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Volumn 990, Issue , 2013, Pages 1-35

Mass spectrometry-based proteomics: Basic principles and emerging technologies and directions

Author keywords

2 dimensional gel electrophoresis; Electrospray ionization; ESI; Glycosylation; Isotope labeling; MALDI; Mascot; Mass spectrometry; Matrix assisted laser desorption ionization; NanoLC; Nanoscale reversed phase liquid chromatography; Peptide identification; Peptide sequencing; Phosphorylation; Proteome; Sequence database; SEQUEST

Indexed keywords

PEPTIDE DERIVATIVE; PEPTIDE; PROTEOME;

EID: 84934436152     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-7-5896-4_1     Document Type: Article
Times cited : (26)

References (230)
  • 1
    • 0036545614 scopus 로고    scopus 로고
    • Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
    • Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 1(4):323-333
    • (2002) Mol Cell Proteomics , vol.1 , Issue.4 , pp. 323-333
    • Griffin, T.J.1    Gygi, S.P.2    Ideker, T.3    Rist, B.4    Eng, J.5    Hood, L.6    Aebersold, R.7
  • 2
    • 0037453060 scopus 로고    scopus 로고
    • Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae
    • doi:10.1073/pnas.0634629100 0634629100 [pii]
    • Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR 3rd (2003) Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100(6):3107-3112. doi:10.1073/pnas.0634629100 0634629100 [pii]
    • (2003) Proc Natl Acad Sci U S a , vol.100 , Issue.6 , pp. 3107-3112
    • Washburn, M.P.1    Koller, A.2    Oshiro, G.3    Ulaszek, R.R.4    Plouffe, D.5    Deciu, C.6    Winzeler, E.7    Yates III, J.R.8
  • 3
    • 84984042980 scopus 로고
    • Protein and polymer analyses up to m/z 100,000 by laser ionization timeof-flight mass spectrometry
    • Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T, Matsuo T (1988) Protein and polymer analyses up to m/z 100,000 by laser ionization timeof-flight mass spectrometry. Rapid Comm Mass Spectrom 2(8):151-153
    • (1988) Rapid Comm Mass Spectrom , vol.2 , Issue.8 , pp. 151-153
    • Tanaka, K.1    Waki, H.2    Ido, Y.3    Akita, S.4    Yoshida, Y.5    Yoshida, T.6    Matsuo, T.7
  • 4
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246(4926):64-71
    • (1989) Science , vol.246 , Issue.4926 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 7
    • 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 JRI (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.I.3
  • 8
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • doi:10.1002/(SICI)1522-2683(19991201)20:18 <3551::AID-ELPS3551> 3.0.CO;2-2 [pii] 10.1002/ (SICI)1522-2683(19991201)20:18 <3551:: AIDELPS3551> 3.0.CO;2-2
    • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551-3567. doi:10.1002/(SICI)1522-2683(19991201)20: 18 3.0.CO;2-2 [pii] 10.1002/(SICI)1522-2683(19991201)20:18 3.0.CO;2-2
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 9
    • 0036391454 scopus 로고    scopus 로고
    • Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags
    • Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R (2002) Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J Proteome Res 1(1): 47-54
    • (2002) J Proteome Res , vol.1 , Issue.1 , pp. 47-54
    • Gygi, S.P.1    Rist, B.2    Griffin, T.J.3    Eng, J.4    Aebersold, R.5
  • 11
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242-247
    • (2001) Nat Biotechnol , vol.19 , Issue.3 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 12
    • 0034662907 scopus 로고    scopus 로고
    • Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
    • Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci U S A 97(17): 9390-9395
    • (2000) Proc Natl Acad Sci U S a , vol.97 , Issue.17 , pp. 9390-9395
    • Gygi, S.P.1    Corthals, G.L.2    Zhang, Y.3    Rochon, Y.4    Aebersold, R.5
  • 14
    • 0035067251 scopus 로고    scopus 로고
    • Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome
    • Oda Y, Nagasu T, Chait BT (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19(4): 379-382
    • (2001) Nat Biotechnol , vol.19 , Issue.4 , pp. 379-382
    • Oda, Y.1    Nagasu, T.2    Chait, B.T.3
  • 15
    • 0035072715 scopus 로고    scopus 로고
    • A systematic approach to the analysis of protein phosphorylation
    • Zhou H, Watts JD, Aebersold R (2001) A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 19(4):375-378
    • (2001) Nat Biotechnol , vol.19 , Issue.4 , pp. 375-378
    • Zhou, H.1    Watts, J.D.2    Aebersold, R.3
  • 16
    • 0038699625 scopus 로고    scopus 로고
    • Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    • Zhang H, Li XJ, Martin DB, Aebersold R (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 21(6):660-666
    • (2003) Nat Biotechnol , vol.21 , Issue.6 , pp. 660-666
    • Zhang, H.1    Li, X.J.2    Martin, D.B.3    Aebersold, R.4
  • 17
    • 0012578783 scopus 로고    scopus 로고
    • Advances in quantitative proteomics using stable isotope tags
    • Flory MR, Griffin TJ, Martin D, Aebersold R (2002) Advances in quantitative proteomics using stable isotope tags. Trends Biotechnol 20(12 Suppl): S23-S29
    • (2002) Trends Biotechnol , vol.20 , Issue.12 SUPPL.
    • Flory, M.R.1    Griffin, T.J.2    Martin, D.3    Aebersold, R.4
  • 18
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • doi:10.1002/pmic.200300744
    • Creasy DM, Cottrell JS (2004) Unimod: protein modifications for mass spectrometry. Proteomics 4(6):1534-1536. doi:10.1002/pmic.200300744
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 19
    • 79953719716 scopus 로고    scopus 로고
    • More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS
    • doi:10.1021/pr101060v
    • Michalski A, Cox J, Mann M (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 10(4):1785-1793. doi:10.1021/pr101060v
    • (2011) J Proteome Res , vol.10 , Issue.4 , pp. 1785-1793
    • Michalski, A.1    Cox, J.2    Mann, M.3
  • 20
    • 57449099068 scopus 로고    scopus 로고
    • Precision proteomics: The case for high resolution and high mass accuracy
    • doi:10.1073/pnas.0800788105
    • Mann M, Kelleher NL (2008) Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A 105(47):18132-18138. doi:10.1073/pnas.0800788105
    • (2008) Proc Natl Acad Sci U S a , vol.105 , Issue.47 , pp. 18132-18138
    • Mann, M.1    Kelleher, N.L.2
  • 21
    • 2742576125 scopus 로고    scopus 로고
    • Accuracy requirements for peptide characterization by monoisotopic molecular mass measurements
    • doi:10.1021/ac9604651
    • Zubarev RA, Hakansson P, Sundqvist B (1996) Accuracy requirements for peptide characterization by monoisotopic molecular mass measurements. Anal Chem 68(22):4060-4063. doi:10.1021/ac9604651
    • (1996) Anal Chem , vol.68 , Issue.22 , pp. 4060-4063
    • Zubarev, R.A.1    Hakansson, P.2    Sundqvist, B.3
  • 23
    • 83655164803 scopus 로고    scopus 로고
    • Improving proteomics mass accuracy by dynamic offline lock mass
    • doi:10.1021/ac201867h
    • Zhang Y, Wen Z, Washburn MP, Florens LA (2011) Improving proteomics mass accuracy by dynamic offline lock mass. Anal Chem. doi:10.1021/ac201867h
    • (2011) Anal Chem.
    • Zhang, Y.1    Wen, Z.2    Washburn, M.P.3    Florens, L.A.4
  • 24
    • 0842285056 scopus 로고
    • The interpretation of collision-induced dissociation tandem mass-spectra of peptides
    • doi:10.1002/mas.1280140104
    • Papayannopoulos IA (1995) The interpretation of collision-induced dissociation tandem mass-spectra of peptides. Mass Spectrom Rev 14(1):49-73. doi:10.1002/mas.1280140104
    • (1995) Mass Spectrom Rev , vol.14 , Issue.1 , pp. 49-73
    • Papayannopoulos, I.A.1
  • 25
    • 0037398266 scopus 로고    scopus 로고
    • Interfacing the orbitrap mass analyzer to an electrospray ion source
    • doi:10.1021/ac0258047
    • Hardman M, Makarov AA (2003) Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal Chem. 75(7):1699-1705. doi:10.1021/ac0258047
    • (2003) Anal Chem. , vol.75 , Issue.7 , pp. 1699-1705
    • Hardman, M.1    Makarov, A.A.2
  • 26
    • 0041408938 scopus 로고    scopus 로고
    • Electrostatic axially harmonic orbital trapping: A high-performance technique of mass analysis
    • doi:10.1021/ac991131p
    • Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72(6):1156-1162. doi:10.1021/ac991131p
    • (2000) Anal Chem , vol.72 , Issue.6 , pp. 1156-1162
    • Makarov, A.1
  • 27
    • 33645654439 scopus 로고    scopus 로고
    • Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer
    • doi:10.1021/ac0518811
    • Makarov A, Denisov E, Kholomeev A, Baischun W, Lange O, Strupat K, Horning S (2006) Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem 78(7):2113-2120. doi:10.1021/ac0518811
    • (2006) Anal Chem , vol.78 , Issue.7 , pp. 2113-2120
    • Makarov, A.1    Denisov, E.2    Kholomeev, A.3    Baischun, W.4    Lange, O.5    Strupat, K.6    Horning, S.7
  • 29
    • 67650711335 scopus 로고    scopus 로고
    • Performance evaluation of a high-field orbitrap mass analyzer
    • doi:10.1016/j.jasms.2009.01.005
    • Makarov A, Denisov E, Lange O (2009) Performance evaluation of a high-field orbitrap mass analyzer. J Am Soc Mass Spectrom 20(8):1391-1396. doi:10.1016/j.jasms.2009.01.005
    • (2009) J Am Soc Mass Spectrom , vol.20 , Issue.8 , pp. 1391-1396
    • Makarov, A.1    Denisov, E.2    Lange, O.3
  • 31
    • 79959958529 scopus 로고    scopus 로고
    • Performance characteristics of a New hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600)
    • doi:10.1021/ac200812d
    • Andrews GL, Simons BL, Young JB, Hawkridge AM, Muddiman DC (2011) Performance characteristics of a New hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal Chem 83(13):5442-5446. doi:10.1021/ac200812d
    • (2011) Anal Chem , vol.83 , Issue.13 , pp. 5442-5446
    • Andrews, G.L.1    Simons, B.L.2    Young, J.B.3    Hawkridge, A.M.4    Muddiman, D.C.5
  • 33
    • 33645128611 scopus 로고    scopus 로고
    • Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel
    • doi:10.1016/j.jasms.2005.12.013
    • Page JS, Tolmachev AV, Tang KQ, Smith RD (2006) Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel. J Am Soc Mass Spectrom 17(4):586-592. doi:10.1016/j.jasms.2005.12.013
    • (2006) J Am Soc Mass Spectrom , vol.17 , Issue.4 , pp. 586-592
    • Page, J.S.1    Tolmachev, A.V.2    Tang, K.Q.3    Smith, R.D.4
  • 35
  • 36
    • 77951028799 scopus 로고    scopus 로고
    • The ion funnel: Theory, implementations, and applications
    • doi:10.1002/mas.20232
    • Kelly RT, Tolmachev AV, Page JS, Tang KQ, Smith RD (2010) The ion funnel: theory, implementations, and applications. Mass Spectrom Rev 29(2):294-312. doi:10.1002/mas.20232
    • (2010) Mass Spectrom Rev , vol.29 , Issue.2 , pp. 294-312
    • Kelly, R.T.1    Tolmachev, A.V.2    Page, J.S.3    Tang, K.Q.4    Smith, R.D.5
  • 37
    • 0029924432 scopus 로고    scopus 로고
    • Stacked-ring electrostatic ion guide
    • doi:10.1016/1044-0305(95)00605-2
    • Guan SH, Marshall AG (1996) Stacked-ring electrostatic ion guide. J Am Soc Mass Spectrom 7(1):101-106. doi:10.1016/1044-0305(95)00605-2
    • (1996) J Am Soc Mass Spectrom , vol.7 , Issue.1 , pp. 101-106
    • Guan, S.H.1    Marshall, A.G.2
  • 38
    • 49049117384 scopus 로고    scopus 로고
    • Nanoelectrospray emitter arrays providing interemitter electric field uniformity
    • doi:10.1021/ac800508q
    • Kelly RT, Page JS, Marginean I, Tang KQ, Smith RD (2008) Nanoelectrospray emitter arrays providing interemitter electric field uniformity. Anal Chem 80(14):5660-5665. doi:10.1021/ac800508q
    • (2008) Anal Chem , vol.80 , Issue.14 , pp. 5660-5665
    • Kelly, R.T.1    Page, J.S.2    Marginean, I.3    Tang, K.Q.4    Smith, R.D.5
  • 39
    • 41149088254 scopus 로고    scopus 로고
    • Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry
    • doi:10.1021/ac702354b
    • Page JS, Tang K, Kelly RT, Smith RD (2008) Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry. Anal Chem 80(5):1800-1805. doi:10.1021/ac702354b
    • (2008) Anal Chem , vol.80 , Issue.5 , pp. 1800-1805
    • Page, J.S.1    Tang, K.2    Kelly, R.T.3    Smith, R.D.4
  • 40
    • 34548127562 scopus 로고    scopus 로고
    • Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface
    • doi:10.1016/j.jasms.2007.05.018
    • Page JS, Kelly RT, Tang K, Smith RD (2007) Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface. J Am Soc Mass Spectrom 18(9):1582-1590. doi:10.1016/j.jasms.2007.05.018
    • (2007) J Am Soc Mass Spectrom , vol.18 , Issue.9 , pp. 1582-1590
    • Page, J.S.1    Kelly, R.T.2    Tang, K.3    Smith, R.D.4
  • 41
    • 80052681763 scopus 로고    scopus 로고
    • Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface
    • doi:10.1007/s13361-011-0135-7
    • Tang KQ, Page JS, Marginean I, Kelly RT, Smith RD (2011) Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface. J Am Soc Mass Spectrom 22(8):1318-1325. doi:10.1007/s13361-011-0135-7
    • (2011) J Am Soc Mass Spectrom , vol.22 , Issue.8 , pp. 1318-1325
    • Tang, K.Q.1    Page, J.S.2    Marginean, I.3    Kelly, R.T.4    Smith, R.D.5
  • 42
    • 78449279144 scopus 로고    scopus 로고
    • Achieving 50% ionization efficiency in subambient pressure ionization with nanoelectrospray
    • doi:10.1021/ac1019123
    • Marginean I, Page JS, Tolmachev AV, Tang KQ, Smith RD (2010) Achieving 50% ionization efficiency in subambient pressure ionization with nanoelectrospray. Anal Chem 82(22):9344-9349. doi:10.1021/ac1019123
    • (2010) Anal Chem , vol.82 , Issue.22 , pp. 9344-9349
    • Marginean, I.1    Page, J.S.2    Tolmachev, A.V.3    Tang, K.Q.4    Smith, R.D.5
  • 43
    • 79952520637 scopus 로고    scopus 로고
    • Ion/neutral, ion/electron, ion/photon, and ion/Ion interactions in tandem mass spectrometry: Do we need them all? Are they enough?
    • doi:10.1007/s13361-010-0004-9
    • McLuckey SA, Mentinova M (2011) Ion/neutral, ion/electron, ion/photon, and ion/Ion interactions in tandem mass spectrometry: do we need them all? Are they enough? J Am Soc Mass Spectrom 22(1):3-12. doi:10.1007/s13361-010-0004-9
    • (2011) J Am Soc Mass Spectrom , vol.22 , Issue.1 , pp. 3-12
    • McLuckey, S.A.1    Mentinova, M.2
  • 44
    • 75749136525 scopus 로고    scopus 로고
    • Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification
    • doi:10.1021/ac902005s
    • McAlister GC, Phanstiel D, Wenger CD, Lee MV, Coon JJ (2010) Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal Chem 82(1):316-322. doi:10.1021/ac902005s
    • (2010) Anal Chem , vol.82 , Issue.1 , pp. 316-322
    • McAlister, G.C.1    Phanstiel, D.2    Wenger, C.D.3    Lee, M.V.4    Coon, J.J.5
  • 45
    • 0023386279 scopus 로고
    • Instrumentation, applications, and energy deposition in quadrupole ion-trap tandem mass-spectrometry
    • doi:10.1021/ac00140a021
    • Louris JN, Cooks RG, Syka JEP, Kelley PE, Stafford GC, Todd JFJ (1987) Instrumentation, applications, and energy deposition in quadrupole ion-trap tandem mass-spectrometry. Anal Chem 59(13):1677-1685. doi:10.1021/ac00140a021
    • (1987) Anal Chem , vol.59 , Issue.13 , pp. 1677-1685
    • Louris, J.N.1    Cooks, R.G.2    Syka, J.E.P.3    Kelley, P.E.4    Stafford, G.C.5    Todd, J.F.J.6
  • 47
    • 12444345515 scopus 로고    scopus 로고
    • Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
    • doi:10.1021/ac0262560
    • Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Hamon C (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75(8):1895-1904. doi:10.1021/ac0262560
    • (2003) Anal Chem , vol.75 , Issue.8 , pp. 1895-1904
    • Thompson, A.1    Schafer, J.2    Kuhn, K.3    Kienle, S.4    Schwarz, J.5    Schmidt, G.6    Neumann, T.7    Hamon, C.8
  • 48
    • 36348987990 scopus 로고    scopus 로고
    • ITRAQ reagentbased quantitative proteomic analysis on a linear ion trap mass spectrometer
    • doi:10.1021/pr070291b
    • Griffin TJ, Xie HW, Bandhakavi S, Popko J, Mohan A, Carlis JV, Higgins L (2007) iTRAQ reagentbased quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res 6(11):4200-4209. doi:10.1021/pr070291b
    • (2007) J Proteome Res , vol.6 , Issue.11 , pp. 4200-4209
    • Griffin, T.J.1    Xie, H.W.2    Bandhakavi, S.3    Popko, J.4    Mohan, A.5    Carlis, J.V.6    Higgins, L.7
  • 49
    • 52649098504 scopus 로고    scopus 로고
    • Robust and sensitive iTRAQ quantification on an LTQ orbitrap mass spectrometer
    • doi:10.1074/mcp.M800029-MCP200
    • Bantscheff M, Boesche M, Eberhard D, Matthieson T, Sweetman G, Kuster B (2008) Robust and sensitive iTRAQ quantification on an LTQ orbitrap mass spectrometer. Mol Cell Proteomics 7(9):1702-1713. doi:10.1074/mcp.M800029-MCP200
    • (2008) Mol Cell Proteomics , vol.7 , Issue.9 , pp. 1702-1713
    • Bantscheff, M.1    Boesche, M.2    Eberhard, D.3    Matthieson, T.4    Sweetman, G.5    Kuster, B.6
  • 50
    • 79951635872 scopus 로고    scopus 로고
    • Improved precision of iTRAQ and TMT quantification by an axial extraction field in an orbitrap HCD cell
    • doi:10.1021/ac102265w
    • Pichler P, Kocher T, Holzmann J, Mohring T, Ammerer G, Mechtler K (2011) Improved precision of iTRAQ and TMT quantification by an axial extraction field in an orbitrap HCD cell. Anal Chem 83(4):1469-1474. doi:10.1021/ac102265w
    • (2011) Anal Chem , vol.83 , Issue.4 , pp. 1469-1474
    • Pichler, P.1    Kocher, T.2    Holzmann, J.3    Mohring, T.4    Ammerer, G.5    Mechtler, K.6
  • 51
    • 78649849874 scopus 로고    scopus 로고
    • Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation
    • doi:10.1021/pr100637q
    • Nagaraj N, D'Souza RCJ, Cox J, Olsen JV, Mann M (2010) Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 9(12):6786-6794. doi:10.1021/pr100637q
    • (2010) J Proteome Res , vol.9 , Issue.12 , pp. 6786-6794
    • Nagaraj, N.1    D'Souza, R.C.J.2    Cox, J.3    Olsen, J.V.4    Mann, M.5
  • 52
    • 0000944563 scopus 로고    scopus 로고
    • Electron capture dissociation of multiply charged protein cations. A nonergodic process
    • doi:10.1021/ja973478k
    • Zubarev RA, Kelleher NL, McLafferty FW (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. J Am Chem Soc 120(13):3265-3266. doi:10.1021/ja973478k
    • (1998) J Am Chem Soc , vol.120 , Issue.13 , pp. 3265-3266
    • Zubarev, R.A.1    Kelleher, N.L.2    McLafferty, F.W.3
  • 53
    • 33745684811 scopus 로고    scopus 로고
    • Electron capture dissociation mass spectrometry in characterization of peptides and proteins
    • doi:10.1007/s10529-006-9065-z
    • Bakhtiar R, Guan ZQ (2006) Electron capture dissociation mass spectrometry in characterization of peptides and proteins. Biotechnol Lett 28(14):1047-1059. doi:10.1007/s10529-006-9065-z
    • (2006) Biotechnol Lett , vol.28 , Issue.14 , pp. 1047-1059
    • Bakhtiar, R.1    Guan, Z.Q.2
  • 55
    • 3042789073 scopus 로고    scopus 로고
    • Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
    • doi:10.1073/pnas.0402700101
    • Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 101(26):9528-9533. doi:10.1073/pnas. 0402700101
    • (2004) Proc Natl Acad Sci U S a , vol.101 , Issue.26 , pp. 9528-9533
    • Syka, J.E.P.1    Coon, J.J.2    Schroeder, M.J.3    Shabanowitz, J.4    Hunt, D.F.5
  • 57
    • 0038610834 scopus 로고    scopus 로고
    • Reactions of polypeptide ions with electrons in the gas phase
    • doi:10.1002/mas.10042
    • Zubarev RA (2003) Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom Rev 22(1):57-77. doi:10.1002/mas.10042
    • (2003) Mass Spectrom Rev , vol.22 , Issue.1 , pp. 57-77
    • Zubarev, R.A.1
  • 58
    • 55849104839 scopus 로고    scopus 로고
    • Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications
    • doi:10.1002/ pmic.200800329
    • Wiesner J, Premsler T, Sickmann A (2008) Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8(21):4466-4483. doi:10.1002/ pmic.200800329
    • (2008) Proteomics , vol.8 , Issue.21 , pp. 4466-4483
    • Wiesner, J.1    Premsler, T.2    Sickmann, A.3
  • 59
    • 70349113034 scopus 로고    scopus 로고
    • Determination of glycosylation sites and site-specific heterogeneity in glycoproteins
    • doi:10.1016/j.cbpa.2009.07.022
    • An HJ, Froehlich JW, Lebrilla CB (2009) Determination of glycosylation sites and site-specific heterogeneity in glycoproteins. Curr Opin Chem Biol 13(4):421-426. doi:10.1016/j.cbpa.2009.07.022
    • (2009) Curr Opin Chem Biol , vol.13 , Issue.4 , pp. 421-426
    • An, H.J.1    Froehlich, J.W.2    Lebrilla, C.B.3
  • 60
    • 67649213067 scopus 로고    scopus 로고
    • Phosphopeptide fragmentation and analysis by mass spectrometry
    • doi:10.1002/jms.1599
    • Boersema PJ, Mohammed S, Heck AJR (2009) Phosphopeptide fragmentation and analysis by mass spectrometry. J Mass Spectrom 44(6):861-878. doi:10.1002/jms.1599
    • (2009) J Mass Spectrom , vol.44 , Issue.6 , pp. 861-878
    • Boersema, P.J.1    Mohammed, S.2    Heck, A.J.R.3
  • 61
    • 55849105589 scopus 로고    scopus 로고
    • Quantitative phosphoproteomics: An emerging key technology in signal-transduction research
    • doi:10.1002/pmic. 200800132
    • Schreiber TB, Mausbacher N, Breitkopf SB, Grundner-Culemann K, Daub H (2008) Quantitative phosphoproteomics: an emerging key technology in signal-transduction research. Proteomics 8(21):4416-4432. doi:10.1002/pmic. 200800132
    • (2008) Proteomics , vol.8 , Issue.21 , pp. 4416-4432
    • Schreiber, T.B.1    Mausbacher, N.2    Breitkopf, S.B.3    Grundner-Culemann, K.4    Daub, H.5
  • 62
    • 7244221587 scopus 로고    scopus 로고
    • Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociation of peptides in a quadrupole ion trap with selective IRMPD of phosphopeptides
    • doi:10.1016/j.jasms.2004.07.016
    • Crowe MC, Brodbelt JS (2004) Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociation of peptides in a quadrupole ion trap with selective IRMPD of phosphopeptides. J Am Soc Mass Spectrom 15(11):1581-1592. doi:10.1016/j.jasms.2004.07.016
    • (2004) J Am Soc Mass Spectrom , vol.15 , Issue.11 , pp. 1581-1592
    • Crowe, M.C.1    Brodbelt, J.S.2
  • 63
    • 24644456406 scopus 로고    scopus 로고
    • Differentiation of phosphorylated and unphosphorylated peptides by high-performance liquid chromatographyelectrospray ionization-infrared multiphoton dissociation in a quadrupole ion trap
    • doi:10.1021/ac0509410
    • Crowe MC, Brodbelt JS (2005) Differentiation of phosphorylated and unphosphorylated peptides by high-performance liquid chromatographyelectrospray ionization-infrared multiphoton dissociation in a quadrupole ion trap. Anal Chem 77(17):5726-5734. doi:10.1021/ac0509410
    • (2005) Anal Chem , vol.77 , Issue.17 , pp. 5726-5734
    • Crowe, M.C.1    Brodbelt, J.S.2
  • 64
    • 66149102368 scopus 로고    scopus 로고
    • Infrared multiphoton dissociation in quadrupole ion traps
    • doi:10.1002/mas.20216
    • Brodbelt JS, Wilson JJ (2009) Infrared multiphoton dissociation in quadrupole ion traps. Mass Spectrom Rev 28(3):390-424. doi:10.1002/mas.20216
    • (2009) Mass Spectrom Rev , vol.28 , Issue.3 , pp. 390-424
    • Brodbelt, J.S.1    Wilson, J.J.2
  • 65
    • 0027997748 scopus 로고
    • Infrared multiphoton dissociation of large multiply-charged ions for biomolecule sequencing
    • doi:10.1021/ac00090a004
    • Little DP, Speir JP, Senko MW, Oconnor PB, McLafferty FW (1994) Infrared multiphoton dissociation of large multiply-charged ions for biomolecule sequencing. Anal Chem 66(18):2809-2815. doi:10.1021/ac00090a004
    • (1994) Anal Chem , vol.66 , Issue.18 , pp. 2809-2815
    • Little, D.P.1    Speir, J.P.2    Senko, M.W.3    Oconnor, P.B.4    McLafferty, F.W.5
  • 66
    • 70349917570 scopus 로고    scopus 로고
    • Ultraviolet photodissociation: Developments towards applications for massspectrometry-based proteomics
    • doi:10.1002/anie.200900613
    • Ly T, Julian RR (2009) Ultraviolet photodissociation: developments towards applications for massspectrometry-based proteomics. Angew Chem Int Ed 48(39):7130-7137. doi:10.1002/anie.200900613
    • (2009) Angew Chem Int Ed , vol.48 , Issue.39 , pp. 7130-7137
    • Ly, T.1    Julian, R.R.2
  • 67
    • 66149151341 scopus 로고    scopus 로고
    • Ultraviolet photofragmentation of biomolecular ions
    • doi:10.1002/mas.20214
    • Reilly JP (2009) Ultraviolet photofragmentation of biomolecular ions. Mass Spectrom Rev 28(3):425-447. doi:10.1002/mas.20214
    • (2009) Mass Spectrom Rev , vol.28 , Issue.3 , pp. 425-447
    • Reilly, J.P.1
  • 68
    • 0034652301 scopus 로고    scopus 로고
    • Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry
    • doi:10.1021/ac991025n
    • Gatlin CL, Eng JK, Cross ST, Detter JC, Yates JR (2000) Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal Chem 72(4):757-763. doi:10.1021/ac991025n
    • (2000) Anal Chem , vol.72 , Issue.4 , pp. 757-763
    • Gatlin, C.L.1    Eng, J.K.2    Cross, S.T.3    Detter, J.C.4    Yates, J.R.5
  • 69
    • 0034655385 scopus 로고    scopus 로고
    • Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures
    • doi:10.1021/ac991133C 70.
    • Masselon C, Anderson GA, Harkewicz R, Bruce JE, Pasa-Tolic L, Smith RD (2000) Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal Chem 72(8):1918-1924. doi:10.1021/ac991133C 70.
    • (2000) Anal Chem , vol.72 , Issue.8 , pp. 1918-1924
    • Masselon, C.1    Anderson, G.A.2    Harkewicz, R.3    Bruce, J.E.4    Pasa-Tolic, L.5    Smith, R.D.6
  • 70
    • 0038047154 scopus 로고    scopus 로고
    • Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer
    • doi:10.1002/pmic.200300362
    • Purvine S, Eppel JT, Yi EC, Goodlett DR (2003) Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3(6):847-850. doi:10.1002/pmic.200300362
    • (2003) Proteomics , vol.3 , Issue.6 , pp. 847-850
    • Purvine, S.1    Eppel, J.T.2    Yi, E.C.3    Goodlett, D.R.4
  • 72
    • 77957990113 scopus 로고    scopus 로고
    • Proteomics on an orbitrap benchtop mass spectrometer using All-ion fragmentation
    • doi:10.1074/mcp.M110.001537
    • Geiger T, Cox J, Mann M (2010) Proteomics on an orbitrap benchtop mass spectrometer using All-ion fragmentation. Mol Cell Proteomics 9(10):2252-2261. doi:10.1074/mcp.M110.001537
    • (2010) Mol Cell Proteomics , vol.9 , Issue.10 , pp. 2252-2261
    • Geiger, T.1    Cox, J.2    Mann, M.3
  • 73
    • 20244381257 scopus 로고    scopus 로고
    • Highthroughput peptide identification from protein digests using data-dependent multiplexed tandem FTICR mass spectrometry coupled with capillary liquid chromatography
    • doi:10.1021/ac010192w
    • Li LJ, Masselon CD, Anderson GA, Pasa-Tolic L, Lee SW, Shen YF, Zhao R, Lipton MS, Conrads TP, Tolic N, Smith RD (2001) Highthroughput peptide identification from protein digests using data-dependent multiplexed tandem FTICR mass spectrometry coupled with capillary liquid chromatography. Anal Chem 73(14):3312-3322. doi:10.1021/ac010192w
    • (2001) Anal Chem , vol.73 , Issue.14 , pp. 3312-3322
    • Li, L.J.1    Masselon, C.D.2    Anderson, G.A.3    Pasa-Tolic, L.4    Lee, S.W.5    Shen, Y.F.6    Zhao, R.7    Lipton, M.S.8    Conrads, T.P.9    Tolic, N.10    Smith, R.D.11
  • 74
    • 68049114653 scopus 로고    scopus 로고
    • Precursor acquisition independent from ion count: How to dive deeper into the proteomics ocean
    • doi:10.1021/ac900888s
    • Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR (2009) Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem 81(15):6481-6488. doi:10.1021/ac900888s
    • (2009) Anal Chem , vol.81 , Issue.15 , pp. 6481-6488
    • Panchaud, A.1    Scherl, A.2    Shaffer, S.A.3    Von Haller, P.D.4    Kulasekara, H.D.5    Miller, S.I.6    Goodlett, D.R.7
  • 75
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • doi:10.1038/nmeth705
    • Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 1(1):39-45. doi:10.1038/nmeth705
    • (2004) Nat Methods , vol.1 , Issue.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 76
    • 79954569537 scopus 로고    scopus 로고
    • Faster, quantitative, and accurate precursor acquisition independent from ion count
    • doi:10.1021/ac103079q
    • Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR (2011) Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem 83(6):2250-2257. doi:10.1021/ac103079q
    • (2011) Anal Chem , vol.83 , Issue.6 , pp. 2250-2257
    • Panchaud, A.1    Jung, S.2    Shaffer, S.A.3    Aitchison, J.D.4    Goodlett, D.R.5
  • 77
    • 0035226437 scopus 로고    scopus 로고
    • Towards defining the urinary proteome using liquid chromatographytandem mass spectrometry - II. Limitations of complex mixture analyses
    • doi:10.1002/1615-9861(200101)1:1 <108:aidprot108> 3.0.co;2-5
    • Davis MT, Spahr CS, McGinley MD, Robinson JH, Bures EJ, Beierle J, Mort J, Yu W, Luethy R, Patterson SD (2001) Towards defining the urinary proteome using liquid chromatographytandem mass spectrometry - II. Limitations of complex mixture analyses. Proteomics 1(1):108-117. doi:10.1002/1615-9861(200101)1: 1<108:aidprot108>3.0.co;2-5
    • (2001) Proteomics , vol.1 , Issue.1 , pp. 108-117
    • Davis, M.T.1    Spahr, C.S.2    McGinley, M.D.3    Robinson, J.H.4    Bures, E.J.5    Beierle, J.6    Mort, J.7    Yu, W.8    Luethy, R.9    Patterson, S.D.10
  • 78
    • 0034016574 scopus 로고    scopus 로고
    • Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition
    • doi:10.1038/sj.cdd.4400640
    • Patterson SD, Spahr CS, Daugas E, Susin SA, Irinopoulou T, Koehler C, Kroemer G (2000) Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition. Cell Death Differ 7(2):137-144. doi:10.1038/sj.cdd.4400640
    • (2000) Cell Death Differ , vol.7 , Issue.2 , pp. 137-144
    • Patterson, S.D.1    Spahr, C.S.2    Daugas, E.3    Susin, S.A.4    Irinopoulou, T.5    Koehler, C.6    Kroemer, G.7
  • 80
    • 0036747350 scopus 로고    scopus 로고
    • Approaching complete peroxisome characterization by gas-phase fractionation
    • doi:10.1002/1522-2683(200209)23:18 <3205::aidelps3205> 3.0.co;2-y
    • Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR (2002) Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis 23(18):3205-3216. doi:10.1002/1522-2683(200209) 23:18<3205::aidelps3205>3.0.co;2-y
    • (2002) Electrophoresis , vol.23 , Issue.18 , pp. 3205-3216
    • Yi, E.C.1    Marelli, M.2    Lee, H.3    Purvine, S.O.4    Aebersold, R.5    Aitchison, J.D.6    Goodlett, D.R.7
  • 81
    • 39449111536 scopus 로고    scopus 로고
    • Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides
    • doi:10.1021/ ac701680f
    • Scherl A, Shaffer SA, Taylor GK, Kulasekara HD, Miller SI, Goodlett DR (2008) Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. Anal Chem 80(4):1182-1191. doi:10.1021/ ac701680f
    • (2008) Anal Chem , vol.80 , Issue.4 , pp. 1182-1191
    • Scherl, A.1    Shaffer, S.A.2    Taylor, G.K.3    Kulasekara, H.D.4    Miller, S.I.5    Goodlett, D.R.6
  • 82
    • 79961185259 scopus 로고    scopus 로고
    • Ion mobility mass spectrometry for peptide analysis
    • doi:10.1016/j.ymeth. 2011.05.004
    • Harvey SR, MacPhee CE, Barran PE (2011) Ion mobility mass spectrometry for peptide analysis. Methods 54(4):454-461. doi:10.1016/j.ymeth. 2011.05.004
    • (2011) Methods , vol.54 , Issue.4 , pp. 454-461
    • Harvey, S.R.1    Macphee, C.E.2    Barran, P.E.3
  • 83
    • 0035891934 scopus 로고    scopus 로고
    • Multidimensional separations of complex peptide mixtures: A combined high-performance liquid chromatography/ion mobility/time-of-flight mass spectrometry approach
    • doi:10.1016/s1387-3806(01) 00511-5
    • Valentine SJ, Kulchania M, Barnes CAS, Clemmer DE (2001) Multidimensional separations of complex peptide mixtures: a combined high-performance liquid chromatography/ion mobility/time-of-flight mass spectrometry approach. Int J Mass Spectrom 212(1-3):97-109. doi:10.1016/s1387-3806(01) 00511-5
    • (2001) Int J Mass Spectrom , vol.212 , Issue.1-3 , pp. 97-109
    • Valentine, S.J.1    Kulchania, M.2    Barnes, C.A.S.3    Clemmer, D.E.4
  • 84
    • 0033567898 scopus 로고    scopus 로고
    • Gas phase separations of electrosprayed peptide libraries
    • doi:10.1021/ac9903757
    • Srebalus CA, Li JW, Marshall WS, Clemmer DE (1999) Gas phase separations of electrosprayed peptide libraries. Anal Chem 71(18):3918-3927. doi:10.1021/ac9903757
    • (1999) Anal Chem , vol.71 , Issue.18 , pp. 3918-3927
    • Srebalus, C.A.1    Li, J.W.2    Marshall, W.S.3    Clemmer, D.E.4
  • 85
    • 77949801007 scopus 로고    scopus 로고
    • High-resolution differential ion mobility separations using helium-rich gases
    • doi:10.1021/ac902852a
    • Shvartsburg AA, Danielson WF, Smith RD (2010) High-resolution differential ion mobility separations using helium-rich gases. Anal Chem 82(6):2456-2462. doi:10.1021/ac902852a
    • (2010) Anal Chem , vol.82 , Issue.6 , pp. 2456-2462
    • Shvartsburg, A.A.1    Danielson, W.F.2    Smith, R.D.3
  • 86
    • 75749092642 scopus 로고    scopus 로고
    • Differential ion mobility separations of peptides with resolving power exceeding 50
    • doi:10.1021/ac902133n
    • Shvartsburg AA, Tang KQ, Smith RD (2010) Differential ion mobility separations of peptides with resolving power exceeding 50. Anal Chem 82(1):32-35. doi:10.1021/ac902133n
    • (2010) Anal Chem , vol.82 , Issue.1 , pp. 32-35
    • Shvartsburg, A.A.1    Tang, K.Q.2    Smith, R.D.3
  • 87
    • 77956574893 scopus 로고    scopus 로고
    • High-resolution differential ion mobility separations using planar analyzers at elevated dispersion fields
    • doi:10.1021/ac101413k
    • Shvartsburg AA, Prior DC, Tang KQ, Smith RD (2010) High-resolution differential ion mobility separations using planar analyzers at elevated dispersion fields. Anal Chem 82(18):7649-7655. doi:10.1021/ac101413k
    • (2010) Anal Chem , vol.82 , Issue.18 , pp. 7649-7655
    • Shvartsburg, A.A.1    Prior, D.C.2    Tang, K.Q.3    Smith, R.D.4
  • 88
    • 33744949963 scopus 로고    scopus 로고
    • High-resolution field asymmetric waveform ion mobility spectrometry using new planar geometry analyzers
    • doi:10.1021/ac052020v
    • Shvartsburg AA, Li FM, Tang KQ, Smith RD (2006) High-resolution field asymmetric waveform ion mobility spectrometry using new planar geometry analyzers. Anal Chem 78(11):3706-3714. doi:10.1021/ac052020v
    • (2006) Anal Chem , vol.78 , Issue.11 , pp. 3706-3714
    • Shvartsburg, A.A.1    Li, F.M.2    Tang, K.Q.3    Smith, R.D.4
  • 89
    • 79959964339 scopus 로고    scopus 로고
    • Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues
    • doi:10.1021/ac200985s
    • Shvartsburg AA, Singer D, Smith RD, Hoffmann R (2011) Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues. Anal Chem 83(13):5078-5085. doi:10.1021/ac200985s
    • (2011) Anal Chem , vol.83 , Issue.13 , pp. 5078-5085
    • Shvartsburg, A.A.1    Singer, D.2    Smith, R.D.3    Hoffmann, R.4
  • 91
    • 33846811132 scopus 로고    scopus 로고
    • An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument
    • doi:10.1016/j.ijms.2006.07.021
    • Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, Bateman RH, Bowers MT, Scrivens JH (2007) An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom 261(1):1-12. doi:10.1016/j.ijms.2006.07.021
    • (2007) Int J Mass Spectrom , vol.261 , Issue.1 , pp. 1-12
    • Pringle, S.D.1    Giles, K.2    Wildgoose, J.L.3    Williams, J.P.4    Slade, S.E.5    Thalassinos, K.6    Bateman, R.H.7    Bowers, M.T.8    Scrivens, J.H.9
  • 92
    • 70549084975 scopus 로고    scopus 로고
    • Directed mass spectrometry: Towards hypothesisdriven proteomics
    • doi:10.1016/j.cbpa.2009.08.016
    • Schmidt A, Claassen M, Aebersold R (2009) Directed mass spectrometry: towards hypothesisdriven proteomics. Curr Opin Chem Biol 13(5-6):510-517. doi:10.1016/j.cbpa.2009.08.016
    • (2009) Curr Opin Chem Biol , vol.13 , Issue.5-6 , pp. 510-517
    • Schmidt, A.1    Claassen, M.2    Aebersold, R.3
  • 93
    • 55349134214 scopus 로고    scopus 로고
    • The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline
    • doi:10.1002/prca.200780174
    • Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P (2008) The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin Appl 2(10-11):1386-1402. doi:10.1002/prca.200780174
    • (2008) Proteomics Clin Appl , vol.2 , Issue.10-11 , pp. 1386-1402
    • Paulovich, A.G.1    Whiteaker, J.R.2    Hoofnagle, A.N.3    Wang, P.4
  • 94
    • 68749094119 scopus 로고    scopus 로고
    • Full dynamic range proteome analysis of S. Cerevisiae by targeted proteomics
    • doi:10.1016/ j.cell.2009.05.051
    • Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R (2009) Full dynamic range proteome analysis of S. Cerevisiae by targeted proteomics. Cell 138(4):795-806. doi:10.1016/ j.cell.2009.05.051
    • (2009) Cell , vol.138 , Issue.4 , pp. 795-806
    • Picotti, P.1    Bodenmiller, B.2    Mueller, L.N.3    Domon, B.4    Aebersold, R.5
  • 95
    • 59849093889 scopus 로고    scopus 로고
    • Prediction of high-responding peptides for targeted protein assays by mass spectrometry
    • doi:10.1038/nbt.1524
    • Fusaro VA, Mani DR, Mesirov JP, Carr SA (2009) Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol 27(2):190-198. doi:10.1038/nbt.1524
    • (2009) Nat Biotechnol , vol.27 , Issue.2 , pp. 190-198
    • Fusaro, V.A.1    Mani, D.R.2    Mesirov, J.P.3    Carr, S.A.4
  • 97
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • doi:10.1038/embor.2008.56
    • Deutsch EW, Lam H, Aebersold R (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 9(5):429-434. doi:10.1038/embor.2008.56
    • (2008) EMBO Rep , vol.9 , Issue.5 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 101
    • 79955069761 scopus 로고    scopus 로고
    • Applying selected reaction monitoring to targeted proteomics
    • doi:10.1586/epr.11.11
    • Calvo E, Camafeita E, Fernandez-Gutierrez B, Lopez JA (2011) Applying selected reaction monitoring to targeted proteomics. Expert Rev Proteomics 8(2):165-173. doi:10.1586/epr.11.11
    • (2011) Expert Rev Proteomics , vol.8 , Issue.2 , pp. 165-173
    • Calvo, E.1    Camafeita, E.2    Fernandez-Gutierrez, B.3    Lopez, J.A.4
  • 102
    • 77952408229 scopus 로고    scopus 로고
    • Recent progress in selected reaction monitoring MS-driven plasma protein biomarker analysis
    • doi:10.4155/bio.09.56
    • Chiu CL, Randall S, Molloy MP (2009) Recent progress in selected reaction monitoring MS-driven plasma protein biomarker analysis. Bioanalysis 1(4):847-855. doi:10.4155/bio.09.56
    • (2009) Bioanalysis , vol.1 , Issue.4 , pp. 847-855
    • Chiu, C.L.1    Randall, S.2    Molloy, M.P.3
  • 103
    • 78751675280 scopus 로고    scopus 로고
    • Targeted proteomics by selected reaction monitoring mass spectrometry: Applications to systems biology and biomarker discovery
    • doi:10.1039/c0mb00159g
    • Elschenbroich S, Kislinger T (2011) Targeted proteomics by selected reaction monitoring mass spectrometry: applications to systems biology and biomarker discovery. Mol Biosyst 7(2):292-303. doi:10.1039/c0mb00159g
    • (2011) Mol Biosyst , vol.7 , Issue.2 , pp. 292-303
    • Elschenbroich, S.1    Kislinger, T.2
  • 105
    • 57049144338 scopus 로고    scopus 로고
    • MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments
    • doi:10.1074/mcp.M700504-MCP200
    • Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M (2008) MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics 7(11):2270-2278. doi:10.1074/mcp.M700504-MCP200
    • (2008) Mol Cell Proteomics , vol.7 , Issue.11 , pp. 2270-2278
    • Martin, D.B.1    Holzman, T.2    May, D.3    Peterson, A.4    Eastham, A.5    Eng, J.6    McIntosh, M.7
  • 106
    • 66149134917 scopus 로고    scopus 로고
    • MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions
    • doi:10.1074/mcp.M800192-MCP200
    • Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C (2009) MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics 8(4):696-705. doi:10.1074/mcp.M800192-MCP200
    • (2009) Mol Cell Proteomics , vol.8 , Issue.4 , pp. 696-705
    • Mead, J.A.1    Bianco, L.2    Ottone, V.3    Barton, C.4    Kay, R.G.5    Lilley, K.S.6    Bond, N.J.7    Bessant, C.8
  • 109
    • 78650355102 scopus 로고    scopus 로고
    • Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry
    • doi:10.1021/ac102179j
    • MacLean B, Tomazela DM, Abbatiello SE, Zhang SC, Whiteaker JR, Paulovich AG, Carr SA, Mac-Coss MJ (2010) Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Anal Chem 82(24):10116-10124. doi:10.1021/ac102179j
    • (2010) Anal Chem , vol.82 , Issue.24 , pp. 10116-10124
    • Maclean, B.1    Tomazela, D.M.2    Abbatiello, S.E.3    Zhang, S.C.4    Whiteaker, J.R.5    Paulovich, A.G.6    Carr, S.A.7    Mac-Coss, M.J.8
  • 110
    • 67049132416 scopus 로고    scopus 로고
    • Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development
    • doi:10.1021/pr801028b
    • Prakash A, Tomazela DM, Frewen B, MacLean B, Merrihew G, Peterman S, MacCoss MJ (2009) Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res 8(6):2733-2739. doi:10.1021/pr801028b
    • (2009) J Proteome Res , vol.8 , Issue.6 , pp. 2733-2739
    • Prakash, A.1    Tomazela, D.M.2    Frewen, B.3    Maclean, B.4    Merrihew, G.5    Peterman, S.6    Maccoss, M.J.7
  • 112
    • 52949099571 scopus 로고    scopus 로고
    • Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data
    • doi:btn398 [pii] 10.1093/bioinformatics/btn398
    • Cruz-Marcelo A, Guerra R, Vannucci M, Li Y, Lau CC, Man TK (2008) Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. Bioinformatics 24(19):2129-2136. doi:btn398 [pii] 10.1093/bioinformatics/btn398
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2129-2136
    • Cruz-Marcelo, A.1    Guerra, R.2    Vannucci, M.3    Li, Y.4    Lau, C.C.5    Man, T.K.6
  • 113
    • 79953139278 scopus 로고    scopus 로고
    • Protein mass spectra data analysis for clinical biomarker discovery: A global review
    • doi:bbq019 [pii] 10.1093/bib/bbq019
    • Roy P, Truntzer C, Maucort-Boulch D, Jouve T, Molinari N (2011) Protein mass spectra data analysis for clinical biomarker discovery: a global review. Brief Bioinform 12(2):176-186. doi:bbq019 [pii] 10.1093/bib/bbq019
    • (2011) Brief Bioinform , vol.12 , Issue.2 , pp. 176-186
    • Roy, P.1    Truntzer, C.2    Maucort-Boulch, D.3    Jouve, T.4    Molinari, N.5
  • 114
    • 77952509680 scopus 로고    scopus 로고
    • Feature detection techniques for preprocessing proteomic data
    • doi:10.1155/2010/896718
    • Sellers KF, Miecznikowski JC (2010) Feature detection techniques for preprocessing proteomic data. Int J Biomed Imaging 2010:896718. doi:10.1155/2010/896718
    • (2010) Int J Biomed Imaging , vol.2010 , pp. 896718
    • Sellers, K.F.1    Miecznikowski, J.C.2
  • 115
    • 67449160970 scopus 로고    scopus 로고
    • Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets
    • doi:1477-5956-7-19 [pii] 10.1186/1477-5956-7-19
    • Wegdam W, Moerland PD, Buist MR, Loren V, van Themaat E, Bleijlevens B, Hoefsloot HC, de Koster CG, Aerts JM (2009) Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Sci 7:19. doi:1477-5956-7-19 [pii] 10.1186/1477-5956-7-19
    • (2009) Proteome Sci , vol.7 , pp. 19
    • Wegdam, W.1    Moerland, P.D.2    Buist, M.R.3    Loren, V.4    Van Themaat, E.5    Bleijlevens, B.6    Hoefsloot, H.C.7    De Koster, C.G.8    Aerts, J.M.9
  • 116
    • 44249092131 scopus 로고    scopus 로고
    • De Novo Peptide de Novo Peptide Sequencing via Manual Interpretation ofMS/MS Spectra
    • Addona T, Clauser K (2002) De Novo Peptide De Novo Peptide Sequencing via Manual Interpretation ofMS/MS Spectra. Curr Protoc Protein Sci 16.11.1-16.11.19
    • (2002) Curr Protoc Protein Sci , pp. 16111-161119
    • Addona, T.1    Clauser, K.2
  • 117
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • doi:10.1093/bioinformatics/bth092
    • Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9):1466-1467. doi:10.1093/bioinformatics/bth092
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 119
    • 79953701087 scopus 로고    scopus 로고
    • Andromeda: A peptide search engine integrated into the MaxQuant environment
    • doi:10.1021/Pr101065j
    • Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10(4):1794-1805. doi:10.1021/Pr101065j
    • (2011) J Proteome Res , vol.10 , Issue.4 , pp. 1794-1805
    • Cox, J.1    Neuhauser, N.2    Michalski, A.3    Scheltema, R.A.4    Olsen, J.V.5    Mann, M.6
  • 120
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • doi:10.1021/Pr0604054
    • Tabb DL, Fernando CG, Chambers MC (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 6(2):654-661. doi:10.1021/Pr0604054
    • (2007) J Proteome Res , vol.6 , Issue.2 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 121
    • 0033565832 scopus 로고    scopus 로고
    • Role of accurate mass measurement (+/ 10 ppm) in protein identification strategies employing MS or MS MS and database searching
    • Clauser KR, Baker P, Burlingame AL (1999) Role of accurate mass measurement (+/ 10 ppm) in protein identification strategies employing MS or MS MS and database searching. Anal Chem 71(14):2871-2882
    • (1999) Anal Chem , vol.71 , Issue.14 , pp. 2871-2882
    • Clauser, K.R.1    Baker, P.2    Burlingame, A.L.3
  • 122
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: Towards highthroughput tandem mass spectrometry data identification
    • doi:10.1002/pmic.200300485
    • Colinge J, Masselot A, Giron M, Dessingy T, Magnin J (2003) OLAV: towards highthroughput tandem mass spectrometry data identification. Proteomics 3(8):1454-1463. doi:10.1002/pmic.200300485
    • (2003) Proteomics , vol.3 , Issue.8 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 123
    • 79953043425 scopus 로고    scopus 로고
    • Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post-translational modifications (vol 11, pg 590, 2011)
    • Casado-Vela J (2011) Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post-translational modifications (vol 11, pg 590, 2011). Proteomics 11(7):1370-1370
    • (2011) Proteomics , vol.11 , Issue.7 , pp. 1370-1370
    • Casado-Vela, J.1
  • 124
    • 77956304093 scopus 로고    scopus 로고
    • Mass spectrometry in highthroughput proteomics: Ready for the big time
    • doi:10.1038/nmeth0910-681
    • Nilsson T, Mann M, Aebersold R, Yates JR, Bairoch A, Bergeron JJM (2010) Mass spectrometry in highthroughput proteomics: ready for the big time. Nat Methods 7(9):681-685. doi:10.1038/nmeth0910-681
    • (2010) Nat Methods , vol.7 , Issue.9 , pp. 681-685
    • Nilsson, T.1    Mann, M.2    Aebersold, R.3    Yates, J.R.4    Bairoch, A.5    Bergeron, J.J.M.6
  • 125
    • 38649114671 scopus 로고    scopus 로고
    • Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies
    • doi:10.1021/Pr070540w
    • Searle BC, Turner M, Nesvizhskii AI (2008) Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. J Proteome Res 7(1):245-253. doi:10.1021/Pr070540w
    • (2008) J Proteome Res , vol.7 , Issue.1 , pp. 245-253
    • Searle, B.C.1    Turner, M.2    Nesvizhskii, A.I.3
  • 127
    • 53049093468 scopus 로고    scopus 로고
    • Enhancing peptide identification confidence by combining search methods
    • doi:10.1021/Pr700798h
    • Alves G, Wu WW, Wang GH, Shen RF, Yu YK (2008) Enhancing peptide identification confidence by combining search methods. J Proteome Res 7(8):3102-3113. doi:10.1021/Pr700798h
    • (2008) J Proteome Res , vol.7 , Issue.8 , pp. 3102-3113
    • Alves, G.1    Wu, W.W.2    Wang, G.H.3    Shen, R.F.4    Yu, Y.K.5
  • 128
    • 84890704446 scopus 로고    scopus 로고
    • Improving computer interpretation of linear ion trap proteomics data using Scaffold
    • Searle BC, Turner M (2006) Improving computer interpretation of linear ion trap proteomics data using Scaffold. Mol Cell Proteomics 5(10): S297-S297
    • (2006) Mol Cell Proteomics , vol.5 , Issue.10
    • Searle, B.C.1    Turner, M.2
  • 129
    • 77949695293 scopus 로고    scopus 로고
    • Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies
    • doi:10.1002/pmic. 200900437
    • Searle BC (2010) Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics 10(6):1265-1269. doi:10.1002/pmic. 200900437
    • (2010) Proteomics , vol.10 , Issue.6 , pp. 1265-1269
    • Searle, B.C.1
  • 130
    • 79959942025 scopus 로고    scopus 로고
    • MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines
    • doi:10.1021/Pr2002116
    • Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM (2011) MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res 10(7):2949-2958. doi:10.1021/Pr2002116
    • (2011) J Proteome Res , vol.10 , Issue.7 , pp. 2949-2958
    • Kwon, T.1    Choi, H.2    Vogel, C.3    Nesvizhskii, A.I.4    Marcotte, E.M.5
  • 131
    • 0032159387 scopus 로고    scopus 로고
    • Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis
    • Yates JR, Morgan SF, Gatlin CL, Griffin PR, Eng JK (1998) Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. Anal Chem 70(17):3557-3565
    • (1998) Anal Chem , vol.70 , Issue.17 , pp. 3557-3565
    • Yates, J.R.1    Morgan, S.F.2    Gatlin, C.L.3    Griffin, P.R.4    Eng, J.K.5
  • 132
    • 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(5):655-667
    • (2007) Proteomics , vol.7 , Issue.5 , 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
  • 133
    • 53249098366 scopus 로고    scopus 로고
    • Building consensus spectral libraries for peptide identification in proteomics
    • doi:10.1038/Nmeth.1254
    • Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R (2008) Building consensus spectral libraries for peptide identification in proteomics. Nat Methods 5(10):873-875. doi:10.1038/Nmeth.1254
    • (2008) Nat Methods , vol.5 , Issue.10 , pp. 873-875
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    Stein, S.E.5    Aebersold, R.6
  • 134
    • 33747626954 scopus 로고    scopus 로고
    • Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
    • doi:10.1021/Ac060279n
    • 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(16):5678-5684. doi:10.1021/Ac060279n
    • (2006) Anal Chem , vol.78 , Issue.16 , pp. 5678-5684
    • Frewen, B.E.1    Merrihew, G.E.2    Wu, C.C.3    Noble, W.S.4    Maccoss, M.J.5
  • 135
    • 33747170146 scopus 로고    scopus 로고
    • Using annotated peptide mass spectrum libraries for protein identification
    • doi:10.1021/Pr0602085
    • Craig R, Cortens JC, Fenyo D, Beavis RC (2006) Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res 5(8):1843-1849. doi:10.1021/Pr0602085
    • (2006) J Proteome Res , vol.5 , Issue.8 , pp. 1843-1849
    • Craig, R.1    Cortens, J.C.2    Fenyo, D.3    Beavis, R.C.4
  • 137
    • 35948937578 scopus 로고    scopus 로고
    • HMMatch: Peptide identification by spectral matching of tandem mass spectra using hidden Markov models
    • doi:10.1089/cmb.2007.0071
    • Wu X, Tseng CW, Edwards N (2007) HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models. J Comput Biol 14(8):1025-1043. doi:10.1089/cmb.2007.0071
    • (2007) J Comput Biol , vol.14 , Issue.8 , pp. 1025-1043
    • Wu, X.1    Tseng, C.W.2    Edwards, N.3
  • 139
    • 76749169902 scopus 로고    scopus 로고
    • A ubiquitin and ubiquitin-like protein spectral library
    • doi:10.1002/pmic.200900627
    • Srikumar T, Jeram SM, Lam H, Raught B (2010) A ubiquitin and ubiquitin-like protein spectral library. Proteomics 10(2):337-342. doi:10.1002/pmic.200900627
    • (2010) Proteomics , vol.10 , Issue.2 , pp. 337-342
    • Srikumar, T.1    Jeram, S.M.2    Lam, H.3    Raught, B.4
  • 143
    • 77957221582 scopus 로고    scopus 로고
    • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
    • doi:S1874-3919(10)00249-6 [pii] 10.1016/ j.jprot.2010.08.009
    • Nesvizhskii AI (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 73(11):2092-2123. doi:S1874-3919(10)00249-6 [pii] 10.1016/ j.jprot.2010.08.009
    • (2010) J Proteomics , vol.73 , Issue.11 , pp. 2092-2123
    • Nesvizhskii, A.I.1
  • 144
    • 66749169317 scopus 로고    scopus 로고
    • Predicting intensity ranks of peptide fragment ions
    • doi:10.1021/Pr800677f
    • Frank AM (2009) Predicting intensity ranks of peptide fragment ions. J Proteome Res 8(5):2226-2240. doi:10.1021/Pr800677f
    • (2009) J Proteome Res , vol.8 , Issue.5 , pp. 2226-2240
    • Frank, A.M.1
  • 145
    • 67650725988 scopus 로고    scopus 로고
    • Computational principles of determining and improving mass precision and accuracy for proteome measurements in an orbitrap
    • doi:10.1016/j.jasms.2009.05.007
    • Cox J, Mann M (2009) Computational principles of determining and improving mass precision and accuracy for proteome measurements in an orbitrap. J Am Soc Mass Spectrom 20(8):1477-1485. doi:10.1016/j.jasms.2009.05.007
    • (2009) J Am Soc Mass Spectrom , vol.20 , Issue.8 , pp. 1477-1485
    • Cox, J.1    Mann, M.2
  • 147
    • 84987398179 scopus 로고
    • Computer-aided peptide sequencing by fast-atom-bombardment mass-spectrometry
    • Ishikawa K, Niwa Y (1986) Computer-aided peptide sequencing by fast-atom-bombardment mass-spectrometry. Biomed Environ Mass 13(7): 373-380
    • (1986) Biomed Environ Mass , vol.13 , Issue.7 , pp. 373-380
    • Ishikawa, K.1    Niwa, Y.2
  • 148
    • 84987395027 scopus 로고
    • Paas-3: A computer-program to determine probable sequence of peptides from mass-spectrometric data
    • Sakurai T, Matsuo T, Matsuda H, Katakuse I (1984) Paas-3: a computer-program to determine probable sequence of peptides from mass-spectrometric data. Biomed Mass Spectrom 11(8):396-399
    • (1984) Biomed Mass Spectrom , vol.11 , Issue.8 , pp. 396-399
    • Sakurai, T.1    Matsuo, T.2    Matsuda, H.3    Katakuse, I.4
  • 149
    • 0003597619 scopus 로고
    • A graphics display-oriented strategy for the amino-acid sequencing of peptides by tandem mass-spectrometry
    • Scoble HA, Biller JE, Biemann K (1987) A graphics display-oriented strategy for the amino-acid sequencing of peptides by tandem mass-spectrometry. Fresen Z Anal Chem 327(2):239-245
    • (1987) Fresen Z Anal Chem , vol.327 , Issue.2 , pp. 239-245
    • Scoble, H.A.1    Biller, J.E.2    Biemann, K.3
  • 150
    • 0024287234 scopus 로고
    • An efficient algorithm for sequencing peptides using fast atom bombardment mass-spectral data
    • Siegel MM, Bauman N (1988) An efficient algorithm for sequencing peptides using fast atom bombardment mass-spectral data. Biomed Environ Mass 15(6):333-343
    • (1988) Biomed Environ Mass , vol.15 , Issue.6 , pp. 333-343
    • Siegel, M.M.1    Bauman, N.2
  • 151
    • 0025038664 scopus 로고
    • Fast algorithm for peptide sequencing by mass-spectroscopy
    • Bartels C (1990) Fast algorithm for peptide sequencing by mass-spectroscopy. Biomed Environ Mass 19(6):363-368
    • (1990) Biomed Environ Mass , vol.19 , Issue.6 , pp. 363-368
    • Bartels, C.1
  • 152
    • 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(11):2594-2604
    • (2001) Anal Chem , vol.73 , Issue.11 , pp. 2594-2604
    • Taylor, J.A.1    Johnson, R.S.2
  • 154
    • 0034814613 scopus 로고    scopus 로고
    • A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry
    • Chen T, Kao MY, Tepel M, Rush J, Church GM (2001) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J Comput Biol 8(3):325-337
    • (2001) J Comput Biol , vol.8 , Issue.3 , pp. 325-337
    • Chen, T.1    Kao, M.Y.2    Tepel, M.3    Rush, J.4    Church, G.M.5
  • 155
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: De novo peptide sequencing via probabilistic network modeling
    • doi:10.1021/Ac048788h
    • Frank A, Pevzner P (2005) PepNovo: De novo peptide sequencing via probabilistic network modeling. Anal Chem 77(4):964-973. doi:10.1021/Ac048788h
    • (2005) Anal Chem , vol.77 , Issue.4 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 157
    • 55249118638 scopus 로고    scopus 로고
    • DirecTag: Accurate sequence tags from peptide MS/MS through statistical scoring
    • doi:10.1021/Pr800154p
    • Tabb DL, Ma ZQ, Martin DB, Ham AJL, Chambers MC (2008) DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res 7(9):3838-3846. doi:10.1021/Pr800154p
    • (2008) J Proteome Res , vol.7 , Issue.9 , pp. 3838-3846
    • Tabb, D.L.1    Ma, Z.Q.2    Martin, D.B.3    Ham, A.J.L.4    Chambers, M.C.5
  • 160
    • 0034213620 scopus 로고    scopus 로고
    • De novo peptide sequencing by two dimensional fragment correlation mass spectrometry
    • Zhang ZQ, McElvain JS (2000) De novo peptide sequencing by two dimensional fragment correlation mass spectrometry. Anal Chem 72(11):2337-2350
    • (2000) Anal Chem , vol.72 , Issue.11 , pp. 2337-2350
    • Zhang, Z.Q.1    McElvain, J.S.2
  • 161
    • 29144437803 scopus 로고    scopus 로고
    • Proteomics-grade de novo sequencing approach
    • doi:10.1021/pr050288x
    • Savitski MM, Nielsen ML, Kjeldsen F, Zubarev RA (2005) Proteomics-grade de novo sequencing approach. J Proteome Res 4(6):2348-2354. doi:10.1021/ pr050288x
    • (2005) J Proteome Res , vol.4 , Issue.6 , pp. 2348-2354
    • Savitski, M.M.1    Nielsen, M.L.2    Kjeldsen, F.3    Zubarev, R.A.4
  • 162
    • 34249826390 scopus 로고    scopus 로고
    • Protein identification by spectral networks analysis
    • doi:10.1073/pnas.0701130104
    • Bandeira N, Tsur D, Frank A, Pevzner PA (2007) Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A 104(15):6140-6145. doi:10.1073/pnas.0701130104
    • (2007) Proc Natl Acad Sci U S a , vol.104 , Issue.15 , pp. 6140-6145
    • Bandeira, N.1    Tsur, D.2    Frank, A.3    Pevzner, P.A.4
  • 163
    • 70349207551 scopus 로고    scopus 로고
    • Spectrum fusion: Using multiple mass spectra for de novo peptide sequencing
    • doi:10.1089/cmb.2009.0122
    • Datta R, Bern M (2009) Spectrum fusion: using multiple mass spectra for de novo peptide sequencing. J Comput Biol 16(8):1169-1182. doi:10.1089/cmb.2009. 0122
    • (2009) J Comput Biol , vol.16 , Issue.8 , pp. 1169-1182
    • Datta, R.1    Bern, M.2
  • 164
    • 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(24):4390-4399
    • (1994) Anal Chem , vol.66 , Issue.24 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 165
    • 0345600791 scopus 로고    scopus 로고
    • GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model
    • doi:10.1021/Ac0347462
    • Tabb DL, Saraf A, Yates JR (2003) GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem 75(23):6415-6421. doi:10.1021/Ac0347462
    • (2003) Anal Chem , vol.75 , Issue.23 , pp. 6415-6421
    • Tabb, D.L.1    Saraf, A.2    Yates, J.R.3
  • 166
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttransiationally modified peptides from tandem mass spectra
    • doi:10.1021/Ac050102d
    • Tanner S, Shu HJ, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V (2005) InsPecT: identification of posttransiationally modified peptides from tandem mass spectra. Anal Chem 77(14):4626-4639. doi:10.1021/Ac050102d
    • (2005) Anal Chem , vol.77 , Issue.14 , pp. 4626-4639
    • Tanner, S.1    Shu, H.J.2    Frank, A.3    Wang, L.C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 167
    • 77950660595 scopus 로고    scopus 로고
    • TagRecon: High-throughput mutation identification through sequence tagging
    • doi:10.1021/pr900850m
    • Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham AJL, Tabb DL (2010) TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res 9(4):1716-1726. doi:10.1021/pr900850m
    • (2010) J Proteome Res , vol.9 , Issue.4 , pp. 1716-1726
    • Dasari, S.1    Chambers, M.C.2    Slebos, R.J.3    Zimmerman, L.J.4    Ham, A.J.L.5    Tabb, D.L.6
  • 168
    • 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
    • doi:10.1074/mcp.T600050-MCP200
    • 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(9):1638-1655. doi:10.1074/mcp.T600050-MCP200
    • (2007) Mol Cell Proteomics , vol.6 , Issue.9 , 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
  • 169
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • Nesvizhskii AI, Aebersold R (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 4(10):1419-1440
    • (2005) Mol Cell Proteomics , vol.4 , Issue.10 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 170
    • 1042266254 scopus 로고    scopus 로고
    • Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS
    • doi:10.1016/S1359-6446(03)02978-7 S1359644603029787 [pii]
    • Nesvizhskii AI, Aebersold R (2004) Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today 9(4):173-181. doi:10.1016/S1359-6446(03)02978-7 S1359644603029787 [pii]
    • (2004) Drug Discov Today , vol.9 , Issue.4 , pp. 173-181
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 171
    • 33644864034 scopus 로고    scopus 로고
    • Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
    • doi:10.1038/Nbt1183
    • States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM (2006) Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 24(3):333-338. doi:10.1038/Nbt1183
    • (2006) Nat Biotechnol , vol.24 , Issue.3 , pp. 333-338
    • States, D.J.1    Omenn, G.S.2    Blackwell, T.W.3    Fermin, D.4    Eng, J.5    Speicher, D.W.6    Hanash, S.M.7
  • 172
    • 0001677717 scopus 로고
    • Controlling the false discovery rate-A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J Roy Stat Soc B Met 57(1):289-300
    • (1995) J Roy Stat Soc B Met , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 173
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by ms/ms and database search
    • Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by ms/ms and database search. Anal Chem 74(20):5383-5392
    • (2002) Anal Chem , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 174
    • 65249143361 scopus 로고    scopus 로고
    • Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets
    • doi:10.1021/Pr800792z
    • Bianco L, Mead JA, Bessant C (2009) Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets. J Proteome Res 8(4):1782-1791. doi:10.1021/Pr800792z
    • (2009) J Proteome Res , vol.8 , Issue.4 , pp. 1782-1791
    • Bianco, L.1    Mead, J.A.2    Bessant, C.3
  • 175
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • doi:10.1021/pr700600n
    • Kall L, Storey JD, MacCoss MJ, Noble WS (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 7(1):29-34. doi:10.1021/pr700600n
    • (2008) J Proteome Res , vol.7 , Issue.1 , pp. 29-34
    • Kall, L.1    Storey, J.D.2    Maccoss, M.J.3    Noble, W.S.4
  • 176
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • doi:10.1073/pnas.1530509100 1530509100 [pii]
    • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100(16):9440-9445. doi:10.1073/pnas.1530509100 1530509100 [pii]
    • (2003) Proc Natl Acad Sci U S a , vol.100 , Issue.16 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 178
    • 0036209134 scopus 로고    scopus 로고
    • Qscore: An algorithm for evaluating SEQUEST database search results
    • Moore RE, Young MK, Lee TD (2002) Qscore: an algorithm for evaluating SEQUEST database search results. J Am Soc Mass Spectrom 13(4):378-386
    • (2002) J Am Soc Mass Spectrom , vol.13 , Issue.4 , pp. 378-386
    • Moore, R.E.1    Young, M.K.2    Lee, T.D.3
  • 179
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75(17):4646-4658
    • (2003) Anal Chem , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 181
    • 78650147228 scopus 로고    scopus 로고
    • The generating function of CID, ETD and CID/ETD pairs of tandem mass spectra: Applications to database search
    • doi:M110.003731 [pii] 10.1074/mcp.M110.003731
    • Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA (2010) The generating function of CID, ETD and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics. doi:M110.003731 [pii] 10.1074/mcp.M110.003731
    • (2010) Mol Cell Proteomics
    • Kim, S.1    Mischerikow, N.2    Bandeira, N.3    Navarro, J.D.4    Wich, L.5    Mohammed, S.6    Heck, A.J.7    Pevzner, P.A.8
  • 182
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • doi:10.1021/Ac0258709
    • Fenyo D, Beavis RC (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 75(4):768-774. doi:10.1021/Ac0258709
    • (2003) Anal Chem , vol.75 , Issue.4 , pp. 768-774
    • Fenyo, D.1    Beavis, R.C.2
  • 183
    • 33845380405 scopus 로고    scopus 로고
    • A capital workshop for the HUPO proteomics standards initiative
    • Taylor CF (2006) A capital workshop for the HUPO proteomics standards initiative. J Proteome Res 5(12):3229-3230
    • (2006) J Proteome Res , vol.5 , Issue.12 , pp. 3229-3230
    • Taylor, C.F.1
  • 184
    • 33750285086 scopus 로고    scopus 로고
    • The HUPO proteomics standards initiativeovercoming the fragmentation of proteomics data
    • doi:10.1002/pmic.200600537
    • Hermjakob H (2006) The HUPO proteomics standards initiativeovercoming the fragmentation of proteomics data. Proteomics 6(1):34-38. doi:10.1002/pmic. 200600537
    • (2006) Proteomics , vol.6 , Issue.1 , pp. 34-38
    • Hermjakob, H.1
  • 185
    • 33748087472 scopus 로고    scopus 로고
    • The work of the human proteome organisation's proteomics standards initiative (HUPO PSI)
    • Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R (2006) The work of the human proteome organisation's proteomics standards initiative (HUPO PSI). Omics 10(2):145-151
    • (2006) Omics , vol.10 , Issue.2 , pp. 145-151
    • Taylor, C.F.1    Hermjakob, H.2    Julian, R.K.3    Garavelli, J.S.4    Aebersold, R.5    Apweiler, R.6
  • 186
    • 0037293360 scopus 로고    scopus 로고
    • Meeting review: The HUPO proteomics standards initiative meeting: Towards common standards for exchanging proteomics dataHinxton, Cambridge, UK, 19-20 October 2002
    • doi:10.1002/Cfg.232
    • Orchard S, Kersey P, Hermjakob H, Apweiler R (2003) Meeting review: The HUPO proteomics standards initiative meeting: towards common standards for exchanging proteomics dataHinxton, Cambridge, UK, 19-20 October 2002. Comp Funct Genom 4(1):16-19. doi:10.1002/Cfg.232
    • (2003) Comp Funct Genom , vol.4 , Issue.1 , pp. 16-19
    • Orchard, S.1    Kersey, P.2    Hermjakob, H.3    Apweiler, R.4
  • 187
    • 0037621728 scopus 로고    scopus 로고
    • Meeting review: Progress in establishing common standards for exchanging proteomics data: The second meeting of the HUPO proteomics standards initiative
    • doi:10.1002/Cfg.279
    • Orchard S, Kersey P, Zhu WM, Montecchi-Palazzi L, Hermjakob H, Apweiler R (2003) Meeting review: progress in establishing common standards for exchanging proteomics data: the second meeting of the HUPO proteomics standards initiative. Comp Funct Genom 4(2):203-206. doi:10.1002/Cfg.279
    • (2003) Comp Funct Genom , vol.4 , Issue.2 , pp. 203-206
    • Orchard, S.1    Kersey, P.2    Zhu, W.M.3    Montecchi-Palazzi, L.4    Hermjakob, H.5    Apweiler, R.6
  • 188
    • 33646907086 scopus 로고    scopus 로고
    • Reporting protein identification datathe next generation of guidelines
    • Bradshaw RA, Burlingame AL, Carr S, Aebersold R (2006) Reporting protein identification datathe next generation of guidelines. Mol Cell Proteomics 5(5):787-788
    • (2006) Mol Cell Proteomics , vol.5 , Issue.5 , pp. 787-788
    • Bradshaw, R.A.1    Burlingame, A.L.2    Carr, S.3    Aebersold, R.4
  • 189
    • 58149396182 scopus 로고    scopus 로고
    • Stable isotopic labeling of proteins for quantitative proteomic applications
    • doi:eln047 [pii] 10.1093/bfgp/eln047
    • Becker GW (2008) Stable isotopic labeling of proteins for quantitative proteomic applications. Brief Funct Genomic Proteomic 7(5):371-382. doi:eln047 [pii] 10.1093/bfgp/eln047
    • (2008) Brief Funct Genomic Proteomic , vol.7 , Issue.5 , pp. 371-382
    • Becker, G.W.1
  • 191
    • 0033535961 scopus 로고    scopus 로고
    • Accurate quantitation of protein expression and site-specific phosphorylation
    • Oda Y, Huang K, Cross FR, Cowburn D, Chait BT (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 96(12):6591-6596
    • (1999) Proc Natl Acad Sci U S a , vol.96 , Issue.12 , pp. 6591-6596
    • Oda, Y.1    Huang, K.2    Cross, F.R.3    Cowburn, D.4    Chait, B.T.5
  • 192
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376-386
    • (2002) Mol Cell Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 193
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994-999
    • (1999) Nat Biotechnol , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 194
    • 42349105213 scopus 로고    scopus 로고
    • Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags
    • doi:10.1021/ac702422x
    • Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC (2008) Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem 80(8):2921-2931. doi:10.1021/ac702422x
    • (2008) Anal Chem , vol.80 , Issue.8 , pp. 2921-2931
    • Dayon, L.1    Hainard, A.2    Licker, V.3    Turck, N.4    Kuhn, K.5    Hochstrasser, D.F.6    Burkhard, P.R.7    Sanchez, J.C.8
  • 196
    • 45949104657 scopus 로고    scopus 로고
    • Quantitative protein analysis using proteolytic [18O] water labeling
    • doi:10.1002/0471140864.ps2304s34
    • Reynolds KJ, Fenselau C (2004) Quantitative protein analysis using proteolytic [18O] water labeling. Curr Protoc Protein Sci 23:23-24. doi:10.1002/0471140864.ps2304s34
    • (2004) Curr Protoc Protein Sci , vol.23 , pp. 23-24
    • Reynolds, K.J.1    Fenselau, C.2
  • 197
    • 41949139372 scopus 로고    scopus 로고
    • Quantitative shotgun proteomics of enriched heterocysts from Nostoc sp. PCC 7120 using 8-plex isobaric peptide tags
    • doi:10.1021/pr700604v
    • Ow SY, Cardona T, Taton A, Magnuson A, Lindblad P, Stensjo K, Wright PC (2008) Quantitative shotgun proteomics of enriched heterocysts from Nostoc sp. PCC 7120 using 8-plex isobaric peptide tags. J Proteome Res 7(4):1615-1628. doi:10.1021/pr700604v
    • (2008) J Proteome Res , vol.7 , Issue.4 , pp. 1615-1628
    • Ow, S.Y.1    Cardona, T.2    Taton, A.3    Magnuson, A.4    Lindblad, P.5    Stensjo, K.6    Wright, P.C.7
  • 198
    • 4444346217 scopus 로고    scopus 로고
    • Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis
    • Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR 3rd (2004) Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem 76(17): 4951-4959
    • (2004) Anal Chem , vol.76 , Issue.17 , pp. 4951-4959
    • Wu, C.C.1    Maccoss, M.J.2    Howell, K.E.3    Matthews, D.E.4    Yates III, J.R.5
  • 199
    • 82555185589 scopus 로고    scopus 로고
    • Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on orbitrap-type mass spectrometers
    • doi:10.1021/ac201760x
    • Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M (2011) Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on orbitrap-type mass spectrometers. Anal Chem 83(23):8959-8967. doi:10.1021/ac201760x
    • (2011) Anal Chem , vol.83 , Issue.23 , pp. 8959-8967
    • Savitski, M.M.1    Sweetman, G.2    Askenazi, M.3    Marto, J.A.4    Lang, M.5    Zinn, N.6    Bantscheff, M.7
  • 201
    • 40349092949 scopus 로고    scopus 로고
    • Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
    • doi:0706983105 [pii] 10.1073/pnas.0706983105
    • Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP (2008) Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A 105(5):1454-1459. doi:0706983105 [pii] 10.1073/pnas.0706983105
    • (2008) Proc Natl Acad Sci U S a , vol.105 , Issue.5 , pp. 1454-1459
    • Sardiu, M.E.1    Cai, Y.2    Jin, J.3    Swanson, S.K.4    Conaway, R.C.5    Conaway, J.W.6    Florens, L.7    Washburn, M.P.8
  • 202
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • doi:M500061-MCP200 [pii] 10.1074/mcp.M500061-MCP200
    • Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4(9):1265-1272. doi:M500061-MCP200 [pii] 10.1074/mcp.M500061-MCP200
    • (2005) Mol Cell Proteomics , vol.4 , Issue.9 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 203
    • 0036674269 scopus 로고    scopus 로고
    • Large-scale proteomic analysis of the human spliceosome
    • doi:10.1101/gr.473902
    • Rappsilber J, Ryder U, Lamond AI, Mann M (2002) Large-scale proteomic analysis of the human spliceosome. Genome Res 12(8):1231-1245. doi:10.1101/gr.473902
    • (2002) Genome Res , vol.12 , Issue.8 , pp. 1231-1245
    • Rappsilber, J.1    Ryder, U.2    Lamond, A.I.3    Mann, M.4
  • 206
    • 77951650200 scopus 로고    scopus 로고
    • Role of spectral counting in quantitative proteomics
    • doi:10.1586/epr.09.69
    • Lundgren DH, Hwang SI, Wu L, Han DK (2010) Role of spectral counting in quantitative proteomics. Expert Rev Proteomics 7(1):39-53. doi:10.1586/epr.09.69
    • (2010) Expert Rev Proteomics , vol.7 , Issue.1 , pp. 39-53
    • Lundgren, D.H.1    Hwang, S.I.2    Wu, L.3    Han, D.K.4
  • 207
    • 34247642450 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors
    • doi:0606379103 [pii] 10.1073/pnas.0606379103
    • Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP (2006) Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A 103(50):18928-18933. doi:0606379103 [pii] 10.1073/pnas.0606379103
    • (2006) Proc Natl Acad Sci U S a , vol.103 , Issue.50 , pp. 18928-18933
    • Paoletti, A.C.1    Parmely, T.J.2    Tomomori-Sato, C.3    Sato, S.4    Zhu, D.5    Conaway, R.C.6    Conaway, J.W.7    Florens, L.8    Washburn, M.P.9
  • 208
    • 38149103492 scopus 로고    scopus 로고
    • The chicken egg yolk plasma and granule proteomes
    • doi:10.1002/pmic.200700790
    • Mann K, Mann M (2008) The chicken egg yolk plasma and granule proteomes. Proteomics 8(1):178-191. doi:10.1002/pmic.200700790
    • (2008) Proteomics , vol.8 , Issue.1 , pp. 178-191
    • Mann, K.1    Mann, M.2
  • 210
    • 41549117597 scopus 로고    scopus 로고
    • A quantitative analysis software tool for mass spectrometry-based proteomics
    • doi:nmeth.1195 [pii] 10.1038/nmeth.1195
    • Park SK, Venable JD, Xu T, Yates JR 3rd (2008) A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods 5(4):319-322. doi:nmeth.1195 [pii] 10.1038/nmeth.1195
    • (2008) Nat Methods , vol.5 , Issue.4 , pp. 319-322
    • Park, S.K.1    Venable, J.D.2    Xu, T.3    Yates III, J.R.4
  • 211
    • 77954205753 scopus 로고    scopus 로고
    • PepC: Proteomics software for identifying differentially expressed proteins based on spectral counting
    • doi:btq171 [pii] 10.1093/bioinformatics/btq171
    • Heinecke NL, Pratt BS, Vaisar T, Becker L (2010) PepC: proteomics software for identifying differentially expressed proteins based on spectral counting. Bioinformatics 26(12):1574-1575. doi:btq171 [pii] 10.1093/ bioinformatics/btq171
    • (2010) Bioinformatics , vol.26 , Issue.12 , pp. 1574-1575
    • Heinecke, N.L.1    Pratt, B.S.2    Vaisar, T.3    Becker, L.4
  • 212
    • 74049132731 scopus 로고    scopus 로고
    • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
    • doi:nbt.1592 [pii] 10.1038/nbt.1592
    • Griffin NM, Yu J, Long F, Oh P, Shore S, Li Y, Koziol JA, Schnitzer JE (2010) Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat Biotechnol 28(1):83-89. doi:nbt.1592 [pii] 10.1038/nbt.1592
    • (2010) Nat Biotechnol , vol.28 , Issue.1 , pp. 83-89
    • Griffin, N.M.1    Yu, J.2    Long, F.3    Oh, P.4    Shore, S.5    Li, Y.6    Koziol, J.A.7    Schnitzer, J.E.8
  • 213
    • 76649139789 scopus 로고    scopus 로고
    • IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation
    • doi:M900177-MCP200 [pii] 10.1074/mcp.M900177-MCP200
    • Tsou CC, Tsai CF, Tsui YH, Sudhir PR, Wang YT, Chen YJ, Chen JY, Sung TY, Hsu WL (2010) IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol Cell Proteomics 9(1):131-144. doi:M900177-MCP200 [pii] 10.1074/mcp.M900177- MCP200
    • (2010) Mol Cell Proteomics , vol.9 , Issue.1 , pp. 131-144
    • Tsou, C.C.1    Tsai, C.F.2    Tsui, Y.H.3    Sudhir, P.R.4    Wang, Y.T.5    Chen, Y.J.6    Chen, J.Y.7    Sung, T.Y.8    Hsu, W.L.9
  • 214
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized P.P.B.-Range mass accuracies and proteome-wide protein quantification
    • doi:nbt.1511 [pii] 10.1038/nbt.1511
    • Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367-1372. doi:nbt.1511 [pii] 10.1038/nbt.1511
    • (2008) Nat Biotechnol , vol.26 , Issue.12 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 216
    • 77954772536 scopus 로고    scopus 로고
    • MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
    • doi:1471-2105-11-395 [pii] 10.1186/1471-2105-11-395
    • Pluskal T, Castillo S, Villar-Briones A, Oresic M (2010) MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11:395. doi:1471-2105-11-395 [pii] 10.1186/1471-2105-11-395
    • (2010) BMC Bioinformatics , vol.11 , pp. 395
    • Pluskal, T.1    Castillo, S.2    Villar-Briones, A.3    Oresic, M.4
  • 217
    • 33750615386 scopus 로고    scopus 로고
    • PEPPeR, a platform for experimental proteomic pattern recognition
    • doi:M600222-MCP200 [pii] 10.1074/mcp.M600222-MCP200
    • Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA (2006) PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5(10):1927-1941. doi:M600222-MCP200 [pii] 10.1074/mcp.M600222-MCP200
    • (2006) Mol Cell Proteomics , vol.5 , Issue.10 , pp. 1927-1941
    • Jaffe, J.D.1    Mani, D.R.2    Leptos, K.C.3    Church, G.M.4    Gillette, M.A.5    Carr, S.A.6
  • 219
    • 0037106398 scopus 로고    scopus 로고
    • Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry
    • Bondarenko PV, Chelius D, Shaler TA (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 74(18):4741-4749
    • (2002) Anal Chem , vol.74 , Issue.18 , pp. 4741-4749
    • Bondarenko, P.V.1    Chelius, D.2    Shaler, T.A.3
  • 220
    • 0036665581 scopus 로고    scopus 로고
    • Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
    • Chelius D, Bondarenko PV (2002) Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 1(4):317-323
    • (2002) J Proteome Res , vol.1 , Issue.4 , pp. 317-323
    • Chelius, D.1    Bondarenko, P.V.2
  • 221
    • 79251595677 scopus 로고    scopus 로고
    • Data processing pipelines for comprehensive profiling of proteomics samples by labelfree LC-MS for biomarker discovery
    • doi:S0039-9140(10)00825-8 [pii] 10.1016/j.talanta.2010.10.029
    • Christin C, Bischoff R, Horvatovich P (2011) Data processing pipelines for comprehensive profiling of proteomics samples by labelfree LC-MS for biomarker discovery. Talanta 83(4):1209-1224. doi:S0039-9140(10)00825-8 [pii] 10.1016/j.talanta.2010.10.029
    • (2011) Talanta , vol.83 , Issue.4 , pp. 1209-1224
    • Christin, C.1    Bischoff, R.2    Horvatovich, P.3
  • 222
    • 77957367167 scopus 로고    scopus 로고
    • Ultra-high performance liquid chromatographymass spectrometry for the fast profiling of histone post-translational modifications
    • doi:10.1021/pr100497a
    • Contrepois K, Ezan E, Mann C, Fenaille F (2010) Ultra-high performance liquid chromatographymass spectrometry for the fast profiling of histone post-translational modifications. J Proteome Res 9(10):5501-5509. doi:10.1021/pr100497a
    • (2010) J Proteome Res , vol.9 , Issue.10 , pp. 5501-5509
    • Contrepois, K.1    Ezan, E.2    Mann, C.3    Fenaille, F.4
  • 223
  • 224
    • 71049194213 scopus 로고    scopus 로고
    • Development and eval uation of normalization methods for label-free relative quantification of endogenous peptides
    • doi:M800514-MCP200 [pii] 10.1074/mcp. M800514-MCP200
    • Kultima K, Nilsson A, Scholz B, Rossbach UL, Falth M, Andren PE (2009) Development and eval uation of normalization methods for label-free relative quantification of endogenous peptides. Mol Cell Proteomics 8(10):2285-2295. doi:M800514-MCP200 [pii] 10.1074/mcp. M800514-MCP200
    • (2009) Mol Cell Proteomics , vol.8 , Issue.10 , pp. 2285-2295
    • Kultima, K.1    Nilsson, A.2    Scholz, B.3    Rossbach, U.L.4    Falth, M.5    Andren, P.E.6
  • 225
    • 63849247205 scopus 로고    scopus 로고
    • Proteomics strategies for target identification and biomarker discovery in cancer
    • doi:3452 [pii]
    • Rajcevic U, Niclou SP, Jimenez CR (2009) Proteomics strategies for target identification and biomarker discovery in cancer. Front Biosci 14:3292-3303. doi:3452 [pii]
    • (2009) Front Biosci , vol.14 , pp. 3292-3303
    • Rajcevic, U.1    Niclou, S.P.2    Jimenez, C.R.3
  • 226
    • 74049115774 scopus 로고    scopus 로고
    • Mass spectrometry-based label-free quantitative proteomics
    • doi:10.1155/2010/840518
    • Zhu W, Smith JW, Huang CM (2010) Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol 2010:840518. doi:10.1155/2010/ 840518
    • (2010) J Biomed Biotechnol , vol.2010 , pp. 840518
    • Zhu, W.1    Smith, J.W.2    Huang, C.M.3
  • 227
    • 64549128284 scopus 로고    scopus 로고
    • Robustness and accuracy of high speed LC-MS separations for global peptide quantitation and biomarker discovery
    • doi:S1570-0232(09)00138-X [pii] 10.1016/j.jchromb.2009.02.052
    • Lengqvist J, Andrade J, Yang Y, Alvelius G, Lewensohn R, Lehtio J (2009) Robustness and accuracy of high speed LC-MS separations for global peptide quantitation and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 877(13):1306-1316. doi:S1570-0232(09)00138-X [pii] 10.1016/j.jchromb.2009. 02.052
    • (2009) J Chromatogr B Analyt Technol Biomed Life Sci , vol.877 , Issue.13 , pp. 1306-1316
    • Lengqvist, J.1    Andrade, J.2    Yang, Y.3    Alvelius, G.4    Lewensohn, R.5    Lehtio, J.6
  • 228
    • 84880037648 scopus 로고    scopus 로고
    • LC/MSbased quantitative proteomic analysis of paraffinembedded archival melanomas reveals potential proteomic biomarkers associated with metastasis
    • doi:10.1371/journal.pone. 0004430
    • Huang SK, Darfler MM, Nicholl MB, You J, Bemis KG, Tegeler TJ, Wang M, Wery JP, Chong KK, Nguyen L, Scolyer RA, Hoon DS (2009) LC/MSbased quantitative proteomic analysis of paraffinembedded archival melanomas reveals potential proteomic biomarkers associated with metastasis. PLoS One 4(2)):e4430. doi:10.1371/journal.pone. 0004430
    • (2009) PLoS One , vol.4 , Issue.2
    • Huang, S.K.1    Darfler, M.M.2    Nicholl, M.B.3    You, J.4    Bemis, K.G.5    Tegeler, T.J.6    Wang, M.7    Wery, J.P.8    Chong, K.K.9    Nguyen, L.10    Scolyer, R.A.11    Hoon, D.S.12
  • 229
    • 33847252481 scopus 로고    scopus 로고
    • CSF biomarker discovery using label-free nano-LC-MS based proteomic profiling: Technical aspects
    • Huang JT, McKenna T, Hughes C, Leweke FM, Schwarz E, Bahn S (2007) CSF biomarker discovery using label-free nano-LC-MS based proteomic profiling: technical aspects. J Sep Sci 30(2): 214-225
    • (2007) J Sep Sci , vol.30 , Issue.2 , pp. 214-225
    • Huang, J.T.1    McKenna, T.2    Hughes, C.3    Leweke, F.M.4    Schwarz, E.5    Bahn, S.6
  • 230
    • 42649131100 scopus 로고    scopus 로고
    • Statistical similarities between transcriptomics and quantitative shotgun proteomics data
    • doi:M700240-MCP200 [pii] 10.1074/mcp.M700240-MCP200
    • Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP (2008) Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics 7(4):631-644. doi:M700240-MCP200 [pii] 10.1074/mcp.M700240-MCP200
    • (2008) Mol Cell Proteomics , vol.7 , Issue.4 , pp. 631-644
    • Pavelka, N.1    Fournier, M.L.2    Swanson, S.K.3    Pelizzola, M.4    Ricciardi-Castagnoli, P.5    Florens, L.6    Washburn, M.P.7


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