Table of Contents
ISRN Computational Biology
Volume 2014 (2014), Article ID 960902, 7 pages
http://dx.doi.org/10.1155/2014/960902
Research Article

In Silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA

Received 4 February 2014; Accepted 17 March 2014; Published 22 April 2014

Academic Editors: Y. Cai and J. Ruan

Copyright © 2014 Jesse G. Meyer. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Y. Zhang, B. R. Fonslow, B. Shan, M.-C. Baek, and J. R. Yates, “Protein analysis by shotgun/bottom-up proteomics,” Chemical Reviews, vol. 113, no. 4, pp. 2343–2394, 2013. View at Publisher · View at Google Scholar
  2. B. Meyer, D. G. Papasotiriou, and M. Karas, “100% protein sequence coverage: a modern form of surrealism in proteomics,” Amino Acids, vol. 41, no. 2, pp. 291–310, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. J. M. Gilmore and M. P. Washburn, “Advances in shotgun proteomics and the analysis of membrane proteomes,” Journal of Proteomics, vol. 73, no. 11, pp. 2078–2091, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Rey, H. Mrázek, P. Pompach et al., “Effective removal of nonionic detergents in protein mass spectrometry, hydrogen/deuterium exchange, and proteomics,” Analytical Chemistry, vol. 82, no. 12, pp. 5107–5116, 2010. View at Publisher · View at Google Scholar · View at Scopus
  5. A. Motoyama and J. R. Yates III, “Multidimensional LC separations in shotgun proteomics,” Analytical Chemistry, vol. 80, no. 19, pp. 7187–7193, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. Y. Wang, F. Yang, M. A. Gritsenko et al., “Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells,” Proteomics, vol. 11, no. 10, pp. 2019–2026, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. L. H. Betancourt, P.-J. de Bock, A. Staes et al., “SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping,” Journal of Proteomics, vol. 91, pp. 164–171, 2013. View at Publisher · View at Google Scholar
  8. A. Michalski, E. Damoc, J.-P. Hauschild et al., “Mass spectrometry-based proteomics using Q exactive, a high-performance benchtop quadrupole orbitrap mass spectrometer,” Molecular & Cellular Proteomics, vol. 10, no. 9, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. J. V. Olsen, J. C. Schwartz, J. Griep-Raming et al., “A dual pressure linear ion trap orbitrap instrument with very high sequencing speed,” Molecular & Cellular Proteomics, vol. 8, no. 12, pp. 2759–2769, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. C. K. Frese, A. F. M. Altelaar, M. L. Hennrich et al., “Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap velos,” Journal of Proteome Research, vol. 10, no. 5, pp. 2377–2388, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. R. J. Chalkley, P. R. Baker, K. F. Medzihardszky, A. J. Lynn, and A. L. Burlingame, “In-depth analysis of tandem mass spectrometry data from disparate instrument types,” Molecular & Cellular Proteomics, vol. 7, no. 12, pp. 2386–2398, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. Y. Shen, N. Tolić, S. O. Purvine, and R. D. Smith, “Improving collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD) fourier transform MS/MS degradome-peptidome identifications using high accuracy mass information,” Journal of Proteome Research, vol. 11, no. 2, pp. 668–677, 2012. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Kim, N. Mischerikow, N. Bandeira et al., “The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search,” Molecular & Cellular Proteomics, vol. 9, no. 12, pp. 2840–2852, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Linnarsson, “Recent advances in DNA sequencing methods—general principles of sample preparation,” Experimental Cell Research, vol. 316, no. 8, pp. 1339–1343, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. B. Rietschel, T. N. Arrey, B. Meyer et al., “Elastase digests: new ammunition for shotgun membrane proteomics,” Molecular & Cellular Proteomics, vol. 8, no. 5, pp. 1029–1043, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. G. Choudhary, S.-L. Wu, P. Shieh, and W. S. Hancock, “Multiple enzymatic digestion for enhanced sequence coverage of proteins in complex proteomic mixtures using capillary LC with ion trap MS/MS,” Journal of Proteome Research, vol. 2, no. 1, pp. 59–67, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. H. Moura, R. R. Terilli, A. R. Woolfitt et al., “Proteomic analysis and label-free quantification of the large Clostridium difficile toxins,” International Journal of Proteomics, vol. 2013, Article ID 293782, 10 pages, 2013. View at Publisher · View at Google Scholar
  18. B. Q. Tran, C. Hernandez, P. Waridel et al., “Addressing trypsin bias in large scale (Phospho)proteome analysis by size exclusion chromatography and secondary digestion of large post-trypsin peptides,” Journal of Proteome Research, vol. 10, no. 2, pp. 800–811, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. N. Neuhauser, N. Nagaraj, P. McHardy et al., “High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome,” Journal of Proteome Research, vol. 12, no. 6, pp. 2858–2868, 2013. View at Publisher · View at Google Scholar
  20. D. L. Swaney, C. D. Wenger, and J. J. Coon, “Value of using multiple proteases for large-scale mass spectrometry-based proteomics,” Journal of Proteome Research, vol. 9, no. 3, pp. 1323–1329, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. J. R. Wiśniewski and M. Mann, “Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis,” Analytical Chemistry, vol. 84, no. 6, pp. 2631–2637, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. J. R. Wiśniewski, A. Zougman, N. Nagaraj, and M. Mann, “Universal sample preparation method for proteome analysis,” Nature Methods, vol. 6, no. 5, pp. 359–362, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. R Development Core Team, R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, 2008.
  24. D. L. Crimmins, S. M. Mische, and N. D. Denslow, “Chemical cleavage of proteins in solution,” in Current Protocols in Protein Science, John Wiley & Sons, New York, NY, USA, 2001. View at Google Scholar
  25. R. Kaiser and L. Metzka, “Enhancement of cyanogen bromide cleavage yields for methionyl-serine and methionyl-threonine peptide bonds,” Analytical Biochemistry, vol. 266, no. 1, pp. 1–8, 1999. View at Publisher · View at Google Scholar · View at Scopus
  26. Y. A. Andreev, S. A. Kozlov, A. A. Vassilevski, and E. V. Grishin, “Cyanogen bromide cleavage of proteins in salt and buffer solutions,” Analytical Biochemistry, vol. 407, no. 1, pp. 144–146, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. M. M. Vestling, M. A. Kelly, and C. Fenselau, “Optimization by mass spectrometry of a tryptophan-specific protein cleavage reaction,” Rapid Communications in Mass Spectrometry, vol. 8, no. 9, pp. 786–790, 1994. View at Google Scholar · View at Scopus
  28. G. R. Jacobson, M. H. Schaffer, G. R. Stark, and T. C. Vanaman, “Specific chemical cleavage in high yield at the amino peptide bonds of cysteine and cystine residues,” The Journal of Biological Chemistry, vol. 248, no. 19, pp. 6583–6591, 1973. View at Google Scholar · View at Scopus
  29. M. Iwasaki, T. Masuda, M. Tomita, and Y. Ishihama, “Chemical cleavage-assisted tryptic digestion for membrane proteome analysis,” Journal of Proteome Research, vol. 8, no. 6, pp. 3169–3175, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. J. G. Meyer, S. Kim, D. Maltby, M. Ghassemian, N. Bandeira, and E. A. Komives, “Expanding proteome coverage with orthogonal-specificity alpha-lytic proteases,” Molecular & Cellular Proteomics, vol. 13, no. 3, pp. 823–835, 2014. View at Google Scholar
  31. J. R. Wiśniewski, D. F. Zielinska, and M. Mann, “Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method,” Analytical Biochemistry, vol. 410, no. 2, pp. 307–309, 2011. View at Publisher · View at Google Scholar · View at Scopus
  32. J. E. P. Syka, J. J. Coon, M. J. Schroeder, J. Shabanowitz, and D. F. Hunt, “Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 26, pp. 9528–9533, 2004. View at Publisher · View at Google Scholar · View at Scopus