Skip to main content
SpringerLink
Log in

De Novo Sequencing Methods in Proteomics

  • Protocol
  • First Online:
Proteome Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 604))

Abstract

The review describes methods of de novo sequencing of peptides by mass spectrometry. De novo methods utilize computational approaches to deduce the sequence or partial sequence of peptides directly from the experimental MS/MS spectra. The concepts behind a number of de novo sequencing methods are discussed. The other approach to identify peptides by tandem mass spectrometry is to match the fragment ions with virtual peptide ions generated from a genomic or protein database. De novo methods are essential to identify proteins when the genomes are not known but they are also extremely useful even when the genomes are known since they are not affected by errors in a search database. Another advantage of de novo methods is that the partial sequence can be used to search for posttranslation modifications or for the identification of mutations by homology based software.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Aebersold, R. and M. Mann, (2003). Mass spectrometry-based proteomics. Nature, 422 (6928): p. 198-207.

    Article  PubMed  CAS  Google Scholar 

  2. Domon, B. and R. Aebersold, (2006). Mass spectrometry and protein analysis. Science, 312(5771): p. 212-7.

    Article  PubMed  CAS  Google Scholar 

  3. Wisniewski, J.R., (2008). Mass spectrometry-based proteomics: principles, perspectives, and challenges. Arch Pathol Lab Med, 132(10): p. 1566-9.

    PubMed  CAS  Google Scholar 

  4. Reinders, J., et al., (2004). Challenges in mass spectrometry-based proteomics. Proteomics, 4(12): p. 3686-703.

    Article  PubMed  CAS  Google Scholar 

  5. Fenn, J.B., et al., (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science, 246(4926): p. 64-71.

    Article  PubMed  CAS  Google Scholar 

  6. Karas, M. and F. Hillenkamp, (1988). Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem, 60(20): p. 2299-301.

    Article  PubMed  CAS  Google Scholar 

  7. Whitehouse, C.M., et al., (1985). Electrospray interface for liquid chromatographs and mass spectrometers. Anal Chem, 57(3): p. 675-9.

    Article  PubMed  CAS  Google Scholar 

  8. Chernushevich, I.V., A.V. Loboda, and B.A. Thomson, (2001). An introduction to quadrupole-time-of-flight mass spectrometry. J Mass Spectrom, 36(8): p. 849-65.

    Article  PubMed  CAS  Google Scholar 

  9. Roepstorff, P., (2000). MALDI-TOF mass spectrometry in protein chemistry. EXS, 88: p. 81-97.

    PubMed  CAS  Google Scholar 

  10. Yost, R.A., and R.K. Boyd, (1990). Tandem mass-spectrometry - quadrupole and hybrid instruments. Methods Enzymol, 193: p. 154-200.

    Article  PubMed  CAS  Google Scholar 

  11. Peterman, S.M., C.P. Dufresne, and S. Horning, (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(2): p. 112-24.

    PubMed  Google Scholar 

  12. Gizzi, G., et al., (2005). Determination of dioxins (PCDDs/PCDFs) and PCBs in food and feed using the DR CALUX (R) bioassay: results of an international validation study. Food Addit Contam, 22(5): p. 472-81.

    Article  PubMed  CAS  Google Scholar 

  13. Delahunty, C. and J.R. Yates, (2005). Protein identification using 2D-LC-MS/MS. Methods, 35(3): p. 248-55.

    Article  PubMed  CAS  Google Scholar 

  14. Steen, H. and M. Mann, (2004). The ABC’s (and XYZ’s) of peptide sequencing. Nat Rev Mol Cell Biol, 5(9): p. 699-711.

    Article  PubMed  CAS  Google Scholar 

  15. Hayes, R.N. and M.L. Gross, (1990). Collision-Induced Dissociation. Methods Enzymol, 193: p. 237-63.

    Article  PubMed  CAS  Google Scholar 

  16. McLuckey, S.A., D.E. Goeringer, and G.L. Glish, (1992). Collisional activation with random noise in ion trap mass spectrometry. Anal Chem, 64(13): p. 1455-60.

    Article  PubMed  CAS  Google Scholar 

  17. Morris, H.R., et al., (1996). High sensitivity collisionally-activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun Mass Spectrom, 10(8): p. 889-96.

    Article  PubMed  CAS  Google Scholar 

  18. Savitski, M.M., et al., (2007). Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation. J Proteome Res, 6(7): p. 2669-73.

    Article  PubMed  CAS  Google Scholar 

  19. Biemann, K., (1988). Contributions of mass spectrometry to peptide and protein structure. Biomed Environ Mass Spectrom, 16(1-12): p. 99-111.

    Article  PubMed  CAS  Google Scholar 

  20. Breci, L.A., et al., (2003). Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal Chem, 75(9): p. 1963-71.

    Article  PubMed  CAS  Google Scholar 

  21. Huang, Y., et al., (2005). Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal Chem, 77(18): p. 5800-13.

    Article  PubMed  CAS  Google Scholar 

  22. Mann, M., C.K. Meng, and J.B. Fenn, (1989). Interpreting mass-spectra of multiply charged ions. Anal Chem, 61(15): p. 1702-08.

    Article  CAS  Google Scholar 

  23. Paizs, B. and S. Suhai, (2004). Towards understanding the tandem mass spectra of protonated oligopeptides. 1: mechanism of amide bond cleavage. J Am Soc Mass Spectrom, 15(1): p. 103-13.

    Google Scholar 

  24. Paizs, B. and S. Suhai, (2005). Fragmentation pathways of protonated peptides. Mass Spectrom Rev, 24(4): p. 508-48.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  26. Tabb, D.L., et al., (2003). Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem, 75(5): p. 1155-63.

    Article  PubMed  CAS  Google Scholar 

  27. Wysocki, V.H., et al., (2000). Mobile and localized protons: a framework for understanding peptide dissociation. J Mass Spectrom, 35(12): p. 1399-406.

    Article  PubMed  CAS  Google Scholar 

  28. Zhang, Z., (2004). Prediction of low-energy collision-induced dissociation spectra of peptides. Anal Chem, 76(14): p. 3908-22.

    Article  PubMed  CAS  Google Scholar 

  29. Zhong, H., et al., (2004). Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis. Nat Biotechnol, 22(10): p. 1291-6.

    Article  PubMed  CAS  Google Scholar 

  30. Appella, E. and C.W. Anderson, (2007). New prospects for proteomics - electron-capture (ECD) and electron-transfer dissociation (ETD) fragmentation techniques and combined fractional diagonal chromatography (COFRADIC). FEBS J, 274(24): p. 6255.

    PubMed  CAS  Google Scholar 

  31. Zubarev, R.A., (2004). Electron-capture dissociation tandem mass spectrometry. Curr Opin Biotechnol, 15(1): p. 12-6.

    Article  PubMed  CAS  Google Scholar 

  32. Zubarev, R.A., et al., (2000). Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem, 72(3): p. 563-73.

    Article  PubMed  CAS  Google Scholar 

  33. Lin, D., D.L. Tabb, and J.R. Yates, (2003). Large-scale protein identification using mass spectrometry. Biochim Biophys Acta, 1646(1-2): p. 1-10.

    PubMed  CAS  Google Scholar 

  34. MacCoss, M.J., (2005). Computational analysis of shotgun proteomics data. Curr Opin Chem Biol, 9(1): p. 88-94.

    Article  PubMed  CAS  Google Scholar 

  35. Johnson, R.S., et al., (2005). Informatics for protein identification by mass spectrometry. Methods, 35(3): p. 223-36.

    Article  PubMed  CAS  Google Scholar 

  36. Forner, F., L.J. Foster, and S. Toppo, (2007). Mass spectrometry data analysis in the proteomics era. Curr Bioinform, 2(1): p. 63-93.

    Article  CAS  Google Scholar 

  37. Pedrioli, P.G., et al., (2004). A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol, 22(11): p. 1459-66.

    Article  PubMed  CAS  Google Scholar 

  38. Ma, B., et al., (2003). PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom, 17(20): p. 2337-42.

    Article  PubMed  CAS  Google Scholar 

  39. Perkins, D.N., et al., (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20(18): p. 3551-67.

    Article  PubMed  CAS  Google Scholar 

  40. Eng, J.K., A.L. Mccormack, and J.R. Yates, (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(11): p. 976-89.

    Article  CAS  Google Scholar 

  41. Yates, J.R., III, J.K. Eng, and A.L. McCormack, (1995). Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem, 67(18): p. 3202-10.

    Article  PubMed  CAS  Google Scholar 

  42. Craig, R., J.P. Cortens, and R.C. Beavis, (2005). The use of proteotypic peptide libraries for protein identification. Rapid Commun Mass Spectrom, 19(13): p. 1844-50.

    Article  PubMed  CAS  Google Scholar 

  43. Frewen, B.E., et al., (2006). Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem, 78(16): p. 5678-84.

    Article  PubMed  CAS  Google Scholar 

  44. Sadygov, R.G., D. Cociorva, and J.R. Yates, III, (2004). Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods, 1(3): p. 195-202.

    Article  PubMed  CAS  Google Scholar 

  45. Sadygov, R.G., H.B. Liu, and J.R. Yates, (2004). Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal Chem, 76(6): p. 1664-71.

    Article  PubMed  CAS  Google Scholar 

  46. Yates, J.R., III, et al., (1995). Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem, 67(8): p. 1426-36.

    Article  PubMed  CAS  Google Scholar 

  47. Eng, J.K., et al., (2008). A fast SEQUEST cross correlation algorithm. J Proteome Res, 7(10): p. 4598-602.

    Article  PubMed  CAS  Google Scholar 

  48. Elias, J.E., et al., (2005). Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods, 2(9): p. 667-75.

    Article  PubMed  CAS  Google Scholar 

  49. Stein, S.E. and D.R. Scott, (1994). Optimization and testing of mass-spectral library search algorithms for compound identification. J Am Soc Mass Spectrom, 5(9): p. 859-66.

    Article  CAS  Google Scholar 

  50. Kapp, E.A., et al., (2005). An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics, 5(13): p. 3475-90.

    Article  PubMed  CAS  Google Scholar 

  51. Craig, R. and R.C. Beavis, (2004). TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20(9): p. 1466-7.

    Article  PubMed  CAS  Google Scholar 

  52. Craig, R. and R.C. Beavis, (2003). A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom, 17(20): p. 2310-6.

    Article  PubMed  CAS  Google Scholar 

  53. Craig, R., J.P. Cortens, and R.C. Beavis, (2004). Open source system for analyzing, validating, and storing protein identification data. J Proteome Res, 3(6): p. 1234-42.

    Article  PubMed  CAS  Google Scholar 

  54. Geer, L.Y., et al., (2004). Open mass spectrometry search algorithm. J Proteome Res, 3(5): p. 958-64.

    Article  PubMed  CAS  Google Scholar 

  55. Zhang, N., R. Aebersold, and B. Schwilkowski, (2002). ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics, 2(10): p. 1406-12.

    Article  PubMed  CAS  Google Scholar 

  56. Colinge, J., et al., (2003). OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics, 3(8): p. 1454-63.

    Article  PubMed  CAS  Google Scholar 

  57. Field, H.I., D. Fenyo, and R.C. Beavis, (2002). RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics, 2(1): p. 36-47.

    Article  PubMed  CAS  Google Scholar 

  58. Nesvizhskii, A.I., O. Vitek, and R. Aebersold, (2007). Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods, 4(10): p. 787-97.

    Article  PubMed  CAS  Google Scholar 

  59. Lam, H., et al., (2007). Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics, 7(5): p. 655-67.

    Article  PubMed  CAS  Google Scholar 

  60. Mann, M. and M. Wilm, (1994). Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem, 66(24): p. 4390-9.

    Article  PubMed  CAS  Google Scholar 

  61. Xu, C. and B. Ma, (2006). Software for computational peptide identification from MS-MS data. Drug Discov Today, 11(13-14): p. 595-600.

    Article  PubMed  CAS  Google Scholar 

  62. Dancik, V., et al., (1999). De novo peptide sequencing via tandem mass spectrometry. J Comput Biol, 6(3-4): p. 327-42.

    Article  PubMed  CAS  Google Scholar 

  63. Johnson, R.S. and J.A. Taylor, (2002). Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol Biotechnol, 22(3): p. 301-15.

    Article  PubMed  CAS  Google Scholar 

  64. Taylor, J.A. and R.S. Johnson, (1997). Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom, 11(9): p. 1067-75.

    Article  PubMed  CAS  Google Scholar 

  65. Taylor, J.A. and R.S. Johnson, (2001). Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem, 73(11): p. 2594-604.

    Article  PubMed  CAS  Google Scholar 

  66. Lu, B. and T. Chen, (2003). A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry. J Comput Biol, 10(1): p. 1-12.

    Article  PubMed  CAS  Google Scholar 

  67. Samgina, T.Y., et al., (2008). De novo sequencing of peptides secreted by the skin glands of the Caucasian Green Frog Rana ridibunda. Rapid Commun Mass Spectrom, 22(22): p. 3517-25.

    Article  PubMed  CAS  Google Scholar 

  68. Standing, K.G., (2003). Peptide and protein de novo sequencing by mass spectrometry. Curr Opin Struct Biol, 13(5): p. 595-601.

    Article  PubMed  CAS  Google Scholar 

  69. Xu, C. and B. Ma, (2006). Complexity and scoring function of MS/MS peptide de novo sequencing. Comput Syst Bioinformatics Conf: p. 361-9.

    Google Scholar 

  70. Frank, A. and P. Pevzner, (2005). PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem, 77(4): p. 964-73.

    Article  PubMed  CAS  Google Scholar 

  71. Pitzer, E., A. Masselot, and J. Colinge, (2007). Assessing peptide de novo sequencing algorithms performance on large and diverse data sets. Proteomics, 7(17): p. 3051-4.

    Article  PubMed  CAS  Google Scholar 

  72. Pevtsov, S., et al., (2006). Performance evaluation of existing de novo sequencing algorithms. J Proteome Res, 5(11): p. 3018-28.

    Article  PubMed  CAS  Google Scholar 

  73. Chen, T., et al., (2001). A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J Comput Biol, 8(3): p. 325-37.

    Article  PubMed  CAS  Google Scholar 

  74. Fernandez-de-Cossio, J., et al., (1998). Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by ‘SeqMS’, a software aid for de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom, 12(23): p. 1867-78.

    Article  PubMed  CAS  Google Scholar 

  75. Han, Y., B. Ma, and K. Zhang, (2004). SPIDER: software for protein identification from sequence tags with de novo sequencing error. Proc IEEE Comput Syst Bioinform Conf: p. 206-15.

    Google Scholar 

  76. Han, Y., B. Ma, and K. Zhang, (2005). SPIDER: software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol, 3(3): p. 697-716.

    Article  PubMed  CAS  Google Scholar 

  77. Alves, G. and Y.K. Yu, (2005). Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics, 21(19): p. 3726-32.

    Article  PubMed  CAS  Google Scholar 

  78. Zubarev, R.A., A.R. Zubarev, and M.M. Savitski, (2008). Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet? J Am Soc Mass Spectrom, 19(6): p. 753-61.

    Article  PubMed  CAS  Google Scholar 

  79. Kjeldsen, F., et al., (2003). Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem, 75(6): p. 1267-74.

    Article  PubMed  CAS  Google Scholar 

  80. Cantin, G.T. and J.R. Yates, III, (2004). Strategies for shotgun identification of post-translational modifications by mass spectrometry. J Chromatogr A, 1053(1-2): p. 7-14.

    PubMed  CAS  Google Scholar 

  81. Kelleher, N.L., et al., (1999). Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. Anal Chem, 71(19): p. 4250-3.

    Article  PubMed  CAS  Google Scholar 

  82. Nielsen, M.L., M.M. Savitski, and R.A. Zubarev, (2005). Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry. Mol Cell Proteomics, 4(6): p. 835-45.

    Article  PubMed  CAS  Google Scholar 

  83. Savitski, M.M., M.L. Nielsen, and R.A. Zubarev, (2007). Side-chain losses in electron capture dissociation to improve peptide identification. Anal Chem, 79(6): p. 2296-302.

    Article  PubMed  CAS  Google Scholar 

  84. Silivra, O.A., et al., (2005). Electron capture dissociation of polypeptides in a three-dimensional quadrupole ion trap: Implementation and first results. J Am Soc Mass Spectrom, 16(1): p. 22-7.

    Article  PubMed  CAS  Google Scholar 

  85. Reinders, J. and A. Sickmann, (2005). State-of-the-art in phosphoproteomics. Proteomics, 5(16): p. 4052-61.

    Article  PubMed  CAS  Google Scholar 

  86. Savitski, M.M., et al., (2007). Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides. J Am Soc Mass Spectrom, 18(1): p. 113-20.

    Article  PubMed  CAS  Google Scholar 

  87. Savitski, M.M., et al., (2005). Proteomics-grade de novo sequencing approach. J Proteome Res, 4(6): p. 2348-54.

    Article  PubMed  CAS  Google Scholar 

  88. Savitski, M.M., M.L. Nielsen, and R.A. Zubarev, (2005). New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol Cell Proteomics, 4(8): p. 1180-8.

    Article  PubMed  CAS  Google Scholar 

  89. Clauser, K.R., P. Baker, and A.L. Burlingame, (1999). Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem, 71(14): p. 2871-82.

    Article  PubMed  CAS  Google Scholar 

  90. Falth, M., et al., (2007). SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides. J Proteome Res, 6(10): p. 4063-7.

    Article  PubMed  CAS  Google Scholar 

  91. Zubarev, R. and M. Mann, (2007). On the proper use of mass accuracy in proteomics. Mol Cell Proteomics, 6(3): p. 377-81.

    PubMed  CAS  Google Scholar 

  92. Frank, A.M., et al., (2007). De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res, 6(1): p. 114-23.

    Article  PubMed  CAS  Google Scholar 

  93. Benjamini, Y. and Y. Hochberg, (1995). Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol, 57(1): p. 289-300.

    Google Scholar 

  94. Balgley, B.M., et al., (2007). Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics, 6(9): p. 1599-608.

    Article  PubMed  CAS  Google Scholar 

  95. Choi, H., D. Ghosh, and A.I. Nesvizhskii, (2008). Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res, 7(1): p. 286-92.

    Article  PubMed  CAS  Google Scholar 

  96. Elias, J.E. and S.P. Gygi, (2007). Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods, 4(3): p. 207-14.

    Article  PubMed  CAS  Google Scholar 

  97. States, D.J., et al., (2006). Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol, 24(3): p. 333-8.

    Article  PubMed  CAS  Google Scholar 

  98. Peng, J., et al., (2003). Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res, 2(1): p. 43-50.

    Article  PubMed  CAS  Google Scholar 

  99. Beer, I., et al., (2004). Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics, 4(4): p. 950-60.

    Article  PubMed  CAS  Google Scholar 

  100. Carr, S., et al., (2004). The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics, 3(6): p. 531-3.

    Article  PubMed  CAS  Google Scholar 

  101. Nesvizhskii, A.I. and R. Aebersold, (2005). Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics, 4(10): p. 1419-40.

    Article  PubMed  CAS  Google Scholar 

  102. Klammer, A.A., et al., (2007). Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Anal Chem, 79(16): p. 6111-8.

    Article  PubMed  CAS  Google Scholar 

  103. Fenyo, D. and R.C. Beavis, (2003). A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem, 75(4): p. 768-74.

    Article  PubMed  CAS  Google Scholar 

  104. MacLean, B., et al., (2006). General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics, 22(22): p. 2830-2.

    Article  PubMed  CAS  Google Scholar 

  105. Nesvizhskii, A.I., et al., (2003). A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem, 75(17): p. 4646-58.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Western Ontario, London, ON, Canada

    Christopher Hughes & Gilles A. Lajoie

  2. David Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada

    Bin Ma

Authors
  1. Christopher Hughes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bin Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gilles A. Lajoie
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gilles A. Lajoie .

Editor information

Editors and Affiliations

  1. Fac. Life Sciences, University of Manchester, Oxford Rd., Manchester, M13 9PT, United Kingdom

    Simon J. Hubbard

  2. Fac. Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, United Kingdom

    Andrew R. Jones

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Hughes, C., Ma, B., Lajoie, G.A. (2010). De Novo Sequencing Methods in Proteomics. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-444-9_8

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-443-2

  • Online ISBN: 978-1-60761-444-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation