Molecular phylogenetics by direct comparison of tandem mass spectra

Rapid Communications in Mass Spectrometry

Volumn 26, Issue 7, 2012, Pages 728-732

  Palmblad, Magnus ^a   Deelder, André M ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALS; MASS SPECTROMETERS; MASS SPECTROMETRY;

BACTERIAL IDENTIFICATIONS; BONE MATERIALS; DISTANCE METRICS; GREAT APES; MOLECULAR PHYLOGENETICS; PAIR-WISE COMPARISON; PHYLOGENETIC ANALYSIS; TANDEM MASS SPECTRA; TRYPTIC DIGESTS;

PROTEINS;

EID: 84857522815     PISSN: 09514198     EISSN: 10970231     Source Type: Journal    
DOI: 10.1002/rcm.6162     Document Type: Article

References (34)

1. E. Zuckerkandl, R. T. Jones, L. Pauling,. A comparison of animal hemoglobins by tryptic peptide pattern analysis. Proc. Natl. Acad. Sci. USA 1960, 46, 1349.
2. E. Zuckerkandl, L. Pauling, in Horizons in Biochemistry, (Eds:, M. Kasha, B. Pullman,). Academic Press, New York, 1962, pp. 189-225.
3. E. Zuckerkandl, L. Pauling,. Molecules as documents of evolutionary history. J. Theor. Biol. 1965, 8, 357.
4. R. E. Green, J. Krause, A. W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M. H. Fritz, N. F. Hansen, E. Y. Durand, A. S. Malaspinas, J. D. Jensen, T. Marques-Bonet, C. Alkan, K. Prufer, M. Meyer, H. A. Burbano, J. M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Hober, B. Hoffner, M. Siegemund, A. Weihmann, C. Nusbaum, E. S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, C. Verna, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, V.B. Doronichev, L. V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R. W. Schmitz, P. L. Johnson, E. E. Eichler, D. Falush, E. Birney, J. C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich, S. Paabo,. A draft sequence of the Neandertal genome. Science 2010, 328, 710.
5. R. D. Holland, J. G. Wilkes, F. Rafii, J. B. Sutherland, C. C. Persons, K. J. Voorhees, J. O. Lay Jr,. Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10, 1227.
6. T. Krishnamurthy, P. L. Ross, U. Rajamani,. Detection of pathogenic and non-pathogenic bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10, 883.
7. Y. P. Ho, P. M. Reddy,. Identification of pathogens by mass spectrometry. Clin. Chem. 2010, 56, 525.
8. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley,. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 2007, 316, 280.
9. M. Buckley, A. Walker, S. Y. Ho, Y. Yang, C. Smith, P. Ashton, J. T. Oates, E. Cappellini, H. Koon, K. Penkman, B. Elsworth, D. Ashford, C. Solazzo, P. Andrews, J. Strahler, B. Shapiro, P. Ostrom, H. Gandhi, W. Miller, B. Raney, M. I. Zylber, M. T. Gilbert, R.V. Prigodich, M. Ryan, K.F. Rijsdijk, A. Janoo, M. J. Collins,. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 2008, 319, 33; author reply 33.
10. P. A. Pevzner, S. Kim, J. Ng,. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 2008, 321, 1040; author reply 1040.
11. M. Bern, B. S. Phinney, D. Goldberg,. Reanalysis of Tyrannosaurus rex mass spectra. J. Proteome Res. 2009, 8, 4328.
12. A. Chambery, A. Di Maro, C. Sanges, V. Severino, M. Tarantino, A. Lamberti, A. Parente, P. Arcari,. Improved procedure for protein binder analysis in mural painting by LC-ESI/Q-q-TOF mass spectrometry: detection of different milk species by casein proteotypic peptides. Anal. Bioanal. Chem. 2009, 395, 2281.
13. C. Guarino, F. Fuselli, A. La Mantia, L. Longo, A. Faberi, R. M. Marianella,. Peptidomic approach, based on liquid chromatography/electrospray ionization tandem mass spectrometry, for detecting sheep's milk in goat's and cow's cheeses. Rapid Commun. Mass Spectrom. 2010, 24, 705.
14. M. Carrera, B. Canas, C. Pineiro, J. Vazquez, J. M. Gallardo,. De novo mass spectrometry sequencing and characterization of species-specific peptides from nucleoside diphosphate kinase B for the classification of commercial fish species belonging to the family Merlucciidae. J. Proteome Res. 2007, 6, 3070.
15. M. Buckley, M. Collins, J. Thomas-Oates, J. C. Wilson,. Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2009, 23, 3843.
16. J. M. Wells, S. A. McLuckey,. Collision-induced dissociation (CID) of peptides and proteins. Meth. Enzymol. 2005, 402, 148.
17. R. Craig, J. C. Cortens, D. Fenyo, R. C. Beavis,. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 2006, 5, 1843.
18. B. E. Frewen, G. E. Merrihew, C. C. Wu, W. S. Noble, M. J. MacCoss,. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 2006, 78, 5678.
19. H. Lam, R. Aebersold,. Spectral library searching for peptide identification via tandem MS. Methods Mol. Biol. 2010, 604, 95.
20. P. G. Pedrioli, J. K. Eng, R. Hubley, M. Vogelzang, E. W. Deutsch, B. Raught, B. Pratt, E. Nilsson, R. H. Angeletti, R. Apweiler, K. Cheung, C. E. Costello, H. Hermjakob, S. Huang, R. K. Julian, E. Kapp, M. E. McComb, S. G. Oliver, G. Omenn, N. W. Paton, R. Simpson, R. Smith, C. F. Taylor, W. Zhu, R. Aebersold,. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459.
21. UniProt website:.
22. R. Craig, R. C. Beavis,. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466.
23. A. Keller, J. Eng, N. Zhang, X. J. Li, R. Aebersold,. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 2005 0017.
24. A. Keller, A. I. Nesvizhskii, E. Kolker, R. Aebersold,. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383.
25. A. Frank, P. Pevzner,. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964.
26. Z. B. Alfassi,. On the normalization of a mass spectrum for comparison of two spectra. J. Am. Soc. Mass Spectrom. 2004, 15, 385.
27. D. R. Maddison, D. L. Swofford, W. P. Maddison,. NEXUS: an extensible file format for systematic information. Syst. Biol. 1997, 46, 590.
28. A. Dress, D. Huson, V. Moulton,. Analyzing and visualizing sequence and distance data using SPLITSTREE. Disc. Appl. Math. 1996, 71, 95.
29. R. Sokal, C. Michener,. A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 1958, 38, 1409.
30. C. G. Sibley, J. E. Ahlquist,. The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J. Mol. Evol. 1984, 20, 2.
31. N. Takahata, Y. Satta, J. Klein,. Divergence time and population-size in the lineage leading to modern humans. Theor. Popul. Biol. 1995, 48, 198.
32. F. C. Chen, W. H. Li,. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 2001, 68, 444.
33. S. Kumar, A. Filipski, V. Swarna, A. Walker, S. B. Hedges,. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc. Natl. Acad. Sci. USA 2005, 102, 18842.
34. P. A. Rudnick, K. R. Clauser, L. E. Kilpatrick, D. V. Tchekhovskoi, P. Neta, N. Blonder, D. D. Billheimer, R. K. Blackman, D. M. Bunk, H. L. Cardasis, A. J. Ham, J. D. Jaffe, C. R. Kinsinger, M. Mesri, T. A. Neubert, B. Schilling, D. L. Tabb, T. J. Tegeler, L. Vega-Montoto, A. M. Variyath, M. Wang, P. Wang, J. R. Whiteaker, L. J. Zimmerman, S. A. Carr, S. J. Fisher, B. W. Gibson, A. G. Paulovich, F. E. Regnier, H. Rodriguez, C. Spiegelman, P. Tempst, D. C. Liebler, S. E. Stein,. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteomics 2010, 9, 225.