Analytical Chemistry
Article
linkers: d - and d -DMDSSO. DMDSSO cross-linked peptides
(11) Tang, X.; Munske, G. R.; Siems, W. F.; Bruce, J. E. Anal. Chem.
0
10
2
(
005, 77, 311−318.
preserve the same characteristic MS2 fragmentation patterns
distinctive to cross-link types as DSSO cross-linked peptides,
thus facilitating the detection and identification of cross-linked
peptides. In combination with MS3 sequencing, MS1 mass
mapping and isotopic profiling, the nature and identity of cross-
linked peptides can be determined readily and unambiguously.
This work further demonstrates the robustness of sulfoxide-
containing MS-cleavable cross-linkers in XL-MS studies and
provides a strong basis for us to further develop new DSSO
derivatives and fully define protein−protein interactions. In
addition, we have shown the flexibility in using d - and d -
12) Kao, A.; Chiu, C. L.; Vellucci, D.; Yang, Y.; Patel, V. R.; Guan,
S.; Randall, A.; Baldi, P.; Rychnovsky, S. D.; Huang, L. Mol. Cell.
Proteomics 2011, 10, M110 002212.
(
13) Back, J. W.; Notenboom, V.; de Koning, L. J.; Muijsers, A. O.;
Sixma, T. K.; de Koster, C. G.; de Jong, L. Anal. Chem. 2002, 74,
417−4422.
14) Muller, D. R.; Schindler, P.; Towbin, H.; Wirth, U.; Voshol, H.;
4
(
Hoving, S.; Steinmetz, M. O. Anal. Chem. 2001, 73, 1927−1934.
(15) Seebacher, J.; Mallick, P.; Zhang, N.; Eddes, J. S.; Aebersold, R.;
Gelb, M. H. J. Proteome Res. 2006, 5, 2270−2282.
(16) Krauth, F.; Ihling, C. H.; Ruttinger, H. H.; Sinz, A. Rapid
0
10
Commun. Mass Spectrom. 2009, 23, 2811−2818.
17) Petrotchenko, E. V.; Serpa, J. J.; Borchers, C. H. Mol. Cell.
Proteomics 2011, 10, M110 001420.
18) Rinner, O.; Seebacher, J.; Walzthoeni, T.; Mueller, L. N.; Beck,
M.; Schmidt, A.; Mueller, M.; Aebersold, R. Nat. Methods 2008, 5,
DMDSSO for quantitative analysis of cross-linked peptides,
thus establishing a solid foundation for our future studies
toward the understanding of structural dynamics of protein
complexes.
(
(
3
15−318.
ASSOCIATED CONTENT
Supporting Information
■
(19) Petrotchenko, E.; Borchers, C. BMC Bioinf. 2010, 11, 64.
(20) Yang, B.; Wu, Y. J.; Zhu, M.; Fan, S. B.; Lin, J.; Zhang, K.; Li, S.;
*
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. Nat.
Methods 2012, 9, 904−906.
(
21) Singh, P.; Shaffer, S. A.; Scherl, A.; Holman, C.; Pfuetzner, R. A.;
AUTHOR INFORMATION
949) 824-8540.
■
Larson Freeman, T. J.; Miller, S. I.; Hernandez, P.; Appel, R. D.;
Goodlett, D. R. Anal. Chem. 2008, 80, 8799−8806.
(22) Chu, F.; Baker, P. R.; Burlingame, A. L.; Chalkley, R. J. Mol. Cell.
Proteomics 2010, 9, 25−31.
*
(
(
23) Soderblom, E. J.; Goshe, M. B. Anal. Chem. 2006, 78, 8059−
068.
24) Lu, Y.; Tanasova, M.; Borhan, B.; Reid, G. E. Anal. Chem. 2008,
0, 9279−9287.
25) Leonard, N. M.; Brunckova, J. J. Org. Chem. 2011, 76, 9169−
174.
26) Lee, Y. J.; Lackner, L. L.; Nunnari, J. M.; Phinney, B. S. J.
Proteome Res. 2007, 6, 3908−3917.
Notes
8
(
8
(
9
(
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We wish to thank members of the Huang and Rychnovsky
Laboratory, especially Eric Novitsky, for their help during this
study. We would like to thank Prof. A. L. Burlingame, Drs.
Robert Chalkley, Shenheng Guan, and Peter Baker at UCSF for
using Protein Prospector. We would also like to thank Tonya
Second and Dr. Michael Senko at ThermoFisher Scientific for
their help in improving data acquisition. This work was
supported by National Institutes of Health Grants
RO1GM074830 and R21CA161807 to L.H., R01GM106003
to L.H. and S. R., and R01AI099190-01 to Haoping Liu.
REFERENCES
■
(
(
1) Wells, J. A.; McClendon, C. L. Nature 2007, 450, 1001−1009.
2) Guerrero, C.; Tagwerker, C.; Kaiser, P.; Huang, L. Mol. Cell.
Proteomics 2006, 5, 366−378.
3) Guerrero, C.; Milenkovic, T.; Przulj, N.; Kaiser, P.; Huang, L.
Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 13333−13338.
4) Fang, L.; Kaake, R. M.; Patel, V. R.; Yang, Y.; Baldi, P.; Huang, L.
Mol. Cell. Proteomics 2012, 11, 138−147.
5) Leitner, A.; Walzthoeni, T.; Kahraman, A.; Herzog, F.; Rinner,
O.; Beck, M.; Aebersold, R. Mol. Cell. Proteomics 2010, 9, 1634−1649.
6) Herzog, F.; Kahraman, A.; Boehringer, D.; Mak, R.; Bracher, A.;
(
(
(
(
Walzthoeni, T.; Leitner, A.; Beck, M.; Hartl, F. U.; Ban, N.;
Malmstrom, L.; Aebersold, R. Science 2012, 337, 1348−1352.
(
7) Lasker, K.; Forster, F.; Bohn, S.; Walzthoeni, T.; Villa, E.;
Unverdorben, P.; Beck, F.; Aebersold, R.; Sali, A.; Baumeister, W. Proc.
Natl. Acad. Sci. U.S.A. 2012, 109, 1380−1387.
(
8) Kao, A.; Randall, A.; Yang, Y.; Patel, V. R.; Kandur, W.; Guan, S.;
Rychnovsky, S. D.; Baldi, P.; Huang, L. Mol. Cell. Proteomics 2012, 11,
566−1577.
9) Kalisman, N.; Adams, C. M.; Levitt, M. Proc. Natl. Acad. Sci.
U.S.A. 2012, 109, 2884−2889.
10) Chu, F.; Mahrus, S.; Craik, C. S.; Burlingame, A. L. J. Am. Chem.
Soc. 2006, 128, 10362−10363.
1
(
(
2
106
dx.doi.org/10.1021/ac403636b | Anal. Chem. 2014, 86, 2099−2106