Decoding Split and Pool Combinatorial Libraries with Electron-Transfer Dissociation Tandem Mass Spectrometry
详细信息 查看全文
- 作者：Mohosin Sarkar (1)
Bruce D. Pascal (3) (4)
Caitlin Steckler (4)
Claudio Aquino (1)
Glenn C. Micalizio (1)
Thomas Kodadek (1) (2)
Michael J. Chalmers (4) (5) - 关键词：MS ; MS/MS ; ETD ; ECD ; COPA ; Combinatorial library ; Split and pool synthesis
- 刊名：Journal of The American Society for Mass Spectrometry
- 出版年：2013
- 出版时间：July 2013
- 年：2013
- 卷：24
- 期：7
- 页码：1026-1036
- 全文大小：714KB
- 参考文献：1. Lam, K.S., Salmon, S.E., Hersh, E.M., Hruby, V.J., Kazmierski, W.M., Knapp, R.J.: A new type of synthetic peptide library for identifying ligand-binding activity. / Nature 354, 82-4 (1991) CrossRef
2. Lam, K.S., Lebl, M., Krchnak, V.: The "one-bead-one-compound" combinatorial library method. / Chem. Rev. 97, 411-48 (1997) CrossRef
3. Ramnarayanan, R., Chan, B.C., Salvitti, M.A., Mallouk, T.E., Falih, F.M., Davis, J., Galloway, D.B., Bare, S.R., Willis, R.R.: Directed-sorting method for synthesis of bead-based combinatorial libraries of heterogeneous catalysts. / J. Combinat. Chem. 8, 199-12 (2006) CrossRef
4. 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. Combinat. Chem. 11, 294-02 (2009) CrossRef
5. Simpson, L.S., Kodadek, T.: A cleavable scaffold strategy for the synthesis of one-bead one-compound cyclic peptoid libraries that can be sequenced by tandem mass spectrometry. / Tetrahedron Lett. 53, 2341-344 (2012) CrossRef
6. Aditya, A., Kodadek, T.: Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries. / ACS Combinat. Sci. 14, 164-69 (2012) CrossRef
7. Ruijtenbeek, R., Versluis, C., Heck, A.J., Redegeld, F.A., Nijkamp, F.P., Liskamp, R.M.: Characterization of a phosphorylated peptide and peptoid and peptoid-peptide hybrids by mass spectrometry. / J. Mass Spectrom. 37, 47-5 (2002) CrossRef
8. Syka, J.E., Coon, J.J., Schroeder, M.J., Shabanowitz, J., Hunt, D.F.: Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. / Proc. Natl. Acad. Sci. USA 101, 9528-533 (2004) CrossRef
9. Zubarev, R.A., Kelleher, N.L., McLafferty, F.W.: Electron capture dissociation of multiply charged protein cations. A nonergodic process. / J. Am. Chem. Soc. 120, 3265-266 (1998) CrossRef
10. Udeshi, N.D., Shabanowitz, J., Hunt, D.F., Rose, K.L.: Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS. / FEBS J. 274, 6269-276 (2007) CrossRef
11. Cooper, H.J., Hakansson, K., Marshall, A.G.: The role of electron capture dissociation in biomolecular analysis. / Mass Spectrom. Rev. 24, 201-22 (2005) CrossRef
12. Hakansson, K., Chalmers, M.J., Quinn, J.P., McFarland, M.A., Hendrickson, C.L., Marshall, A.G.: Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. / Anal. Chem. 75, 3256-262 (2003) CrossRef
13. Wiesner, J., Premsler, T., Sickmann, A.: Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. / Proteomics 8, 4466-483 (2008) CrossRef
14. Chalmers, M.J., Hakansson, K., Johnson, R., Smith, R., Shen, J.W., Emmett, M.R., Marshall, A.G.: Protein kinase A phosphorylation characterized by tandem Fourier transform ion cyclotron resonance mass spectrometry. / Proteomics 4, 970-81 (2004) CrossRef
15. Swaney, D.L., McAlister, G.C., Wirtala, M., Schwartz, J.C., Syka, J.E., Coon, J.J.: Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. / Anal. Chem. 79, 477-85 (2007) CrossRef
16. Aquino, C., Sarkar, M., Chalmers, M.J., Mendes, K., Kodadek, T., Micalizio, G.: A biomimetic polyketide-inspired approach to small-molecule ligand discovery. / Nat. Chem. 4, 99-04 (2012) CrossRef
17. Burkoth, T.S., Fafarman, A.T., Charych, D.H., Connolly, M.D., Zuckermann, R.N.: Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis. / J. Am. Chem. Soc. 125, 8841-845 (2003) CrossRef
18. Olivos, H.J., Alluri, P.G., Reddy, M.M., Salony, D., Kodadek, T.: Microwave-assisted solid-phase synthesis of peptoids. / Org. Lett. 4, 4057-059 (2002) CrossRef
19. Zuckermann, R.N., Kerr, J.M., Kent, S.B.H., Moos, W.H.: Efficient method for the preparation of peptoids [oligo( / N-substituted glycines)] by submonomer solid-phase synthesis. / J. Am. Chem. Soc. 114, 10646-0647 (1992) CrossRef
20. Rockwood, A.L., Haimi, P.: Efficient calculation of accurate masses of isotopic peaks. / J. Am. Soc. Mass Spectrom. 17, 415-19 (2006) CrossRef
21. Rockwood, A.L., Van Orman, J.R., Dearden, D.V.: Isotopic compositions and accurate masses of single isotopic peaks. / J. Am. Soc. Mass Spectrom. 15, 12-1 (2004) CrossRef
22. Roepstorff, P., Fohlman, J.: Letter to the editors. / Biol. Mass Spectrom. 11, 601-01 (1984) CrossRef - 作者单位：Mohosin Sarkar (1)
Bruce D. Pascal (3) (4)
Caitlin Steckler (4)
Claudio Aquino (1)
Glenn C. Micalizio (1)
Thomas Kodadek (1) (2)
Michael J. Chalmers (4) (5)
1. Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
3. TRI Informatics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
4. Mass Spectrometry and Proteomics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
2. Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
5. Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
文摘
Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening “hit-are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described “chiral oligomers of pentenoic amides (COPAs)-yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated 79Br/81Br isotope “tags-to differentiate N- and C-terminal product ions. In addition, we have created “Hit-Find,-a software program that allows users to generate libraries in silico. The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.