De Novo protein sequencing by combining top-down and bottom-up tandem mass spectra

Journal of Proteome Research

Volumn 13, Issue 7, 2014, Pages 3241-3248

  Liu, Xiaowen ^a,b   Dekker, Lennard J M ^c   Wu, Si ^d   Vanduijn, Martijn M ^c   Luider, Theo M ^c   Tolić, Nikola ^d   Kou, Qiang ^a   Dvorkin, Mikhail ^e   Alexandrova, Sonya ^e   Vyatkina, Kira ^e   Paša Tolić, Ljiljana ^d   Pevzner, Pavel A ^f  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c ERASMUS MEDICAL CENTER   (Netherlands)

^d PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^e ST PETERSBURG ACADEMIC UNIVERSITY   (Russian Federation)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALEMTUZUMAB; AMINO ACID; CYSTEINE; IODOACETAMIDE; PROTEIN; CARBONATE DEHYDRATASE II; MONOCLONAL ANTIBODY;

ACCURACY; ALGORITHM; ALKYLATION; AMINO ACID SEQUENCE; ARTICLE; LIGHT CHAIN; MASS; MASS SPECTROMETER; MOLECULE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY; ANIMAL; BOVINAE; CHEMISTRY; MOLECULAR GENETICS; PEPTIDE MAPPING; PROCEDURES;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES, MONOCLONAL, HUMANIZED; CARBONIC ANHYDRASE II; CATTLE; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; SEQUENCE ANALYSIS, PROTEIN; TANDEM MASS SPECTROMETRY;

EID: 84903691273     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr401300m     Document Type: Article

References (33)

1. Eng, J. K.; McCormack, A. L.; Yates, J. R., III An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5, 976-989
2. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-3567
3. Wiles, M.; Andreassen, P. Monoclonals-the billion dollar molecules of the future Drug Discovery World 2006, Fall, 17-23
4. Rai, K.; Hallek, M. Future prospects for alemtuzumab (MabCampath (TM)) Med. Oncol. 2002, 19, S57-S63
5. Lewis, R. J.; Garcia, M. L. Therapeutic potential of venom peptides Nat. Rev. Drug Discovery 2003, 2, 790-802
6. Edman, P. Method for determination of the amino acid sequence in peptides Acta Chem. Scand. 1950, 4, 283-293
7. Thoma, R. S.; Smith, J. S.; Sandoval, W.; Leone, J. W.; Hunziker, P.; Hampton, B.; Linse, K. D.; Denslow, N. D. The ABRF Edman Sequencing Research Group 2008 Study: Investigation into homopolymeric amino acid N-terminal sequence tags and their effects on automated Edman degradation J. Biomol. Tech. 2009, 20, 216-225
8. Bandeira, N.; Pham, V.; Pevzner, P.; Arnott, D.; Lill, J. R. Automated de novo protein sequencing of monoclonal antibodies Nat. Biotechnol. 2008, 26, 1336-1338
9. Thakkar, A.; Cohen, A. S.; Connolly, M. D.; Zuckermann, R. N.; Pei, D. High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial Edman degradation and mass spectrometry J. Comput. Chem. 2009, 11, 294-302
10. Calvete, J. J.; Ghezellou, P.; Paiva, O.; Matainaho, T.; Ghassempour, A.; Goudarzi, H.; Kraus, F.; Sanz, L.; Williams, D. J. Snake venomics of two poorly known Hydrophiinae: Comparative proteomics of the venoms of terrestrial Toxicocalamus longissimus and marine Hydrophis cyanocinctus J. Proteomics 2012, 75, 4091-4101
11. Johnson, R. S.; Biemann, K. The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry Biochemistry 1987, 26, 1209-1214
12. Hopper, S.; Johnson, R. S.; Vath, J. E.; Biemann, K. Glutaredoxin from rabbit bone marrow. Purification, characterization, and amino acid sequence determined by tandem mass spectrometry J. Biol. Chem. 1989, 264, 20438-20447
13. Whaley, B.; Caprioli, R. M. Identification of nearest-neighbor peptides in protease digests by mass spectrometry for construction of sequence-ordered tryptic maps Biol. Mass Spectrom. 1991, 20, 210-214
14. MacCoss, M. J.; McDonald, W. H.; Saraf, A.; Sadygov, R.; Clark, J. M.; Tasto, J. J.; Gould, K. L.; Wolters, D.; Washburn, M.; Weiss, A.; Clark, J. I.; Yates, J. R. Shotgun identification of protein modifications from protein complexes and lens tissue Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7900-7905
15. Englander, J. J.; Del Mar, C.; Li, W.; Englander, S. W.; Kim, J. S.; Stranz, D. D.; Hamuro, Y.; Woods, V. L. Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7057-7062
16. Bandeira, N.; Tang, H.; Bafna, V.; Pevzner, P. Shotgun protein sequencing by tandem mass spectra assembly Anal. Chem. 2004, 76, 7221-7233
17. Pham, V.; Henzel, W. J.; Arnott, D.; Hymowitz, S.; Sandoval, W. N.; Truong, B. T.; Lowman, H.; Lill, J. R. De novo proteomic sequencing of a monoclonal antibody raised against OX40 ligand Anal. Biochem. 2006, 352, 77-86
18. Klammer, A. A.; MacCoss, M. J. Effects of modified digestion schemes on the identification of proteins from complex mixtures J. Proteome Res. 2006, 5, 695-700
19. Bandeira, N.; Clauser, K. R.; Pevzner, P. A. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins Mol. Cell. Proteomics 2007, 6, 1123-1134
20. Guthals, A.; Clauser, K. R.; Bandeira, N. Shotgun protein sequencing with meta-contig assembly Mol. Cell. Proteomics 2012, 11, 1084-1096
21. Castellana, N.; Bafna, V. Proteogenomics to discover the full coding content of genomes: A computational perspective J. Proteomics 2010, 73, 2124-2135
22. Cheung, W. C.; Beausoleil, S. A.; Zhang, X.; Sato, S.; Schieferl, S. M.; Wieler, J. S.; Beaudet, J. G.; Ramenani, R. K.; Popova, L.; Comb, M. J.; Rush, J.; Polakiewicz, R. D. A proteomics approach for the identification and cloning of monoclonal antibodies from serum Nat. Biotechnol. 2012, 30, 447-452
23. Liu, X.; Han, Y.; Yuen, D.; Ma, B. Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy Bioinformatics 2009, 25, 2174-2180
24. Tran, J. C.; Zamdborg, L.; Ahlf, D. R.; Lee, J. E.; Catherman, A. D.; Durbin, K. R.; Tipton, J. D.; Vellaichamy, A.; Kellie, J. F.; Li, M.; Wu, C.; Sweet, S. M. M.; Early, B. P.; Siuti, N.; LeDuc, R. D. Mapping intact protein isoforms in discovery mode using top-down proteomics Nature 2011, 480, 254-258
25. Dekker, L.; Wu, S.; Vanduijn, M.; Tolić, N.; Stingl, C.; Zhao, R.; Luider, T.; Paša-Tolić, L. An integrated top-down and bottom-up proteomic approach to characterize the antigen binding fragment of antibodies Proteomics 2014, 10.1002/pmic.201300366
26. Kim, S.; Gupta, N.; Pevzner, P. A. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases J. Proteome Res. 2008, 7, 3354-3363
27. Liu, X.; Inbar, Y.; Dorrestein, P. C.; Wynne, C.; Edwards, N.; Souda, P.; Whitelegge, J. P.; Bafna, V.; Pevzner, P. A. Deconvolution and database search of complex tandem mass spectra of intact proteins: A combinatorial approach Mol. Cell. Proteomics 2010, 9, 2772-2782
28. Liu, X.; Hengel, S.; Wu, S.; Tolić, N.; Paša-Tolić, L.; Pevzner, P. A. Identification of ultramodified proteins using top-down tandem mass spectra J. Proteome Res. 2013, 12, 5830-5838
29. Pevzner, P. A.; Dančík, V.; Tang, C. L. Mutation-tolerant protein identification by mass spectrometry J. Comput. Biol. 2000, 7, 777-787
30. Ma, B.; Zhang, K.; Hendrie, C.; Liang, C.; Li, M.; Doherty-Kirby, A.; Lajoie, G. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry Rapid Commun. Mass Spectrom. 2003, 17, 2337-2342
31. Frank, A.; Pevzner, P. PepNovo: De novo peptide sequencing via probabilistic network modeling Anal. Chem. 2005, 77, 964-973
32. Chi, H.; Sun, R. X.; Yang, B.; Song, C. Q.; Wang, L. H.; Liu, C.; Fu, Y.; Yuan, Z. F.; Wang, H. P.; He, S. M.; Dong, M. Q. pNovo: de novo peptide sequencing and identification using HCD spectra J. Proteome Res. 2010, 9, 2713-2724
33. Guthals, A.; Clauser, K. R.; Frank, A. M.; Bandeira, N. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides J. Proteome Res. 2013, 12, 2846-2857