Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N

Journal of Proteome Research

Volumn 8, Issue 3, 2009, Pages 1415-1422

  Hohmann, Laura ^a   Sherwood, Carly ^a   Eastham, Ashley ^a   Peterson, Amelia ^b   Eng, Jimmy K ^a,c   Eddes, James S ^d   Shteynberg, David ^a   Martin, Daniel B ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Grifola frondosa; Immonium ion; Lys N; Metalloendoprotease; Sequence tags

Indexed keywords

IMMONIUM; ION; LYSINE; METALLOPROTEINASE; PEPTIDE; TRYPSIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; FRAGMENTATION REACTION; GRIFOLA; ION CURRENT; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

FUNGAL PROTEINS; GRIFOLA; LYSINE; METALLOEXOPEPTIDASES; PEPTIDES; PROTEOME; TRYPSIN;

GRIFOLA FRONDOSA;

EID: 65249153010     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800774h     Document Type: Article

References (34)

1. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422 (6928), 198-207.
2. Hunt, D. F.; Yates, J. R., 3rd.; Shabanowitz, J.; Winston, S.; Hauer, C. R. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 1986, 83 (17), 6233-7.
3. Paizs, B.; Suhai, S. Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2004.
4. Roepstorff, P.; Fohlman, J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 1984, 11 (11), 601.
5. Biemann, K. Appendix 5. Nomenclature for peptide fragment ions (positive ions). Methods Enzymol. 1990, 193, 886-7.
6. Eng, J.; McCormack, A.; Yates III, J. R. An approach to correlate tamdem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, (5), 976989.
7. 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 (18), 355167.
8. Dongre, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model. J. Am. Chem. Soc. 1996, 118 (35), 8365-8374.
9. Tang, X. J.; Boyd, R. K. An investigation of fragmentation mechanisms of doubly protonated tryptic peptides. Rapid Commun. Mass Spectrom. 1992, 6 (11), 651-7.
10. Paizs, B.; Suhai, S. Towards understanding some ion intensity relationships for the tandem mass spectra of protonated peptides. Rapid Commun. Mass Spectrom. 2002, 16 (17), 1699-702.
11. Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 2000, 35 (12), 1399-406.
12. Tabb, D. L.; Huang, Y.; Wysocki, V. H.; Yates, J. R. 3rd, Influence of basic residue content on fragment ion peak intensities in low- energy collision-induced dissociation spectra of peptides. Anal. Chem. 2004, 76 (5), 1243-8.
13. Saito, T.; Dohmae, N.; Tsujimoto, M.; Takio, K. PCR cloning and heterologous expression of cDNA encoding a peptidyl-Lys met- alloendopeptidase precursor of Grifola frondosa. J. Gen. Appl. Microbiol. 2002, 48 (5), 287-92.
14. Hori, T.; Kumasaka, T.; Yamamoto, M.; Nonaka, N.; Tanaka, N.; Hashimoto, Y.; Ueki, U.; Takio, K. Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms. Acta Crystallogr. D: Biol. Crystallogr. 2001, 57 (Pt 3), 361-8.
15. Nonaka, T.; Dohmae, N.; Hashimoto, Y.; Takio, K. Amino acid sequences of metalloendopeptidases specific for acyl-lysine bonds from Grifola frondosa and Pleurotus ostreatus fruiting bodies. J. Biol. Chem. 1997, 272 (48), 30032-9.
16. Nishiwaki, T.; Hayashi, K. Purification and characterization of an aminopeptidase from the edible basidiomycete Grifola frondosa. Biosci. Biotechnol. Biochem. 2001, 65 (2), 424-7.
17. Nonaka, T.; Hashimoto, Y.; Takio, K. Kinetic characterization of lysine-specific metalloendopeptidases from Grifola frondosa and Pleurotus ostreatus fruiting bodies. J. Biochem. 1998, 124 (1), 15762.
18. Barrett, A. J.; Rawlings, N. K.; Woessner, J. F. Handbook of Proteolytic Enzymes; Elsevier Academic Press: London, 2004; Vol. 1.
19. 18O labeling for comparative pro- teomics: application to cytokine/lipolysaccharide-treated human retinal pigment epithelium cell line. Mol. Cell. Proteomics 2005, 4 (10), 1550-7.
20. Taouatas, N.; Drugan, M. M.; Heck, A. J.; Mohammed, S. Straightforward ladder sequencing of peptides using a Lys-N metalloen- dopeptidase. Nat. Methods 2008, 5 (5), 405-7.
21. Klimek, J.; Eddes, J. S.; Hohmann, L.; Jackson, J.; Peterson, A.; Letarte, S.; Gafken, P. R.; Katz, J. E.; Mallick, P.; Lee, H.; Schmidt, A.; Ossola, R.; Eng, J. K.; Aebersold, R.; Martin, D. B. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res. 2008, 7 (1), 96-103.
22. Martin, D. B.; Eng, J. K.; Nesvizhskii, A. I.; Gemmill, A.; Aebersold, R. Investigation of neutral loss during collision-induced dissociation of peptide ions. Anal. Chem. 2005, 77 (15), 4870-82.
23. Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 2005-0017.
24. Horth, P.; Miller, C. A.; Preckel, T.; Wenz, C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol. Cell. Proteomics 2006, 5 (10), 1968-74.
25. Lam, H. T.; Josserand, J.; Lion, N.; Girault, H. H. Modeling the isoelectric focusing of peptides in an OFFGEL multicompartment cell. J. Proteome Res. 2007, 6 (5), 1666-76.
26. Choudhary, G.; Wu, S. L.; Shieh, P.; Hancock, W. S. Multiple enzymatic digestion for enhanced sequence coverage of proteins in complex proteomic mixtures using capillary LC with ion trap MS/MS. J. Proteome Res. 2003, 2 (1), 59-67.
27. Gatlin, C. L.; Eng, J. K.; Cross, S. T.; Detter, J. C.; Yates, J. R. 3rd, Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal. Chem. 2000, 72 (4), 757-63.
28. Wa, C.; Cerny, R.; Hage, D. S. Obtaining high sequence coverage in matrix-assisted laser desorption time-of-flight mass spectrometry for studies of protein modification: analysis of human serum albumin as a model. Anal. Biochem. 2006, 349 (2), 229-41.
29. Polce, M. J.; Ren, D.; Wesdemiotis, C. Dissociation of the peptide bond in protonated peptides. J. Mass Spectrom. 2000, 35 (12), 1391-8.
30. Vachet, R. W.; Ray, K. L.; Glish, G. L. Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap. J. Am. Soc. Mass Spectrom. 1998, 9 (4), 341-4.
31. Hohmann, L. J.; Eng, J. K.; Gemmill, A.; Klimek, J.; Vitek, O.; Reid, G. E.; Martin, D. B. Quantification of the Compositional Information Provided by Immonium Ions on a Quadrupole-Time-of-Flight Mass Spectrometer. Anal. Chem. 2008.
32. Mann, M.; Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66 (24), 4390-9.
33. Tabb, D. L.; Saraf, A.; Yates, J. R. 3rd, GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal. Chem. 2003, 75 (23), 6415-21.
34. Tabb, D. L.; Ma, Z. Q.; Martin, D. B.; Ham, A. J.; Chambers, M. C. DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring. J. Proteome Res. 2008, 7 (9), 3838-46.