fisher, B.1    Burlingame, A.L.2
  • 5
    • 0001481311 scopus 로고
    • Sequential mass spectrometry applied to the study of the formation of "internal" fragment ions of protonated peptides
    • Ballard KD, Gaskell SJ. 1991. Sequential mass spectrometry applied to the study of the formation of "internal" fragment ions of protonated peptides. Int J Mass Spectrom Ion Processes 111:173-189.
    • (1991) Int J Mass Spectrom Ion Processes , vol.111 , pp. 173-189
    • Ballard, K.D.1    Gaskell, S.J.2
  • 7
    • 0019796394 scopus 로고
    • Fast atom bombardment of solids as an ion source in mass spectrometry
    • Barber M, Bordoli RS, Sedgwick RD, Tyler AN. 1981. Fast atom bombardment of solids as an ion source in mass spectrometry. Nature 293:270-275.
    • (1981) Nature , vol.293 , pp. 270-275
    • Barber, M.1    Bordoli, R.S.2    Sedgwick, R.D.3    Tyler, A.N.4
  • 8
    • 0017993988 scopus 로고
    • Detection, identification and structural investigation of biologically important compounds by secondary ion mass spectrometry
    • Benninghoven A, Sichtermann WK. 1978. Detection, identification and structural investigation of biologically important compounds by secondary ion mass spectrometry. Anal Chem 50:1180-1184.
    • (1978) Anal Chem , vol.50 , pp. 1180-1184
    • Benninghoven, A.1    Sichtermann, W.K.2
  • 9
    • 33645965901 scopus 로고    scopus 로고
    • De novo analysis of peptide tandem mass spectra by spectral graph partitioning
    • Bern M, Goldberg D. 2006. De novo analysis of peptide tandem mass spectra by spectral graph partitioning. J Comput Biol 13:364-378.
    • (2006) J Comput Biol , vol.13 , pp. 364-378
    • Bern, M.1    Goldberg, D.2
  • 10
    • 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
  • 11
    • 0025617140 scopus 로고
    • Appendix 5. Nomenclature for peptide fragment ions (positive ions)
    • Biemann K. 1990. Appendix 5. Nomenclature for peptide fragment ions (positive ions). Methods Enzymol 193:886-887.
    • (1990) Methods Enzymol , vol.193 , pp. 886-887
    • Biemann, K.1
  • 12
    • 0023399896 scopus 로고
    • Characterization by tandem mass spectrometry of structural modifications in proteins
    • Biemann K, Scoble HA. 1987. Characterization by tandem mass spectrometry of structural modifications in proteins. Science 237:992-998.
    • (1987) Science , vol.237 , pp. 992-998
    • Biemann, K.1    Scoble, H.A.2
  • 14
    • 0032127904 scopus 로고    scopus 로고
    • N-terminal processing: The methionine aminopeptidase and N alpha-acetyl transferase families
    • Bradshaw RA, Brickey WW, Walker KW. 1998. N-terminal processing: The methionine aminopeptidase and N alpha-acetyl transferase families. Trends Biochem Sci 23:263-267.
    • (1998) Trends Biochem Sci , vol.23 , pp. 263-267
    • Bradshaw, R.A.1    Brickey, W.W.2    Walker, K.W.3
  • 15
    • 38149119842 scopus 로고    scopus 로고
    • De novo sequencing of a 21-kDa cytochrome c4 from Thiocapsa roseopersicina by nanoelectrospray ionization ion-trap and Fourier-transform ion-cyclotron resonance mass spectrometry
    • Branca RM, Bodó G, Bagyinka C, Prokai L. 2007. De novo sequencing of a 21-kDa cytochrome c4 from Thiocapsa roseopersicina by nanoelectrospray ionization ion-trap and Fourier-transform ion-cyclotron resonance mass spectrometry. J Mass Spectrom 42:1569-1582.
    • (2007) J Mass Spectrom , vol.42 , pp. 1569-1582
    • Branca, R.M.1    Bodó, G.2    Bagyinka, C.3    Prokai, L.4
  • 16
    • 0000789037 scopus 로고
    • Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: Evidence for intraionic interactions
    • Burlet O, Yang CY, Gaskell SJ. 1992a. Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: Evidence for intraionic interactions. J Am Soc Mass Spectrom 3:337-344.
    • (1992) J Am Soc Mass Spectrom , vol.3 , pp. 337-344
    • Burlet, O.1    Yang, C.Y.2    Gaskell, S.J.3
  • 18
    • 84873387053 scopus 로고    scopus 로고
    • When target-decoy false discovery rate estimations are inaccurate and how to spot instances
    • Chalkley RJ. 2013. When target-decoy false discovery rate estimations are inaccurate and how to spot instances. J Proteome Res 12:1062-1064.
    • (2013) J Proteome Res , vol.12 , pp. 1062-1064
    • Chalkley, R.J.1
  • 19
    • 33747883123 scopus 로고    scopus 로고
    • Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry
    • Chalkley RJ, Brinkworth CS, Burlingame AL. 2006. Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry. J Am Soc Mass Spectrom 17:1271-1274.
    • (2006) J Am Soc Mass Spectrom , vol.17 , pp. 1271-1274
    • Chalkley, R.J.1    Brinkworth, C.S.2    Burlingame, A.L.3
  • 20
    • 75649110103 scopus 로고    scopus 로고
    • Statistical analysis of peptide electron transfer dissociation fragmentation mass spectrometry
    • Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL. 2010. Statistical analysis of peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem 82:579-584.
    • (2010) Anal Chem , vol.82 , pp. 579-584
    • Chalkley, R.J.1    Medzihradszky, K.F.2    Lynn, A.J.3    Baker, P.R.4    Burlingame, A.L.5
  • 23
    • 33847068627 scopus 로고    scopus 로고
    • Evaluation of low energy CID and ECD fragmentation behavior of mono-oxidized thioether bonds in peptides
    • Chowdhury SM, Munske GR, Ronald RC, Bruce JE. 2007. Evaluation of low energy CID and ECD fragmentation behavior of mono-oxidized thioether bonds in peptides. J Am Soc Mass Spectrom 18:493-501.
    • (2007) J Am Soc Mass Spectrom , vol.18 , pp. 493-501
    • Chowdhury, S.M.1    Munske, G.R.2    Ronald, R.C.3    Bruce, J.E.4
  • 25
    • 0030000913 scopus 로고    scopus 로고
    • Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions
    • Cox KA, Gaskell SJ, Morris M, Whiting AJ. 1996. Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions. J Am Soc Mass Spectrom 7:522-531.
    • (1996) J Am Soc Mass Spectrom , vol.7 , pp. 522-531
    • Cox, K.A.1    Gaskell, S.J.2    Morris, M.3    Whiting, A.J.4
  • 27
    • 70349207551 scopus 로고    scopus 로고
    • Spectrum fusion: Using multiple mass spectra for de novo peptide sequencing
    • Datta R, Bern M. 2009. Spectrum fusion: Using multiple mass spectra for de novo peptide sequencing. J Comput Biol 16:1169-1182.
    • (2009) J Comput Biol , vol.16 , pp. 1169-1182
    • Datta, R.1    Bern, M.2
  • 28
    • 0029810698 scopus 로고    scopus 로고
    • Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: Evidence for the mobile proton model
    • Dongré AR, Jones JL, Somogyi Á, Wysocki VH. 1996. Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: Evidence for the mobile proton model. J Am Chem Soc 118:8365-8374.
    • (1996) J Am Chem Soc , vol.118 , pp. 8365-8374
    • Dongré, A.R.1    Jones, J.L.2    Somogyi, Á.3    Wysocki, V.H.4
  • 29
    • 0000183664 scopus 로고
    • Low-mass ions produced from peptides by high energy collision-induced dissociation in tandem mass spectrometry
    • Falick AM, Hines WM, Medzihradszky KF, Baldwin MA, Gibson BW. 1993. Low-mass ions produced from peptides by high energy collision-induced dissociation in tandem mass spectrometry. J Am Soc Mass Spectrom 4:882-893.
    • (1993) J Am Soc Mass Spectrom , vol.4 , pp. 882-893
    • Falick, A.M.1    Hines, W.M.2    Medzihradszky, K.F.3    Baldwin, M.A.4    Gibson, B.W.5
  • 30
    • 0035860166 scopus 로고    scopus 로고
    • Do all b2 ions have oxazolone structures? Multistage mass spectrometry and ab initio studies on protonated N-acyl amino acid methyl ester model systems
    • Farrugia JM, O'Hair RAJ, Reid GE. 2001. Do all b2 ions have oxazolone structures? Multistage mass spectrometry and ab initio studies on protonated N-acyl amino acid methyl ester model systems. Int J Mass Spectrom 210:71-87.
    • (2001) Int J Mass Spectrom , vol.210 , pp. 71-87
    • Farrugia, J.M.1    O'Hair, R.A.J.2    Reid, G.E.3
  • 31
    • 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
  • 32
    • 84870556977 scopus 로고    scopus 로고
    • Stable isotope N-phosphorylation labeling for peptide de novo sequencing and protein quantification based on organic phosphorus chemistry
    • Gao X, Wu H, Lee KC, Liu H, Zhao Y, Cai Z, Jiang Y. 2012. Stable isotope N-phosphorylation labeling for peptide de novo sequencing and protein quantification based on organic phosphorus chemistry. Anal Chem 84:10236-10244.
    • (2012) Anal Chem , vol.84 , pp. 10236-10244
    • Gao, X.1    Wu, H.2    Lee, K.C.3    Liu, H.4    Zhao, Y.5    Cai, Z.6    Jiang, Y.7
  • 33
    • 77953914157 scopus 로고    scopus 로고
    • Effect of N-terminal glutamic acid and glutamine on fragmentation of peptide ions
    • Godugu B, Neta P, Simón-Manso Y, Stein SE. 2010. Effect of N-terminal glutamic acid and glutamine on fragmentation of peptide ions. J Am Soc Mass Spectrom 21:1169-1176.
    • (2010) J Am Soc Mass Spectrom , vol.21 , pp. 1169-1176
    • Godugu, B.1    Neta, P.2    Simón-Manso, Y.3    Stein, S.E.4
  • 34
    • 36749068401 scopus 로고    scopus 로고
    • Performance characteristics of electron transfer dissociation mass spectrometry
    • Good DM, Wirtala M, McAlister GC, Coon JJ. 2007. Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics 6:1942-1951.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1942-1951
    • Good, D.M.1    Wirtala, M.2    McAlister, G.C.3    Coon, J.J.4
  • 35
    • 0037270746 scopus 로고    scopus 로고
    • Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging
    • Gu S, Pan S, Bradbury EM, Chen X. 2003. Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging J Am Soc Mass Spectrom 14:1-7.
    • (2003) J Am Soc Mass Spectrom , vol.14 , pp. 1-7
    • Gu, S.1    Pan, S.2    Bradbury, E.M.3    Chen, X.4
  • 36
    • 68849096511 scopus 로고    scopus 로고
    • To b or not to b: The ongoing saga of peptide b ions
    • Harrison AG. 2009. To b or not to b: The ongoing saga of peptide b ions. Mass Spectrom Rev 28:640-654.
    • (2009) Mass Spectrom Rev , vol.28 , pp. 640-654
    • Harrison, A.G.1
  • 37
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 38
    • 0000875991 scopus 로고
    • Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra
    • Hines WM, Falick AM, Burlingame AL, Gibson BW. 1992. Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra. J Am Soc Mass Spectrom 3: 326-336.
    • (1992) J Am Soc Mass Spectrom , vol.3 , pp. 326-336
    • Hines, W.M.1    Falick, A.M.2    Burlingame, A.L.3    Gibson, B.W.4
  • 39
    • 20444459841 scopus 로고    scopus 로고
    • Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns
    • Huang Y, Triscari JM, Tseng GC, Pasa-Tolic L, Lipton MS, Smith RD, Wysocki VH. 2005. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal Chem 77:5800-5813.
    • (2005) Anal Chem , vol.77 , pp. 5800-5813
    • Huang, Y.1    Triscari, J.M.2    Tseng, G.C.3    Pasa-Tolic, L.4    Lipton, M.S.5    Smith, R.D.6    Wysocki, V.H.7
  • 41
    • 0016701344 scopus 로고
    • Identification of two related pentapeptides from the brain with potent opiate agonist activity
    • Hughes J, Smith TW, Kosterlitz HW, Fothergill LA, Morgan BA, Morris HR. 1975. Identification of two related pentapeptides from the brain with potent opiate agonist activity. Nature 258:577-580.
    • (1975) Nature , vol.258 , pp. 577-580
    • Hughes, J.1    Smith, T.W.2    Kosterlitz, H.W.3    Fothergill, L.A.4    Morgan, B.A.5    Morris, H.R.6
  • 43
    • 0024639587 scopus 로고
    • Oligopeptide sequence analysis by collision-activated dissociation of multiply-charged ions
    • Hunt DF, Zhu NZ, Shabanowitz J. 1989. Oligopeptide sequence analysis by collision-activated dissociation of multiply-charged ions. Rapid Commun Mass Spectrom 3:122-124.
    • (1989) Rapid Commun Mass Spectrom , vol.3 , pp. 122-124
    • Hunt, D.F.1    Zhu, N.Z.2    Shabanowitz, J.3
  • 45
    • 84922705353 scopus 로고
    • Ph.D. Thesis, MIT, Cambridge, MA.
    • Johnson RS. 1988. Ph.D. Thesis, MIT, Cambridge, MA.
    • (1988)
    • Johnson, R.S.1
  • 46
    • 0023143159 scopus 로고
    • The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry
    • Johnson RS, Biemann K. 1987. The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry. Biochemistry 26:1209-1214.
    • (1987) Biochemistry , vol.26 , pp. 1209-1214
    • Johnson, R.S.1    Biemann, K.2
  • 47
    • 0024427490 scopus 로고
    • Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides
    • Johnson RS, Biemann K. 1989. Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides. Biomed Environ Mass Spectrom 18:945-957.
    • (1989) Biomed Environ Mass Spectrom , vol.18 , pp. 945-957
    • Johnson, R.S.1    Biemann, K.2
  • 48
    • 0002794845 scopus 로고
    • Collision-induced fragmentation of (M + H)+ ions of peptides. Side chain specific sequence ions
    • Johnson RS, Martin SA, Biemann K. 1988. Collision-induced fragmentation of (M + H)+ ions of peptides. Side chain specific sequence ions. Int J Mass Spectrom Ion Processes 86:137-154.
    • (1988) Int J Mass Spectrom Ion Processes , vol.86 , pp. 137-154
    • Johnson, R.S.1    Martin, S.A.2    Biemann, K.3
  • 49
    • 0031014649 scopus 로고    scopus 로고
    • The quadrupole ion trap mass spectrometer - A small solution to a big challenge
    • Jonscher KR, Yates JR III. 1997. The quadrupole ion trap mass spectrometer - A small solution to a big challenge. Anal Biochem 244:1-15.
    • (1997) Anal Biochem , vol.244 , pp. 1-15
    • Jonscher, K.R.1    Yates, J.R.2
  • 50
    • 0242653718 scopus 로고    scopus 로고
    • Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation
    • Kapp EA, Schütz F, Reid GE, Eddes JS, Moritz RL, O'Hair RA, Speed TP, Simpson RJ. 2003. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal Chem 75:6251-6264.
    • (2003) Anal Chem , vol.75 , pp. 6251-6264
    • Kapp, E.A.1    Schütz, F.2    Reid, G.E.3    Eddes, J.S.4    Moritz, R.L.5    O'Hair, R.A.6    Speed, T.P.7    Simpson, R.J.8
  • 51
    • 79959988139 scopus 로고    scopus 로고
    • Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment
    • Kelstrup CD, Hekmat O, Francavilla C, Olsen JV. 2011. Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment. J Proteome Res 10:2937-2948.
    • (2011) J Proteome Res , vol.10 , pp. 2937-2948
    • Kelstrup, C.D.1    Hekmat, O.2    Francavilla, C.3    Olsen, J.V.4
  • 53
    • 59149096107 scopus 로고    scopus 로고
    • Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra
    • Kim S, Gupta N, Bandeira N, Pevzner PA. 2009. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics 8:53-69.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 53-69
    • Kim, S.1    Gupta, N.2    Bandeira, N.3    Pevzner, P.A.4
  • 56
    • 66149174786 scopus 로고    scopus 로고
    • Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides
    • Lau KW, Hart SR, Lynch JA, Wong SC, Hubbard SJ, Gaskell SJ. 2009. Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides. Rapid Commun Mass Spectrom 23:1508-1514.
    • (2009) Rapid Commun Mass Spectrom , vol.23 , pp. 1508-1514
    • Lau, K.W.1    Hart, S.R.2    Lynch, J.A.3    Wong, S.C.4    Hubbard, S.J.5    Gaskell, S.J.6
  • 57
    • 4544368228 scopus 로고    scopus 로고
    • Formation of c1 fragment ions in collision-induced dissociation of glutamine-containing peptide ions: A tip for de novo sequencing
    • Lee YJ, Lee YM. 2004. Formation of c1 fragment ions in collision-induced dissociation of glutamine-containing peptide ions: A tip for de novo sequencing. Rapid Commun Mass Spectrom 18:2069-2076.
    • (2004) Rapid Commun Mass Spectrom , vol.18 , pp. 2069-2076
    • Lee, Y.J.1    Lee, Y.M.2
  • 58
    • 84856692718 scopus 로고    scopus 로고
    • De novo sequencing and homology searching
    • Ma B, Johnson RS. 2012. De novo sequencing and homology searching. Mol Cell Proteomics 11:O111.014902.
    • (2012) Mol Cell Proteomics
    • Ma, B.1    Johnson, R.S.2
  • 60
    • 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
  • 61
    • 30144443840 scopus 로고    scopus 로고
    • Peptide sequence analysis
    • Medzihradszky KF. 2005. Peptide sequence analysis. Methods Enzymol 402:209-244.
    • (2005) Methods Enzymol , vol.402 , pp. 209-244
    • Medzihradszky, K.F.1
  • 62
    • 84862534175 scopus 로고    scopus 로고
    • Partial de novo sequencing and unusual CID fragmentation of a 7 kDa, disulfide-bridged toxin
    • Medzihradszky KF, Bohlen CJ. 2012. Partial de novo sequencing and unusual CID fragmentation of a 7 kDa, disulfide-bridged toxin. J Am Soc Mass Spectrom 23:923-934.
    • (2012) J Am Soc Mass Spectrom , vol.23 , pp. 923-934
    • Medzihradszky, K.F.1    Bohlen, C.J.2
  • 63
    • 84862530454 scopus 로고    scopus 로고
    • Unusual fragmentation of Pro-Ser/Thr-containing peptides detected in collision-induced dissociation spectra
    • Medzihradszky KF, Trinidad JC. 2012. Unusual fragmentation of Pro-Ser/Thr-containing peptides detected in collision-induced dissociation spectra. J Am Soc Mass Spectrom 23:602-607.
    • (2012) J Am Soc Mass Spectrom , vol.23 , pp. 602-607
    • Medzihradszky, K.F.1    Trinidad, J.C.2
  • 64
    • 0026588923 scopus 로고
    • The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family
    • Medzihradszky KF, Gibson BW, Kaur S, Yu ZH, Medzihradszky D, Burlingame AL, Bass NM. 1992. The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family. Eur J Biochem 203:327-339.
    • (1992) Eur J Biochem , vol.203 , pp. 327-339
    • Medzihradszky, K.F.1    Gibson, B.W.2    Kaur, S.3    Yu, Z.H.4    Medzihradszky, D.5    Burlingame, A.L.6    Bass, N.M.7
  • 65
  • 66
    • 0034282457 scopus 로고    scopus 로고
    • Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety
    • Muenchbach M, Quadroni M, Miotto G, James P. 2000. Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal Chem 72:4047-4057.
    • (2000) Anal Chem , vol.72 , pp. 4047-4057
    • Muenchbach, M.1    Quadroni, M.2    Miotto, G.3    James, P.4
  • 67
    • 33645708138 scopus 로고    scopus 로고
    • Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    • Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. 2006. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 5:652-670.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.I.1    Roos, F.F.2    Grossmann, J.3    Vogelzang, M.4    Eddes, J.S.5    Gruissem, W.6    Baginsky, S.7    Aebersold, R.8
  • 68
    • 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
  • 69
    • 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
  • 71
    • 84987419408 scopus 로고
    • Proposal for a common nomenclature for sequence ions in mass spectra of peptides
    • Roepstorff P, Fohlman J. 1984. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11:601.
    • (1984) Biomed Mass Spectrom , vol.11 , pp. 601
    • Roepstorff, P.1    Fohlman, J.2
  • 72
    • 0032106794 scopus 로고    scopus 로고
    • Charge derivatization of peptides for analysis by mass spectrometry
    • Roth KD, Huang ZH, Sadagopan N, Watson JT. 1998. Charge derivatization of peptides for analysis by mass spectrometry. Mass Spectrom Rev 17:255-274.
    • (1998) Mass Spectrom Rev , vol.17 , pp. 255-274
    • Roth, K.D.1    Huang, Z.H.2    Sadagopan, N.3    Watson, J.T.4
  • 75
    • 0036243462 scopus 로고    scopus 로고
    • Patchwork peptide sequencing: Extraction of sequence information from accurate mass data of peptide tandem mass spectra recorded at high resolution
    • Schlosser A, Lehmann WD. 2002. Patchwork peptide sequencing: Extraction of sequence information from accurate mass data of peptide tandem mass spectra recorded at high resolution. Proteomics 2:524-533.
    • (2002) Proteomics , vol.2 , pp. 524-533
    • Schlosser, A.1    Lehmann, W.D.2
  • 76
    • 0030068923 scopus 로고    scopus 로고
    • Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry
    • Schnölzer M, Jedrzejewski P, Lehmann WD. 1996. Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17:945-953.
    • (1996) Electrophoresis , vol.17 , pp. 945-953
    • Schnölzer, M.1    Jedrzejewski, P.2    Lehmann, W.D.3
  • 77
    • 0023655503 scopus 로고
    • Peptide sequencing by magnetic deflection tandem mass spectrometry
    • Scoble HA, Martin SA, Biemann K. 1987. Peptide sequencing by magnetic deflection tandem mass spectrometry. Biochem J 245:621-622.
    • (1987) Biochem J , vol.245 , pp. 621-622
    • Scoble, H.A.1    Martin, S.A.2    Biemann, K.3
  • 79
    • 53249145476 scopus 로고    scopus 로고
    • Peptide sequencing by mass spectrometry for homology searches and cloning of genes
    • Shevchenko A, Wilm M, Mann M. 1997. Peptide sequencing by mass spectrometry for homology searches and cloning of genes. J Protein Chem 16:481-490.
    • (1997) J Protein Chem , vol.16 , pp. 481-490
    • Shevchenko, A.1    Wilm, M.2    Mann, M.3
  • 80
    • 0033649230 scopus 로고    scopus 로고
    • De novo peptide sequencing by nanoelectrospray tandem mass spectrometry using triple quadrupole and quadrupole/time-of-flight instruments
    • Shevchenko A, Chernushevich I, Wilm M, Mann M. 2000. De novo peptide sequencing by nanoelectrospray tandem mass spectrometry using triple quadrupole and quadrupole/time-of-flight instruments. Methods Mol Biol 146:1-16.
    • (2000) Methods Mol Biol , vol.146 , pp. 1-16
    • Shevchenko, A.1    Chernushevich, I.2    Wilm, M.3    Mann, M.4
  • 81
    • 79952506820 scopus 로고    scopus 로고
    • Loss of 45 Da from a2 ions and preferential loss of 48 Da from a2 ions containing methionine in peptide ion tandem mass spectra
    • Simón-Manso Y, Neta P, Yang X, Stein SE. 2011. Loss of 45 Da from a2 ions and preferential loss of 48 Da from a2 ions containing methionine in peptide ion tandem mass spectra. J Am Soc Mass Spectrom 22:280-289.
    • (2011) J Am Soc Mass Spectrom , vol.22 , pp. 280-289
    • Simón-Manso, Y.1    Neta, P.2    Yang, X.3    Stein, S.E.4
  • 82
    • 2342593352 scopus 로고    scopus 로고
    • De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry
    • Spengler B. 2004. De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 15:703-714.
    • (2004) J Am Soc Mass Spectrom , vol.15 , pp. 703-714
    • Spengler, B.1
  • 83
    • 0141884306 scopus 로고    scopus 로고
    • Peptide and protein de novo sequencing by mass spectrometry
    • Standing KG. 2003. Peptide and protein de novo sequencing by mass spectrometry. Curr Opin Struct Biol 13:595-601.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 595-601
    • Standing, K.G.1
  • 84
    • 58149291366 scopus 로고    scopus 로고
    • Factors that contribute to the misidentification of tyrosine nitration by shotgun proteomics
    • Stevens SM, Jr., Prokai-Tatrai K, Prokai L. 2008. Factors that contribute to the misidentification of tyrosine nitration by shotgun proteomics. Mol Cell Proteomics 7:2442-2451.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 2442-2451
    • Stevens, S.M.1    Prokai-Tatrai, K.2    Prokai, L.3
  • 86
    • 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
  • 88
    • 0027918107 scopus 로고
    • Fragmentation reactions of multiply-protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation
    • Tang XJ, Thibault P, Boyd RK. 1993. Fragmentation reactions of multiply-protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation. Anal Chem 65:2824-2834.
    • (1993) Anal Chem , vol.65 , pp. 2824-2834
    • Tang, X.J.1    Thibault, P.2    Boyd, R.K.3
  • 89
    • 0030959279 scopus 로고    scopus 로고
    • Sequence database searches via de novo peptide sequencing by tandem mass spectrometry
    • Taylor JA, Johnson RS. 1997. Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 11:1067-1075.
    • (1997) Rapid Commun Mass Spectrom , vol.11 , pp. 1067-1075
    • Taylor, J.A.1    Johnson, R.S.2
  • 90
    • 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
  • 91
    • 0024689648 scopus 로고
    • Elucidation of some fragmentations of small peptides using sequential mass spectrometry on a hybrid instrument
    • Thorne GC, Gaskell SJ. 1989. Elucidation of some fragmentations of small peptides using sequential mass spectrometry on a hybrid instrument. Rapid Commun Mass Spectrom 3:217-221.
    • (1989) Rapid Commun Mass Spectrom , vol.3 , pp. 217-221
    • Thorne, G.C.1    Gaskell, S.J.2
  • 92
    • 0000590005 scopus 로고
    • Metastable decomposition of peptide [M + H]+ ions via rearrangement involving loss of the C-terminal amino acid residue
    • Thorne GC, Ballard KD, Gaskell SJ. 1990. Metastable decomposition of peptide [M + H]+ ions via rearrangement involving loss of the C-terminal amino acid residue. J Am Soc Mass Spectrom 1:249-257.
    • (1990) J Am Soc Mass Spectrom , vol.1 , pp. 249-257
    • Thorne, G.C.1    Ballard, K.D.2    Gaskell, S.J.3
  • 93
    • 34547153650 scopus 로고    scopus 로고
    • Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing
    • Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. 2007. Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics 7:2318-2329.
    • (2007) Proteomics , vol.7 , pp. 2318-2329
    • Waridel, P.1    Frank, A.2    Thomas, H.3    Surendranath, V.4    Sunyaev, S.5    Pevzner, P.6    Shevchenko, A.7
  • 94
    • 0036636707 scopus 로고    scopus 로고
    • Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) mass spectrometry and its implications for protein identification
    • Wattenberg A, Organ AJ, Schneider K, Tyldesley R, Bordoli R, Bateman RH. 2002. Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) mass spectrometry and its implications for protein identification. J Am Soc Mass Spectrom 13:772-783.
    • (2002) J Am Soc Mass Spectrom , vol.13 , pp. 772-783
    • Wattenberg, A.1    Organ, A.J.2    Schneider, K.3    Tyldesley, R.4    Bordoli, R.5    Bateman, R.H.6
  • 95
    • 0026666837 scopus 로고
    • Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family
    • Wen DX, Livingston BD, Medzihradszky KF, Kelm S, Burlingame AL, Paulson JC. 1992. Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family. J Biol Chem 267:21011-21019.
    • (1992) J Biol Chem , vol.267 , pp. 21011-21019
    • Wen, D.X.1    Livingston, B.D.2    Medzihradszky, K.F.3    Kelm, S.4    Burlingame, A.L.5    Paulson, J.C.6
  • 96
    • 33748294162 scopus 로고    scopus 로고
    • Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches
    • Wielsch N, Thomas H, Surendranath V, Waridel P, Frank A, Pevzner P, Shevchenko A. 2006. Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches. J Proteome Res 5:2448-2456.
    • (2006) J Proteome Res , vol.5 , pp. 2448-2456
    • Wielsch, N.1    Thomas, H.2    Surendranath, V.3    Waridel, P.4    Frank, A.5    Pevzner, P.6    Shevchenko, A.7
  • 97
    • 0034501099 scopus 로고    scopus 로고
    • Mobile and localized protons: A framework for understanding peptide dissociation
    • Wysocki VH, Tsaprailis G, Smith LL, Breci LA. 2000. Mobile and localized protons: A framework for understanding peptide dissociation. J Mass Spectrom 35:1399-1406.
    • (2000) J Mass Spectrom , vol.35 , pp. 1399-1406
    • Wysocki, V.H.1    Tsaprailis, G.2    Smith, L.L.3    Breci, L.A.4
  • 99
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • Zhang Z. 2004. Prediction of low-energy collision-induced dissociation spectra of peptides. Anal Chem 76:3908-3922.
    • (2004) Anal Chem , vol.76 , pp. 3908-3922
    • Zhang, Z.1
  • 100
    • 77749305060 scopus 로고    scopus 로고
    • Prediction of electron-transfer/capture dissociation spectra of peptides
    • Zhang Z. 2010. Prediction of electron-transfer/capture dissociation spectra of peptides. Anal Chem 82:1990-2005.
    • (2010) Anal Chem , vol.82 , pp. 1990-2005
    • Zhang, Z.1
  • 101
    • 81255146358 scopus 로고    scopus 로고
    • Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications
    • Zhang Z. 2011. Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications. Anal Chem 83:8642-8651.
    • (2011) Anal Chem , vol.83 , pp. 8642-8651
    • Zhang, Z.1
  • 104
    • 43549095027 scopus 로고    scopus 로고
    • Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet?
    • Zubarev RA, Zubarev AR, Savitski MM. 2008. Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet? J Am Soc Mass Spectrom 19:753-761.
    • (2008) J Am Soc Mass Spectrom , vol.19 , pp. 753-761
    • Zubarev, R.A.1    Zubarev, A.R.2    Savitski, M.M.3


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