Enrichment of Cross-Linked Peptides Using Charge-Based Fractional Diagonal Chromatography (ChaFRADIC)

Journal of Proteome Research

Volumn 16, Issue 2, 2017, Pages 459-469

  Tinnefeld, Verena ^a   Venne, A Saskia ^a   Sickmann, Albert ^a,b,c   Zahedi, René P ^a  

^a LEIBNIZ INSTITUT FÜR ANALYTISCHE WISSENSCHAFTEN ISAS E V   (Germany)

^b UNIVERSITY OF ABERDEEN   (United Kingdom)

^c RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

ChaFRADIC; enrichment; mass spectrometry; protein cross linking; strong cation exchange chromatography

Indexed keywords

BIOTIN; PEPTIDE; BIS(SULFOSUCCINIMIDYL)SUBERATE; BOVINE SERUM ALBUMIN; CROSS LINKING REAGENT; DRUG MIXTURE; METALLOPROTEINASE; PEPTIDE FRAGMENT; PEPTIDYL-LYS METALLOENDOPEPTIDASE; SUCCINIMIDE DERIVATIVE;

ARTICLE; CELL LYSATE; CELL SIZE; CHARGE BASED FRACTIONAL DIAGONAL CHROMATOGRAPHY; CHROMATOGRAPHY; CROSS LINKING; ENRICHMENT CULTURE; HELA CELL LINE; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CROSS LINKING; SEPARATION TECHNIQUE; ANIMAL; BOVINE; CHEMISTRY; DRUG MIXTURE; HUMAN; ISOLATION AND PURIFICATION; PROCEDURES; PROTEIN DEGRADATION; STATIC ELECTRICITY;

ANIMALS; CATTLE; CHROMATOGRAPHY; CHROMATOGRAPHY, ION EXCHANGE; COMPLEX MIXTURES; CROSS-LINKING REAGENTS; HELA CELLS; HUMANS; METALLOENDOPEPTIDASES; PEPTIDE FRAGMENTS; PROTEOLYSIS; SERUM ALBUMIN, BOVINE; STATIC ELECTRICITY; SUCCINIMIDES;

EID: 85011702051     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.6b00587     Document Type: Article

References (23)

1. Leitner, A.; Walzthoeni, T.; Kahraman, A.; Herzog, F.; Rinner, O.; Beck, M.; Aebersold, R. Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics Mol. Cell. Proteomics 2010, 9, 1634-49 10.1074/mcp.R000001-MCP201
2. Sinz, A. Chemical cross-linking and mass spectreometry to map three-dimensional protein structures and protein-protein interactions Mass Spectrom. Rev. 2006, 25, 663 10.1002/mas.20082
3. Singh, P.; Panchaud, A.; Goodlett, D. R. Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique Anal. Chem. 2010, 82, 2636 10.1021/ac1000724
4. Rappsilber, J. The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and mutli-protein complexes J. Struct. Biol. 2011, 173 (3) 530-540 10.1016/j.jsb.2010.10.014
5. Mayne, S. L.; Patterton, H. G. Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links Briefings Bioinf. 2011, 12 (6) 660-671 10.1093/bib/bbq087
6. Ji, C.; Li, S.; Reilly, J. P.; Radivojac, P.; Tang, H. XL Search: a Probailiistic Database Search Algorithm for Identifying Cross-Linked Peptides J. Proteome Res. 2016, 15 (6) 1830-1841 10.1021/acs.jproteome.6b00004
7. Schweppe, D. K.; Chavez, J. D.; Navare, A. T.; Wu, X.; Ruiz, B.; Eng, J. K.; Lam, H.; Bruce, J. E. Spectral Library Searching To Identify Cross-Linked Peptides J. Proteome Res. 2016, 15 (5) 1725-31 10.1021/acs.jproteome.6b00014
8. Solari, A. S.; Dell'Aica, M.; Sickmann, A.; Zahedi, R. P. Why phosphoproteomics is still a challenge Mol. BioSyst. 2015, 11, 1487-93 10.1039/C5MB00024F
9. Leitner, A.; Reischl, R.; Walzthoeni, T.; Herzog, F.; Bohn, S.; Förster, F.; Aebersold, R. Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography Mol. Cell. Proteomics 2012, 11 (3) M111.014126 10.1074/mcp.M111.014126
10. Herzog, F.; Kahraman, A.; Boehringer, D.; Mak, R.; Bracher, A.; Walzthoeni, T.; Leitner, A.; Beck, M.; Hartl, F.-U.; Ban, N.; Malmström, L.; Aebersold, R. Structural Probing of a Protein Phosphatase 2A Network by chemical Cross-Linking and Mass Spectrometry Science 2012, 337, 1348-1352 10.1126/science.1221483
11. Rampler, E.; Stranzl, T.; Orban-Nemeth, Z.; Hollenstein, D. M.; Hudecz, O.; Schloegelhofer, P.; Mechtler, K. Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2-MND1 J. Proteome Res. 2015, 14, 5048 10.1021/acs.jproteome.5b00903
12. Petrotchenko, E. V.; Olkhovik, V. K.; Borchers, C. H. Isotopically Coded Cleavable Cross-linker for Studying Protein-Protein Interaction and Protein Complexes Mol. Cell. Proteomics 2005, 4 (8) 1167-1179 10.1074/mcp.T400016-MCP200
13. Tan, D.; Li, Q.; Zhang, M. J.; Liu, C.; Ma, C.; Zhang, P.; Ding, Y. H.; Fan, S. B.; Tao, L.; Yang, B.; Li, X.; Ma, S.; Liu, J.; Feng, B.; Liu, X.; Wang, H. W.; He, S. M.; Gao, N.; Ye, K.; Dong, M. Q.; Lei, X. Trifunctional cross-linker for mapping, protein-protein interaction networks and comparing protein conformational states eLife 2016, 5, 1-51 10.7554/eLife.12509
14. Fritzsche, R.; Ihling, C. H.; Götze, M.; Sinz, A. Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis Rapid Commun. Mass Spectrom. 2012, 26, 653-658 10.1002/rcm.6150
15. Taouatas, N.; Altelaar, A.F. M.; Drugan, M. M.; Helbig, A. O.; Mohammed, S.; Heck, A. J. R. Strong Cation Exchange-based Fractionation of Lys-N-generated Peptides Facilitates the Targeted Analysis of Post-translational Modifications Mol. Cell. Proteomics 2009, 8, 190-200 10.1074/mcp.M800285-MCP200
16. Buncherd, H.; Roseboom, W.; Ghavim, B.; Du, W.; de Koning, L. J.; de Koster, C. G.; de Jong, L. Isolation of cross-linked peptides by diagonal strong cation exchange chromatography for protein complex topology studies by peptide fragment fingerprinting from large sequence databases J. Chromatogr. A 2014, 1348, 34-46 10.1016/j.chroma.2014.04.083
17. Venne, S. A.; Vögtle, F.-N.; Meisinger, C.; Sickmann, A.; Zahedi, R. P. Novel Highly Sensitive, Specific and Straightforward Strategy for Comprehensive N-Terminal Proteomics Reveals Unknown Substrates of the Mitochondrial Peptidase Icp55 J. Proteomics Res. 2013, 12, 3823-3830 10.1021/pr400435d
18. Burkhart, J. M.; Schumbrutzki, C.; Wortelkamp, S.; Sickmann, A.; Zahedi, R. P. Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics J. Proteomics 2012, 75 (4) 1454-62 10.1016/j.jprot.2011.11.016
19. Larsen, M. R.; Thingholm, T. E.; Jensen, O. N.; Roepstorff, P.; Jorgensen, T. J. D. Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns Mol. Cell. Proteomics 2005, 4, 873-886 10.1074/mcp.T500007-MCP200
20. Yang, B.; Wu, Y. J.; Zhu, M.; Fan, S. B.; Lin, J.; Zhang, K.; Li, S.; Chi, H.; Li, Y. X.; Chen, H. F.; Luo, S. K.; Ding, Y. H.; Wang, L. H.; Hao, Z.; Xiu, L. Y.; Chen, S.; Ye, K.; He, S. M.; Dong, M. Q. Identification of cross-linked peptides from complex samples Nat. Methods 2012, 9 (9) 904-6 10.1038/nmeth.2099
21. Chambers, M. C.; Maclean, B.; Burke, R.; Amodei, D.; Ruderman, D. L.; Neumann, S.; Gatto, L.; Fischer, B.; Pratt, B.; Egertson, J.; Hoff, K.; Kessner, D.; Tasman, N.; Shulman, N.; Frewen, B.; Baker, T. A.; Brusniak, M. Y.; Paulse, C.; Creasy, D.; Flashner, L.; Kani, K.; Moulding, C.; Seymour, S. L.; Nuwaysir, L. M.; Lefebvre, B.; Kuhlmann, F.; Roark, J.; Rainer, P.; Detlev, S.; Hemenway, T.; Huhmer, A.; Langridge, J.; Connolly, B.; Chadick, T.; Holly, K.; Eckels, J.; Deutsch, E. W.; Moritz, R. L.; Katz, J. E.; Agus, D. B.; MacCoss, M.; Tabb, D. L.; Mallick, P. A cross-platform toolkit for mass spectrometry and proteomics Nat. Biotechnol. 2012, 30 (10) 918-20 10.1038/nbt.2377
22. Bujacz, A. Structures of bovine, equine and leporine serum albumin Acta Crystallogr., Sect. D: Biol. Crystallogr. 2012, 68 (10) 1278-89 10.1107/S0907444912027047
23. Vaudel, M.; Burkhart, J. M.; Sickmann, A.; Martens, L.; Zahedi, R. P. Peptide identification quality control Proteomics 2011, 11 (10) 2105-14 10.1002/pmic.201000704