Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 3, 2013, Pages 444-449

  Merkley, Eric D ^a   Baker, Erin S ^a   Crowell, Kevin L ^a   Orton, Daniel J ^a   Taverner, Thomas ^b   Ansong, Charles ^a   Ibrahim, Yehia M ^a   Burnet, Meagan C ^a   Cort, John R ^a   Anderson, Gordon A ^a   Smith, Richard D ^a   Adkins, Joshua N ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b Mango Solutions   (United Kingdom)

Author keywords

Cross linked peptides; Cross linking; Drift time; Heavy isotope labeling; Ion mobility spectrometry; Liquid chromatography; Mass Spectrometry; Protein structure; Proteins

Indexed keywords

CHEMICAL CROSS-LINKING; DRIFT TIME; ION MOBILITY SPECTROMETRY; ISOTOPE LABELING; MASS SPECTROMETRIC ANALYSIS; PROTEIN STRUCTURES; PROTEIN-PROTEIN INTERACTIONS; QUATERNARY STRUCTURE;

AMINO ACIDS; CROSSLINKING; ISOTOPES; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PEPTIDES; PROTEINS; SEPARATION;

ION MOBILITY SPECTROMETERS;

BACTERIAL PROTEIN; DIMER; SRFN PROTEIN; UNCLASSIFIED DRUG;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ION MOBILITY SPECTROMETRY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PREDICTIVE VALUE; PROCESS DEVELOPMENT; PROTEIN CROSS LINKING; PROTEIN DETERMINATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RESIDUE ANALYSIS; SEPARATION TECHNIQUE; SEQUENCE ANALYSIS; SURFACE PROPERTY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CHROMATOGRAPHY, LIQUID; CROSS-LINKING REAGENTS; ISOTOPE LABELING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SHEWANELLA; TANDEM MASS SPECTROMETRY;

EID: 84875883313     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0565-x     Document Type: Article

References (30)

1. Rappsilber, J.: The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J. Struct. Biol. 173(3), 530-540 (2011)
2. Sinz, A.: Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25(4), 663-682 (2006)
3. 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. 9(8), 1634-1649 (2010)
4. Schilling, B.; Row, R.H.; Gibson, B.W.; Guo, X.; Young, M.M.: MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J. Am. Soc. Mass Spectrom. 14(8), 834-850 (2003)
5. Young, M.M.; Tang, N.; Hempel, J.C.; Oshiro, C.M.; Taylor, E.W.; Kuntz, I.D.; Gibson, B.W.; Dollinger, G.: High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 97(11), 5802-5806 (2000)
6. Walzthoeni, T.; Claassen, M.; Leitner, A.; Herzog, F.; Bohn, S.; Forster, F.; Beck, M.; Aebersold, R.: False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nat. Methods 9(9), 901-903 (2012)
7. 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 9(9), 904-906 (2012)
8. 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 337(6100), 1348-1352 (2012)
9. Taverner, T.; Hall, N.E.; O'Hair, R.A.J.; Simpson, R.J.: Characterization of an antagonist interleukin-6 dimer by stable isotope labeling, cross-linking, and mass spectrometry. J. Biol. Chem. 277(48), 46487-46492 (2002)
10. Santos, L.F.A.; Iglesias, A.H.; Pilau, E.J.; Gomes, A.F.; Gozzo, F.C.: Traveling-Wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from chemical cross-linking. J. Am. Soc. Mass Spectrom. 21(12), 2062-2069 (2010)
11. Smith, D.P.; Anderson, J.; Plante, J.; Ashcroft, A.E.; Radford, S.E.; Wilson, A.J.; Parker, M.J.: Trifluoromethyldiazirine: an effective photo-induced cross-linking probe for exploring amyloid formation. Chem. Commun. (44), 5728-5730 (2008)
12. Kindy, J.M.; Taraszka, J.A.; Regnier, F.E.; Clemmer, D.E.: Quantifying peptides in isotopically labeled protease digests by ion mobility/time-of-flight mass spectrometry. Anal. Chem. 74(5), 950-958 (2002)
13. Soderberg, C.A.G.; Lambert, W.; Kjellstrom, S.; Wiegandt, A.; Wulff, R.P.; Mansson, C.; Rutsdottir, G.; Emanuelsson, C.: Detection of Crosslinks within and between Proteins by LC-MALDI-TOFTOF and the Software FINDX to Reduce the MSMS-Data to Acquire for Validation. PLoS One 7(6), e38927 (2012)
14. Acton, T.B.; Xiao, R.; Anderson, S.; Aramini, J.; Buchwald, W.A.; Ciccosanti, C.; Conover, K.; Everett, J.; Hamilton, K.; Huang, Y.J.; Janjua, H.; Kornhaber, G.; Lau, J.; Lee, D.Y.; Liu, G.H.; Maglaqui, M.; Ma, L.C.; Mao, L.; Patel, D.; Rossi, P.; Sahdev, S.; Shastry, R.; Swapna, G.V.T.; Tang, Y.F.; Tong, S.C.; Wang, D.Y.; Wang, H.; Zhao, L.; Montelione, G.T.: Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol. 493, 21-60 (2011)
15. Cort, J.R.; Selan, U.; Schulte, A.; Grimm, F.; Kennedy, M.A.; Dahl, C.: Allochromatium vinosum DsrC: solution-state NMR structure, redox properties, and interaction with DsrEFH, a protein essential for purple sulfur bacterial sulfur oxidation. J. Mol. Biol. 382(3), 692-707 (2008)
16. Livesay, E.A.; Tang, K.; Taylor, B.K.; Buschbach, M.A.; Hopkins, D.F.; LaMarche, B.L.; Zhao, R.; Shen, Y.; Orton, D.J.; Moore, R.J.; Kelly, R.T.; Udseth, H.R.; Smith, R.D.: Fully Automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. Anal. Chem. 80(1), 294-302 (2007)
17. Ibrahim, Y.; Belov, M.E.; Tolmachev, A.V.; Prior, D.C.; Smith, R.D.: Ion funnel trap interface for orthogonal time-of-flight mass spectrometry. Anal. Chem. 79(20), 7845-7852 (2007)
18. Ibrahim, Y.M.; Prior, D.C.; Baker, E.S.; Smith, R.D.; Belov, M.E.: Characterization of an ion mobility-multiplexed collision-induced dissociation-tandem time-of-flight mass spectrometry approach. Int. J. Mass spectrom. 293(1/3), 34-44 (2010)
19. Jaitly, N.; Mayampurath, A.; Littlefield, K.; Adkins, J. N.; Anderson, G. A.; Smith, R. D.: Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinforma. 10(87), (2009)
20. Crowell K.L.; Shah, A.R.; Slysz, G.; Lamarche, B.L.; Meng, D.; Baker, E.S.; Monroe, M.E.; Anderson, G.A.; Smith, R.D.: LC-IMS-MS feature finder: detecting multidimensional features in IMS-TOF MS data. Proceedings of the American Society for Mass Spectrometry Conference, Denver, CO (June 2011).
21. Mädler, S.; Bich, C.; Touboul, D.; Zenobi, R.: Chemical cross-linking with NHS esters: a systematic study on amino acid reactivities. J. Mass Spectrom. 44(5), 694-706 (2009)
22. Kalkhof, S.; Sinz, A.: Chances and pitfalls of chemical cross-linking with amine-reactive N-hydroxysuccinimide esters. Anal. Bioanal. Chem. 392, 305-312 (2008)
23. Kahraman, A.; Malmström, L.; Aebersold, R.: Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics 27(15), 2163-2164 (2011)
24. 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. Proteom. 11(3) (2012)
25. Chen, Z.A.; Jawhari, A.; Fischer, L.; Buchen, C.; Tahir, S.; Kamenski, T.; Rasmussen, M.; Lariviere, L.; Bukowski-Wills, J.-C.; Nilges, M.; Cramer, P.; Rappsilber, J.: Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 29(4), 717-726 (2010)
26. Fabris, D.; Yu, E.T.: Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. J. Mass Spectrom. 45(8), 841-860 (2010)
27. Li, H.; Wells, S.A.; Jimenez-Roldan, J.E.; Römer, R.A.; Zhao, Y.; Sadler, P.J.; O'Connor, P.B.: Protein flexibility is key to cisplatin crosslinking in calmodulin. Protein Sci. 21(9), 1269-1279 (2012)
28. Valentine, S.J.; Counterman, A.E.; Hoaglund, C.S.; Reilly, J.P.; Clemmer, D.E.: Gas-phase separations of protease digests. J. Am. Soc. Mass Spectrom. 9(11), 1213-1216 (1998)
29. Woods, A.; Koomen, J.; Ruotolo, B.; Gillig, K.; Russel, D.; Fuhrer, K.; Gonin, M.; Egan, T.; Schultz, J.: A study of peptide-peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry. J. Am. Soc. Mass Spectrom. 13(2), 166-169 (2002)
30. Baker, E.S.; Livesay, E.A.; Orton, D.J.; Moore, R.J.; Danielson, W.F.; Prior, D.C.; Ibrahim, Y.M.; LaMarche, B.L.; Mayampurath, A.M.; Schepmoes, A.A.; Hopkins, D.F.; Tang, K.; Smith, R.D.; Belov, M.E.: An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J. Proteome Res. 9(2), 997-1006 (2009)