Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage

Rapid Communications in Mass Spectrometry

Volumn 28, Issue 24, 2014, Pages 2735-2743

  Ebhardt, H Alexander ^a   Nan, Jie ^a   Chaulk, Steven G ^b   Fahlman, Richard P ^b,c   Aebersold, Ruedi ^a,d,e  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ALBERTA   (Canada)

^c UNIVERSITY OF ALBERTA   (Canada)

^d University of Zürich ^*  (Switzerland)

^e UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DISSOCIATION; ELECTROSPRAY IONIZATION; IONS; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

ACIDIC AMINO ACIDS; BASIC AMINO ACIDS; ENZYMATIC GENERATION; ENZYMATIC REACTION; ION SERIES; N TERMINUS; N-TERMINALS; SEQUENCE COVERAGES; SPECTRA'S; SUBSTRATE PEPTIDES;

PEPTIDES;

AMINO ACID; AMINOACYLTRANSFERASE; ARGINYLTRANSFERASE; PEPTIDE;

CHEMISTRY; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY;

AMINO ACIDS, BASIC; AMINOACYLTRANSFERASES; PEPTIDES; SEQUENCE ANALYSIS, PROTEIN; TANDEM MASS SPECTROMETRY;

EID: 84954445952     PISSN: 09514198     EISSN: 10970231     Source Type: Journal    
DOI: 10.1002/rcm.7069     Document Type: Article

References (28)

1. V. H. Wysocki, G. Tsaprailis, L. L. Smith, L. A. Breci,. Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 2000, 35, 1399.
2. B. Domon, R. Aebersold,. Challenges and opportunities in proteomics data analysis. Mol. Cell. Proteomics 2006, 5, 1921.
3. V. Dancik, T. A. Addona, K. R. Clauser, J. E. Vath, P. A. Pevzner,. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 1999, 6, 327.
4. A. M. Frank, M. M. Savitski, M. L. Nielsen, R. A. Zubarev, P. A. Pevzner,. De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 2007, 6, 114.
5. P. L. Ross, Y. N. Huang, J. N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. Bartlet-Jones, F. He, A. Jacobson, D. J. Pappin,. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154.
6. A. Thompson, J. Schafer, K. Kuhn, S. Kienle, J. Schwarz, G. Schmidt, T. Neumann, R. Johnstone, A. K. Mohammed, C. Hamon,. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895.
7. E. Balzi, M. Choder, W. N. Chen, A. Varshavsky, A. Goffeau,. Cloning and functional analysis of the arginyl-tRNA-protein transferase gene ATE1 of Saccharomyces cerevisiae. J. Biol. Chem. 1990, 265, 7464.
8. R. G. Hu, C. S. Brower, H. Wang, I. V. Davydov, J. Sheng, J. Zhou, Y. T. Kwon, A. Varshavsky,. Arginyltransferase, its specificity, putative substrates, bidirectional promoter, and splicing-derived isoforms. J. Biol. Chem. 2006, 281, 32559.
9. A. Varshavsky,. The N-end rule pathway of protein degradation. Genes to Cells: Devoted to Molecular & Cellular Mechanisms 1997, 2, 13.
10. A. Varshavsky,. The N-end rule pathway and regulation by proteolysis. Protein Sci. 2011, 20, 1298.
11. H. A. Ebhardt, Z. Xu, A. W. Fung, R. P. Fahlman,. Quantification of the post-translational addition of amino acids to proteins by MALDI-TOF mass spectrometry. Anal. Chem. 2009, 81, 1937.
12. H. A. Ebhardt, E. Sabido, R. Huttenhain, B. Collins, R. Aebersold,. Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. Proteomics 2012, 12, 1185.
13. A. W. Fung, H. A. Ebhardt, K. S. Krishnakumar, J. Moore, Z. Xu, P. Strazewski, R. P. Fahlman,. Probing the leucyl/phenylalanyl tRNA protein transferase active site with tRNA substrate analogues. Protein Peptide Lett. 2014, 21, 603.
14. A. W. Fung, H. A. Ebhardt, H. Abeysundara, J. Moore, Z. Xu, R. P. Fahlman,. An alternative mechanism for the catalysis of peptide bond formation by L/F transferase: substrate binding and orientation. J. Mol. Biol. 2011, 409, 617.
15. A. Cornish-Bowden,. Fundamentals of Enzyme Kinetics. Butterworths, London, Boston, 1979.
16. B. Schilling, M. J. Rardin, B. X. MacLean, A. M. Zawadzka, B. E. Frewen, M. P. Cusack, D. J. Sorensen, M. S. Bereman, E. Jing, C. C. Wu, E. Verdin, C. R. Kahn, M. J. Maccoss, B. W. Gibson,. Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol. Cell. Proteomics 2012, 11, 202.
17. S. Saha, A. Kashina,. Posttranslational arginylation as a global biological regulator. Dev. Biol. 2011, 358, 1.
18. J. Wang, X. Han, C. C. Wong, H. Cheng, A. Aslanian, T. Xu, P. Leavis, H. Roder, L. Hedstrom, J. R. Yates 3rd, A. Kashina,. Arginyltransferase ATE1 catalyzes midchain arginylation of proteins at side chain carboxylates in vivo. Chem. Biol. 2014, 21, 331.
19. E. Graciet, R. G. Hu, K. Piatkov, J. H. Rhee, E. M. Schwarz, A. Varshavsky,. Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen. Proc. Natl. Acad. Sci. USA 2006, 103, 3078.
20. C. Tuerk, S. MacDougal, L. Gold,. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA 1992, 89, 6988.
21. S. E. St Pierre, L. Ponting, R. Stefancsik, P. McQuilton, C. FlyBase,. FlyBase 102-advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014, 42, D780.
22. S. Yooseph, G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, J. C. Venter,. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007, 5, e16.
23. S. Walter, T. Weinschenk, A. Stenzl, R. Zdrojowy, A. Pluzanska, C. Szczylik, M. Staehler, W. Brugger, P. Y. Dietrich, R. Mendrzyk, N. Hilf, O. Schoor, J. Fritsche, A. Mahr, D. Maurer, V. Vass, C. Trautwein, P. Lewandrowski, C. Flohr, H. Pohla, J. J. Stanczak, V. Bronte, S. Mandruzzato, T. Biedermann, G. Pawelec, E. Derhovanessian, H. Yamagishi, T. Miki, F. Hongo, N. Takaha, K. Hirakawa, H. Tanaka, S. Stevanovic, J. Frisch, A. Mayer-Mokler, A. Kirner, H. G. Rammensee, C. Reinhardt, H. Singh-Jasuja,. Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival. Nat. Med. 2012, 18, 1254.
24. T. Dumrese, S. Stevanovic, F. H. Seeger, N. Yamada, Y. Ishikawa, K. Tokunaga, M. Takiguchi, H. Rammensee,. HLA-A26 subtype A pockets accommodate acidic N-termini of ligands. Immunogenetics 1998, 48, 350.
25. A. Michalski, J. Cox, M. Mann,. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 2011, 10, 1785.
26. B. Meyer, D. G. Papasotiriou, M. Karas,. 100% protein sequence coverage: a modern form of surrealism in proteomics. Amino Acids 2011, 41, 291.
27. M. Konno, T. Sumida, E. Uchikawa, Y. Mori, T. Yanagisawa, S. Sekine, S. Yokoyama,. Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP). FEBS J. 2009, 276, 4763.
28. Available: https://daily.panoramaweb.org/labkey/arg-ms.url.