Skip to main content

Protein identification using mass spectrometry: A method overview

  • Chapter

Part of the Experientia Supplementum book series (EXS,volume 97)

Abstract

With the introduction of soft ionization techniques such as Matrix Assisted Laser Desorption Ionization (MALDI), and Electrospray Ionization (ESI), proteins have become accessible to mass spectrometric analyses. Since then, mass spectrometry has become the method of choice for sensitive, reliable and inexpensive protein and peptide identification. With the increasing number of full genome sequences for a variety of organisms and the numerous protein databases constructed thereof, all the tools necessary for the high-throughput protein identification with mass spectrometry are in place. This chapter highlights the different mass spectrometric techniques currently applied in proteome research by giving a brief overview of methods for identification of posttranslational modifications and discussing their suitability of strategies for automated data analysis.

Keywords

  • Collision Induce Dissociation
  • Electron Capture Dissociation
  • Electron Transfer Dissociation
  • Peptide Mass Fingerprint
  • Method Overview

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-7643-7439-6_7
  • Chapter length: 30 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   169.00
Price excludes VAT (USA)
  • ISBN: 978-3-7643-7439-6
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Hardcover Book
USD   219.99
Price excludes VAT (USA)

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60: 2299–2301

    PubMed  CrossRef  CAS  Google Scholar 

  2. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64–71

    PubMed  CrossRef  CAS  Google Scholar 

  3. Sundqvist B, Kamensky I, Hakansson P, Kjellberg J, Salehpour M, Widdiyasekera S, Fohlman J, Peterson PA, Roepstorff P (1984) Californium-252 plasma desorption time of flight mass spectroscopy of proteins. Biomed Mass Spectrom 11: 242–257

    PubMed  CrossRef  CAS  Google Scholar 

  4. Barber M, Green BN (1987) The analysis of small proteins in the molecular weight range 10–24 kDa by magnetic sector mass spectrometry. Rapid Commun Mass Spectrom 1: 80–83

    PubMed  CrossRef  CAS  Google Scholar 

  5. Karas M, Kruger R (2003) Ion formation in MALDI: the cluster ionization mechanism. Chem Rev 103: 427–440

    PubMed  CrossRef  CAS  Google Scholar 

  6. Takach EJ, Hines WM, Patterson DH, Juhasz P, Falick AM, Vestal ML, Martin SA (1997) Accurate mass measurements using MALDI-TOF with delayed extraction. J Protein Chem 16: 363–369

    PubMed  CrossRef  CAS  Google Scholar 

  7. Bahr U, Stahl-Zeng J, Gleitsmann E, Karas M (1997) Delayed extraction time-of-flight MALDI mass spectrometry of proteins above 25,000 Da. J Mass Spectrom 32: 1111–1116

    PubMed  CrossRef  CAS  Google Scholar 

  8. Karas M, Gluckmann M, Schafer J (2000) Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors. J Mass Spectrom 35: 1–12

    PubMed  CrossRef  CAS  Google Scholar 

  9. Wilm M, Mann M (1996) Analytical properties of the nanoelectrospray ion source. Anal Chem 68: 1–8

    PubMed  CrossRef  CAS  Google Scholar 

  10. Iavarone AT, Jurchen JC, Williams ER (2000) Effects of solvent on the maximum charge state and charge state distribution of protein ions produced by electrospray ionization. J Am Soc Mass Spectrom 11: 976–985

    PubMed  CrossRef  CAS  Google Scholar 

  11. Iavarone AT, Jurchen JC, Williams ER (2001) Supercharged protein and peptide ions formed by electrospray ionization. Anal Chem 73: 1455–1460

    PubMed  CrossRef  CAS  Google Scholar 

  12. Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72: 1156–1162

    CrossRef  CAS  PubMed  Google Scholar 

  13. Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham CR (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40: 430–443

    PubMed  CrossRef  CAS  Google Scholar 

  14. Hardman M, Makarov AA (2003) Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal Chem 75: 1699–1705

    PubMed  CrossRef  CAS  Google Scholar 

  15. Peng WP, Cai Y, Chang HC (2004) Optical detection methods for mass spectrometry of macroions. Mass Spectrom Rev 23: 443–465

    PubMed  CrossRef  CAS  Google Scholar 

  16. Mann M, Hojrup P, Roepstorff P (1993) Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 22: 338–345

    PubMed  CrossRef  CAS  Google Scholar 

  17. James P, Quadroni M, Carafoli E, Gonnet G (1993) Protein identification by mass profile fingerprinting. Biochem Biophys Res Commun 195: 58–64

    PubMed  CrossRef  CAS  Google Scholar 

  18. Pappin DJ, Hojrup P, Bleasby AJ (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3: 327–332

    PubMed  CrossRef  CAS  Google Scholar 

  19. Lipton MS, Pasa-Tolic L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H et al. (2002) Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci USA 99: 11049–11054

    PubMed  CrossRef  CAS  Google Scholar 

  20. Strittmatter EF, Ferguson PL, Tang K, Smith RD (2003) Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J Am Soc Mass Spectrom 14: 980–991

    PubMed  CrossRef  CAS  Google Scholar 

  21. Eng JK, McCormack AL, Yates JR, III (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

    CrossRef  CAS  Google Scholar 

  22. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551–3567

    PubMed  CrossRef  CAS  Google Scholar 

  23. Zhang W, Chait BT (2000) ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 72: 2482–2489

    PubMed  CrossRef  CAS  Google Scholar 

  24. Colinge J, Masselot A, Cusin I, Mahe E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey PA et al. (2004) High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics 4: 1977–1984

    PubMed  CrossRef  CAS  Google Scholar 

  25. Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L (2005) Differential Proteomics via probabilistic peptide identification scores. Anal Chem 77: 596–606

    PubMed  CrossRef  CAS  Google Scholar 

  26. Biemann K (1990) Appendix 5. Nomenclature for peptide fragment ions (positive ions). Methods Enzymol 193: 886–887

    PubMed  CAS  CrossRef  Google Scholar 

  27. Roepstorff P, Fohlman J (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11: 601

    PubMed  CrossRef  CAS  Google Scholar 

  28. Spengler B, Kirsch D, Kaufmann R, Jaeger E (1992) Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. Rapid Commun Mass Spectrom 6: 105–108

    PubMed  CrossRef  CAS  Google Scholar 

  29. Suckau D, Resemann A, Schuerenberg M, Hufnagel P, Franzen J, Holle A (2003) A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem 376: 952–965

    PubMed  CrossRef  CAS  Google Scholar 

  30. Collings BA, Stott WR, Londry FA (2003) Resonant excitation in a low-pressure linear ion trap. J Am Soc Mass Spectrom 14: 622–634

    PubMed  CrossRef  CAS  Google Scholar 

  31. Douglas DJ, Frank AJ, Mao D (2005) Linear ion traps in mass spectrometry. Mass Spectrom Rev 24: 1–29

    PubMed  CrossRef  CAS  Google Scholar 

  32. Hakansson K, Chalmers MJ, Quinn JP, McFarland MA, Hendrickson CL, Marshall AG (2003) Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. Anal Chem 75: 3256–3262

    PubMed  CrossRef  CAS  Google Scholar 

  33. Cooper HJ, Hakansson K, Marshall AG (2005) The role of electron capture dissociation in biomolecular analysis. Mass Spectrom Rev 24: 201–222

    PubMed  CrossRef  CAS  Google Scholar 

  34. Li W, Hendrickson CL, Emmett MR, Marshall AG (1999) Identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and LC ESI infrared multiphoton dissociation Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 71: 4397–4402

    PubMed  CrossRef  CAS  Google Scholar 

  35. Mann M, Wilm M (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66: 4390–4399

    PubMed  CrossRef  CAS  Google Scholar 

  36. Keough T, Lacey MP, Youngquist RS (2002) Solid-phase derivatization of tryptic peptides for rapid protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 16: 1003–1015

    PubMed  CrossRef  CAS  Google Scholar 

  37. Keough T, Lacey MP, Youngquist RS (2000) Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrixassisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 14: 2348–2356

    PubMed  CrossRef  CAS  Google Scholar 

  38. Munchbach M, Quadroni M, Miotto G, James P (2000) Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentationdirecting moiety. Anal Chem 72: 4047–4057

    PubMed  CrossRef  CAS  Google Scholar 

  39. Lindh I, Hjelmqvist L, Bergman T, Sjovall J, Griffiths WJ (2000) De novo sequencing of proteolytic peptides by a combination of C-terminal derivatization and nano-electrospray/collision-induced dissociation mass spectrometry. J Am Soc Mass Spectrom 11: 673–686

    PubMed  CrossRef  CAS  Google Scholar 

  40. Hale JE, Butler JP, Knierman MD, Becker GW (2000) Increased sensitivity of tryptic peptide detection by MALDI-TOF mass spectrometry is achieved by conversion of lysine to homoarginine. Anal Biochem 287: 110–117

    PubMed  CrossRef  CAS  Google Scholar 

  41. Gu S, Pan S, Bradbury EM, Chen X (2002) Use of deuterium-labeled lysine for efficient protein identification and peptide de novo sequencing. Anal Chem 74: 5774–5785

    PubMed  CrossRef  CAS  Google Scholar 

  42. Sonsmann G, Romer A, Schomburg D (2002) Investigation of the influence of charge derivatization on the fragmentation of multiply protonated peptides. J Am Soc Mass Spectrom 13: 47–58

    PubMed  CrossRef  CAS  Google Scholar 

  43. Schnolzer M, Jedrzejewski P, Lehmann WD (1996) Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17: 945–953

    PubMed  CrossRef  CAS  Google Scholar 

  44. Little DP, Speir JP, Senko MW, O’Connor PB, McLafferty FW (1994) Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal Chem 66: 2809–2815

    PubMed  CrossRef  CAS  Google Scholar 

  45. Guilhaus M, Selby D, Mlynski V (2000) Orthogonal acceleration time-of-flight mass spectrometry. Mass Spectrom Rev 19: 65–107

    PubMed  CrossRef  CAS  Google Scholar 

  46. Premstaller A, Oberacher H, Walcher W, Timperio AM, Zolla L, Chervet JP, Cavusoglu N, Van Dorsselaer A, Huber CG (2001) High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. Anal Chem 73: 2390–2396

    PubMed  CrossRef  CAS  Google Scholar 

  47. Peterman SM, Dufresne CP, Horning S (2005) The use of a hybrid linear trap/FT-ICR mass spectrometer for on-line high resolution/high mass accuracy bottom-up sequencing. J Biomol Tech 16: 112–124

    PubMed  Google Scholar 

  48. Sjodahl J, Kempka M, Hermansson K, Thorsen A, Roeraade J (2005) Chip with twin anchors for reduced ion suppression and improved mass accuracy in MALDI-TOF mass spectrometry. Anal Chem 77: 827–832

    PubMed  CrossRef  CAS  Google Scholar 

  49. Mitulovic G, Smoluch M, Chervet JP, Steinmacher I, Kungl A, Mechtler K (2003) An improved method for tracking and reducing the void volume in nano HPLC-MS with micro trapping columns. Anal Bioanal Chem 376: 946–951

    PubMed  CrossRef  CAS  Google Scholar 

  50. Shen Y, Zhao R, Berger SJ, Anderson GA, Rodriguez N, Smith RD (2002) High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal Chem 74: 4235–4249

    PubMed  CrossRef  CAS  Google Scholar 

  51. Mirgorodskaya E, Braeuer C, Fucini P, Lehrach H, Gobom J (2005) Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: sample preparation, data analysis, and application to the analysis of complex peptide mixtures. Proteomics 5: 399–408

    PubMed  CrossRef  CAS  Google Scholar 

  52. Li X, Gong Y, Wang Y, Wu S, Cai Y, He P, Lu Z, Ying W, Zhang Y, Jiao L et al. (2005) Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project. Proteomics 5: 3423–3441

    PubMed  CrossRef  CAS  Google Scholar 

  53. Kalume DE, Molina H, Pandey A (2003) Tackling the phosphoproteome: tools and strategies. Curr Opin Chem Biol 7: 64–69

    PubMed  CrossRef  CAS  Google Scholar 

  54. Sickmann A, Meyer HE (2001) Phosphoamino acid analysis. Proteomics 1: 200–206

    PubMed  CrossRef  CAS  Google Scholar 

  55. Medzihradszky KF, Phillipps NJ, Senderowicz L, Wang P, Turck CW (1997) Synthesis and characterization of histidine-phosphorylated peptides. Protein Sci 6: 1405–1411

    PubMed  CAS  CrossRef  Google Scholar 

  56. Duclos B, Marcandier S, Cozzone AJ (1991) Chemical properties and separation of phosphoamino acids by thin-layer chromatography and/or electrophoresis. Methods Enzymol 201: 10–21

    PubMed  CAS  Google Scholar 

  57. Meyer HE, Eisermann B, Heber M, Hoffmann-Posorske E, Korte H, Weigt C, Wegner A, Hutton T, Donella-Deana A, Perich JW (1993) Strategies for nonradioactive methods in the localization of phosphorylated amino acids in proteins. FASEB J 7: 776–782

    PubMed  CAS  Google Scholar 

  58. McLachlin DT, Chait BT (2001) Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr Opin Chem Biol 5: 591–602

    PubMed  CrossRef  CAS  Google Scholar 

  59. Porath J, Carlsson J, Olsson I, Belfrage G (1975) Metal chelate affinity chromatography, a new approach to protein fractionation. Nature 258: 598–599

    PubMed  CrossRef  CAS  Google Scholar 

  60. Cao P, Stults JT (1999) Phosphopeptide analysis by on-line immobilized metal-ion affinity chromatography-capillary electrophoresis-electrospray ionization mass spectrometry. J Chromatogr A 853: 225–235

    PubMed  CrossRef  CAS  Google Scholar 

  61. Heintz D, Wurtz V, High AA, Van Dorsselaer A, Reski R, Sarnighausen E (2004) An efficient protocol for the identification of protein phosphorylation in a seedless plant, sensitive enough to detect members of signalling cascades. Electrophoresis 25: 1149–1159

    PubMed  CrossRef  CAS  Google Scholar 

  62. Raska CS, Parker CE, Dominski Z, Marzluff WF, Glish GL, Pope RM, Borchers CH (2002) Direct MALDI-MS/MS of phosphopeptides affinity-bound to immobilized metal ion affinity chromatography beads. Anal Chem 74: 3429–3433

    PubMed  CrossRef  CAS  Google Scholar 

  63. Sano A, Nakamura H (2004) Titania as a chemo-affinity support for the column-switching HPLC analysis of phosphopeptides: application to the characterization of phosphorylation sites in proteins by combination with protease digestion and electrospray ionization mass spectrometry. Anal Sci 20: 861–864

    PubMed  CrossRef  CAS  Google Scholar 

  64. Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJ (2005) Highly selective enrichment of phosphorylated peptides from Peptide mixtures using titanium dioxide micro-columns. Mol Cell Proteomics 4: 873–886

    PubMed  CrossRef  CAS  Google Scholar 

  65. Meyer HE, Hoffmann-Posorske E, Korte H, Heilmeyer LM Jr (1986) Sequence analysis of phosphoserine-containing peptides. Modification for picomolar sensitivity. FEBS Lett 204: 61–66

    PubMed  CrossRef  CAS  Google Scholar 

  66. Oda Y, Nagasu T, Chait BT (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19: 379–382

    PubMed  CrossRef  CAS  Google Scholar 

  67. McLachlin DT, Chait BT (2003) Improved beta-elimination-based affinity purification strategy for enrichment of phosphopeptides. Anal Chem 75: 6826–6836

    PubMed  CrossRef  CAS  Google Scholar 

  68. Conrads TP, Issaq HJ, Veenstra TD (2002) New tools for quantitative phosphoproteome analysis. Biochem Biophys Res Commun 290: 885–890

    PubMed  CrossRef  CAS  Google Scholar 

  69. Thompson AJ, Hart SR, Franz C, Barnouin K, Ridley A, Cramer R (2003) Characterization of protein phosphorylation by mass spectrometry using immobilized metal ion affinity chromatography with on-resin beta-elimination and Michael addition. Anal Chem 75: 3232–3243

    PubMed  CrossRef  CAS  Google Scholar 

  70. Hunter T (1995) Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell 80: 225–236

    PubMed  CrossRef  CAS  Google Scholar 

  71. Schlessinger J (1993) Cellular signaling by receptor tyrosine kinases. Harvey Lect 89: 105–123

    PubMed  CAS  Google Scholar 

  72. Yang X, Wu H, Kobayashi T, Solaro RJ, van Breemen RB (2004) Enhanced ionization of phosphorylated peptides during MALDI TOF mass spectrometry. Anal Chem 76: 1532–1536

    PubMed  CrossRef  CAS  Google Scholar 

  73. Kjellstrom S, Jensen ON (2004) Phosphoric acid as a matrix additive for MALDI MS analysis of phosphopeptides and phosphoproteins. Anal Chem 76: 5109–5117

    PubMed  CrossRef  CAS  Google Scholar 

  74. Stensballe A, Jensen ON (2004) Phosphoric acid enhances the performance of Fe(III) affinity chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for recovery, detection and sequencing of phosphopeptides. Rapid Commun Mass Spectrom 18: 1721–1730

    PubMed  CrossRef  CAS  Google Scholar 

  75. Steen H, Kuster B, Mann M (2001) Quadrupole time-of-flight versus triple-quadrupole mass spectrometry for the determination of phosphopeptides by precursor ion scanning. J Mass Spectrom 36: 782–790

    PubMed  CrossRef  CAS  Google Scholar 

  76. Carr SA, Huddleston MJ, Annan RS (1996) Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal Biochem 239: 180–192

    PubMed  CrossRef  CAS  Google Scholar 

  77. Steen H, Mann M (2002) A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode. J Am Soc Mass Spectrom 13: 996–1003

    PubMed  CrossRef  CAS  Google Scholar 

  78. Hogan JM, Pitteri SJ, McLuckey SA (2003) Phosphorylation site identification via ion trap tandem mass spectrometry of whole protein and peptide ions: bovine alpha-crystallin A chain. Anal Chem 75: 6509–6516

    PubMed  CrossRef  CAS  Google Scholar 

  79. Shi SD, Hemling ME, Carr SA, Horn DM, Lindh I, McLafferty FW (2001) Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. Anal Chem 73: 19–22

    PubMed  CrossRef  CAS  Google Scholar 

  80. Silivra OA, Kjeldsen F, Ivonin IA, Zubarev RA (2005) Electron capture dissociation of polypeptides in a three-dimensional quadrupole ion trap: Implementation and first results. J Am Soc Mass Spectrom 16: 22–27

    PubMed  CrossRef  CAS  Google Scholar 

  81. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101: 9528–9533

    PubMed  CrossRef  CAS  Google Scholar 

  82. Chamrad DC, Koerting G, Gobom J, Thiele H, Klose J, Meyer HE, Blueggel M (2003) Interpretation of mass spectrometry data for high-throughput proteomics. Anal Bioanal Chem 376: 1014–1022

    PubMed  CrossRef  CAS  Google Scholar 

  83. Egelhofer V, Gobom J, Seitz H, Giavalisco P, Lehrach H, Nordhoff E (2002) Protein identification by MALDI-TOF-MS peptide mapping: a new strategy. Anal Chem 74: 1760–1771

    PubMed  CrossRef  CAS  Google Scholar 

  84. Lopez-Ferrer D, Martinez-Bartolome S, Villar M, Campillos M, Martin-Maroto F, Vazquez J (2004) Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal Chem 76: 6853–6860

    PubMed  CrossRef  CAS  Google Scholar 

  85. Qian WJ, Liu T, Monroe ME, Strittmatter EF, Jacobs JM, Kangas LJ, Petritis K, Camp DG, Smith RD (2005) Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res 4: 53–62

    PubMed  CrossRef  CAS  Google Scholar 

  86. Boehm AM, Grosse-Coosmann F, Sickmann A (2004) Command line tool for calculating theoretical MS spectra for given sequences. Bioinformatics 20: 2889–2891

    PubMed  CrossRef  CAS  Google Scholar 

  87. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC (2001) Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches. J Biol Chem 276: 28327–28339

    PubMed  CrossRef  CAS  Google Scholar 

  88. Yergey AL, Coorssen JR, Backlund PS Jr, Blank PS, Humphrey GA, Zimmerberg J, Campbell JM, Vestal ML (2002) De novo sequencing of peptides using MALDI/TOF-TOF. J Am Soc Mass Spectrom 13: 784–791

    PubMed  CrossRef  CAS  Google Scholar 

  89. Fernandez-de-Cossio J, Gonzalez J, Satomi Y, Shima T, Okumura N, Besada V, Betancourt L, Padron G, Shimonishi Y, Takao T (2000) Automated interpretation of low-energy collisioninduced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry. Electrophoresis 21: 1694–1699

    PubMed  CrossRef  CAS  Google Scholar 

  90. Johnson RS, Taylor JA (2002) Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol Biotechnol 22: 301–315

    PubMed  CrossRef  CAS  Google Scholar 

  91. Searle BC, Dasari S, Turner M, Reddy AP, Choi D, Wilmarth PA, McCormack AL, David LL, Nagalla SR (2004) High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. Anal Chem 76: 2220–2230

    PubMed  CrossRef  CAS  Google Scholar 

  92. Bruni R, Gianfranceschi G, Koch G (2005) On peptide de novo sequencing: a new approach. J Pept Sci 11: 225–234

    PubMed  CrossRef  CAS  Google Scholar 

  93. Handley J (2002) Software for MS protein identification. Anal Chem 74: 159A–162A

    PubMed  CAS  Google Scholar 

  94. March RE (1997) An introduction to quadrupole ion trap mass spectrometry. J Mass Spec 32: 351–369

    CrossRef  CAS  Google Scholar 

  95. Johnson RS, Martin SA, Biemann K, Stults JT, Watson JT (1987) Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal Chem 59(21): 2621–2625

    PubMed  CrossRef  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2007 Birkhäuser Verlag/Switzerland

About this chapter

Cite this chapter

Schuchardt, S., Sickmann, A. (2007). Protein identification using mass spectrometry: A method overview. In: Baginsky, S., Fernie, A.R. (eds) Plant Systems Biology. Experientia Supplementum, vol 97. Birkhäuser Basel. https://doi.org/10.1007/978-3-7643-7439-6_7

Download citation