De novo sequencing of peptides using MALDI/TOF-TOF

Journal of the American Society for Mass Spectrometry

Volumn 13, Issue 7, 2002, Pages 784-791

  Yergey, Alfred L ^a,c   Coorssen, Jens R ^d   Backlund Jr , Peter S ^a   Blank, Paul S ^a   Humphrey, Glen A ^a   Zimmerberg, Joshua ^a   Campbell, Jennifer M ^b   Vestal, Marvin L ^b  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b Applied Biosystems Framingham   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOLOGICAL MEMBRANES; COMPLEXATION; MASS SPECTROMETRY;

PEPTIDES;

PROTEINS;

MEMBRANE PROTEIN; ANGIOTENSIN I; PEPTIDE; PROTEIN HYDROLYSATE; TRYPSIN;

MASS SPECTROMETRY;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DIGESTION; FRAGMENTATION REACTION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; QUADRUPOLE TIME OF FLIGHT MASS SPECTROMETRY; ANIMAL; CHEMISTRY; MASS SPECTROMETRY; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; SEA URCHIN; SEQUENCE ANALYSIS;

ECHINOIDEA;

ALGORITHMS; ANGIOTENSIN I; ANIMALS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MEMBRANE PROTEINS; PEPTIDES; PROTEIN HYDROLYSATES; SEA URCHINS; SEQUENCE ANALYSIS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 0036633842     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1044-0305(02)00393-8     Document Type: Article

References (28)

1. Mann M., Hoejrup P., Roepstorff P. Use of Mass Spectrometric Molecular Weight Information to Identify Proteins in Sequence Databases. Biol. Mass Spectrom. 22:(6):1993;338-345.
2. Clauser K., Hall S.C., Smith D.M., Webb J.W., Andrews L., Tran H.M., Epstein L.B., Burlingame A.L. Rapid Mass Spectrometric Peptide Sequencing and Mass Matching for Characterization of Human Melanoma Proteins Isolated by Two-Dimensional PAGE. Proc. Natl. Acad. Sci. U.S.A. 92:1995;5072-5076.
3. Zhang W., Chait B. ProFound An Expert System for Protein Identification Using Mass Spectrometric Peptide Mapping Information . Anal. Chem. 72:2000;2482-2489.
4. Eriksson J., Chait B., Fenyo D. A Statistical Approach for Testing the Significance of Mass Spectrometric Protein Identification Results. Anal. Chem. 72:2000;999-1005.
5. Perkins D., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-Based Protein Identification by Searching Sequence Databases Using Mass Spectrometry Data. Electrophoresis. 20:1999;3551-3567.
6. Clauser K., Baker P., Burlingame A. Role of Accurate Mass Measurements (+/- 10 ppm) in Protein Identification Strategies Employing MS and MS/MS. Anal. Chem. 71:1999;2871.
7. Egelhofer V., Bussow K., Luebbert C., Lehrach H., Nodhof E. Improvements in Protein Identification by MALDI-TOF-MS Peptide Mapping. Anal. Chem. 72:2000;2741-2750.
8. 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. 5:1994;976-989.
9. Mann M., Wilm M. Error Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags. Anal. Chem. 66:1994;4390-4399.
10. Tsugita A., van der Broek R., Przybylski M. Exopeptidase Digestion in Combination with Field Desorption Mass Spectrometry for Amino Acid Sequence Determination. FEBS Lett. 137:1982;19-24.
11. Bieman K., Cone C., Webster B.R., Arsenault G.P. Determination of the Amino Acid Sequence in Oligopeptides by Computer Interpretation of High Resolution Mass Spectra. J. Am. Chem. Soc. 88:1966;5598-5606.
12. Siegel M., Bauman N. An Efficient Algorithm for Sequencing Peptides Using Fast Atom Bombardment Mass Spectra. Biomed. Environ. Mass Spectrom. 15:1988;333-343.
13. Johnson R., Bieman K. Computer Program (SEQPEP) to Aid in the Interpretation of High-Energy Collision Tandem Mass Spectra of Peptides. Biomed. Environ. Mass Spectrom. 18:1989;945-957.
14. Yates J., Griffin P., Hood L. Villafranca J. Techniques in Protein Chemistry. Vol. II:1991;477-489 Academic Press, San Diego.
15. Zhang Z., McElvain J. De Novo Peptide Sequencing by Two-Dimensional Fragment Correlation Analysis. Anal. Chem. 72:2000;2337-2350.
16. Taylor J., Johnson R. Sequence Database Searches via de Novo Peptide Sequencing by Tandem Mass Spectrometry. Rapid Commun. Mass Spectrom. 11:1997;1067-1075.
17. Dancik V., Addona T.A., Clauser K.R., Vath J.E., Pevzner P.A. De Novo Peptide Sequencing via Tandem Mass Spectrometry. J. Comp. Biol. 6:1999;327-342.
18. Taylor J., Johnson R. Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry. Anal. Chem. 73:2001;2594-2604.
19. Chen T., Kao M.-Y., Tepel M., Rush J., Church G.M. A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry. J. Comput. Biol. 8:2001;325-337.
20. Hines W.M., Falick A.M., Burlingame A.L., Gibson B.W. Pattern-Based Algorithm for Peptide Sequencing from Tandem High Energy Collision-Induced Dissociation Mass Spectra. J. Am. Soc. Mass Spectrom. 3:1992;326-336.
21. Zimmerberg J., Blank P.S., Kolosova I., Cho M.-S., Tahara M., Coorssen J.R. A Stage-Specific Preparation to Study the Ca2+-Triggered Fusion Steps of Exocytosis Rationale and Perspectives . Biochemie. 82:2000;303-314.
22. Tahara M., Coorssen J.R., Timmers K., Blank P.S., Whalley T., Scheller R., Zimmerberg J. Calcium Can Disrupt the SNARE Protein Complex on Sea Urchin Egg Secretory Vesicles Without Irreversibly Blocking Fusion. J. Biol. Chem. 273:1998;33667-33673.
23. Coorssen J.R., Blank P.S., Tahara M., Zimmerberg J. Biochemical and Functional Studies of Cortical Vesicle Dusion The SNARE Complex and Ca2+ Sensitivity . J. Cell Biol. 143:1998;1845-1847.
24. Facilities A.o.B.R., Representative "In-Gel" Digestion Protocol for Proteins in SDS PAGE Gel www.abrf.org/ABRF/ResearchCommittees/intprotseqrescomm.html 1997.
25. Davis M.T., Stahl D.C., Hefta S.A., Lee T.D. A Microscale Electrospray Interface for On-Line, Capillary Liquid Chromatography/Tandem Mass Spectrometry of Complex Peptide Mixtures. Anal. Chem. 67:1995;4549-4556.
26. Vestal M., Campbell J. Tandem Time-of-Flight Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2002;. unpublished.
27. Vestal M., Juhasz P., Martin S. Delayed Extraction Matrix-assisted Laser Desorption Time-of-Flight Mass Spectrometry. Rapid Commun. Mass Spectrom. 9:1995;1044-1050.
28. MASCOT http://www.matrixscience.com 2001.