Matching cross-linked peptide spectra: Only as good as the worse identification

Molecular and Cellular Proteomics

Volumn 13, Issue 2, 2014, Pages 420-434

  Trnka, Michael J ^a   Baker, Peter R ^a   Robinson, Philip J J ^b   Burlingame, A L ^a   Chalkley, Robert J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE; ELONGATION FACTOR TU; RIBOSOME RNA; RNA POLYMERASE II;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN CROSS LINKING; PROTEIN INTERACTION; RIBOSOME SUBUNIT; SACCHAROMYCES CEREVISIAE; SUPPORT VECTOR MACHINE;

ALGORITHMS; AMINO ACID SEQUENCE; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTATIONAL BIOLOGY; CROSS-LINKING REAGENTS; DATABASES, PROTEIN; HUMANS; MASS SPECTROMETRY; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN;

EID: 84893336659     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.034009     Document Type: Article

References (41)

1. Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., and Aebersold, R. (2010) Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol. Cell. Proteomics 9, 1634-1649
2. Rappsilber, J. (2011) The beginning of a beautiful friendship: cross-linking/ mass spectrometry and modelling of proteins and multi-protein complexes. J. Struct. Biol. 173, 530-540
3. Stengel, F., Aebersold, R., and Robinson, C. V. (2012) Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol. Cell. Proteomics 11, R111.014027
4. Murakami, K., Elmlund, H., Kalisman, N., Bushnell, D. A., Adams, C. M., Azubel, M., Elmlund, D., Levi-Kalisman, Y., Liu, X., Gibbons, B. J., Levitt, M., and Kornberg, R. D. (2013) Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342, 1238724
5. Nguyen, V. Q., Ranjan, A., Stengel, F., Wei, D., Aebersold, R., Wu, C., and Leschziner, A. E. (2013) Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell 154, 1220-1231
6. Tosi, A., Haas, C., Herzog, F., Gilmozzi, A., Berninghausen, O., Ungewickell, C., Gerhold, C. B., Lakomek, K., Aebersold, R., Beckmann, R., and Hopfner, K.-P. (2013) Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 154, 1207-1219
7. Lasker, K., Förster, F., Bohn, S., Walzthoeni, T., Villa, E., Unverdorben, P., Beck, F., Aebersold, R., Sali, A., and Baumeister, W. (2012) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc. Natl. Acad. Sci. U.S.A. 109, 1380-1387
8. Larivie re, L., Plaschka, C., Seizl, M., Petrotchenko, E. V., Wenzeck, L., Borchers, C. H., and Cramer, P. (2013) Model of the Mediator middle module based on protein cross-linking. Nucleic Acids Res. 41, 9266-9273
9. Kalisman, N., Adams, C. M., and Levitt, M. (2012) Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling. Proc. Natl. Acad. Sci. U.S.A. 109, 2884-2889
10. Leitner, A., Joachimiak, L. A., Bracher, A., Mönkemeyer, L., Walzthoeni, T., Chen, B., Pechmann, S., Holmes, S., Cong, Y., Ma, B., Ludtke, S., Chiu, W., Hartl, F. U., Aebersold, R., and Frydman, J. (2012) The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure 20, 814-825
11. Robinson, P. J. J., Bushnell, D. A., Trnka, M. J., Burlingame, A. L., and Kornberg, R. D. (2012) Structure of the Mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A. 109, 17931-17935
12. Lauber, M. A., Rappsilber, J., and Reilly, J. P. (2012) Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Mol. Cell. Proteomics 11, 1965-1976
13. 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., and Rappsilber, J. (2010) Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 29, 717-726
14. Tang, X., Munske, G. R., Siems, W. F., and Bruce, J. E. (2005) Mass spectrometry identifiable cross-linking strategy for studying protein-protein interactions. Anal. Chem. 77, 311-318
15. Soderblom, E. J., and Goshe, M. B. (2006) Collision-induced dissociative chemical cross-linking reagents and methodology: applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 78, 8059-8068
16. Kao, A., Chiu, C., Vellucci, D., Yang, Y., Patel, V. R., Guan, S., Randall, A., Baldi, P., Rychnovsky, S. D., and Huang, L. (2011) Development of a novel cross-linking strategy for fast and accurate identification of crosslinked peptides of protein complexes. Mol. Cell. Proteomics 10, M110.002212
17. Liu, F., Wu, C., Sweedler, J. V., and Goshe, M. B. (2012) An enhanced protein crosslink identification strategy using CID-cleavable chemical crosslinkers and LC/MSn analysis. Proteomics 12, 401-405
18. Luo, J., Fishburn, J., Hahn, S., and Ranish, J. (2012) An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol. Cell. Proteomics 11, M111.008318
19. Maiolica, A., Cittaro, D., Borsotti, D., Sennels, L., Ciferri, C., Tarricone, C., Musacchio, A., and Rappsilber, J. (2007) Structural analysis of multiprotein complexes by cross-linking, mass spectrometry, and database searching. Mol. Cell. Proteomics 6, 2200-2211
20. Rinner, O., Seebacher, J., Walzthoeni, T., Mueller, L., Beck, M., Schmidt, A., Mueller, M., and Aebersold, R. (2008) Identification of cross-linked peptides from large sequence databases. Nat. Methods 5, 315-318
21. Panchaud, A., Singh, P., Shaffer, S. A., and Goodlett, D. R. (2010) xComb: a cross-linked peptide database approach to protein-protein interaction analysis. J. Proteome Res. 9, 2508-2515
22. Xu, H., Hsu, P.-H., Zhang, L., Tsai, M.-D., and Freitas, M. A. (2010) Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry. J. Proteome Res. 9, 3384-3393
23. Chu, F., Baker, P. R., Burlingame, A. L., and Chalkley, R. J. (2010) Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. Mol. Cell. Proteomics 9, 25-31
24. Singh, P., Shaffer, S. A., Scherl, A., Holman, C., Pfuetzner, R. A., Larson Freeman, T. J., Miller, S. I., Hernandez, P., Appel, R. D., and Goodlett, D. R. (2008) Characterization of protein cross-links via mass spectrometry and an open-modification search strategy. Anal. Chem. 80, 8799-8806
25. 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., and Dong, M.-Q. (2012) Identification of cross-linked peptides from complex samples. Nat. Methods 9, 904-906
26. Senko, M. W., Beu, S. C., and McLafferty, F. W. (1995) Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6, 229-233
27. Walzthoeni, T., Claassen, M., Leitner, A., Herzog, F., Bohn, S., Förster, F., Beck, M., and Aebersold, R. (2012) False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nat. Methods 9, 901-903
28. Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
29. Schilling, B., Row, R. H., Gibson, B. W., Guo, X., and Young, M. M. (2003) MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J. Am. Soc. Mass Spectrom. 14, 834-850
30. Iglesias, A. H., Santos, L. F. A., and Gozzo, F. C. (2009) Collision-induced dissociation of lys-lys intramolecular crosslinked peptides. J. Am. Soc. Mass Spectrom. 20, 557-566
31. Chalkley, R. J., Baker, P. R., Medzihradszky, K. F., Lynn, A. J., and Burlingame, A. L. (2008) In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol. Cell. Proteomics 7, 2386-2398
32. Chalkley, R. J., Baker, P. R., Huang, L., Hansen, K. C., Allen, N. P., Rexach, M., and Burlingame, A. L. (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer II. New developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol. Cell. Proteomics 4, 1194-1204
33. Baker, P. R., Medzihradszky, K. F., and Chalkley, R. J. (2010) Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring. Mol. Cell. Proteomics 9, 1795-1803
34. Guan, S., Price, J. C., Prusiner, S. B., Ghaemmaghami, S., and Burlingame, A. L. (2011) A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol. Cell. Proteomics 10, M111.010728
35. Hoopmann, M. R., Finney, G. L., and MacCoss, M. J. (2007) High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal. Chem. 79, 5620-5632
36. Armache, K.-J., Mitterweger, S., Meinhart, A., and Cramer, P. (2005) Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J. Biol. Chem. 280, 7131-7134
37. Krogan, N. J., Peng, W.-T., Cagney, G., Robinson, M. D., Haw, R., Zhong, G., Guo, X., Zhang, X., Canadien, V., Richards, D. P., Beattie, B. K., Lalev, A., Zhang, W., Davierwala, A. P., Mnaimneh, S., Starostine, A., Tikuisis, A. P., Grigull, J., Datta, N., Bray, J. E., Hughes, T. R., Emili, A., and Greenblatt, J. F. (2004) High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13, 225-239
38. Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., and Emili, A. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537
39. Chalkley, R. J. (2013) When target-decoy false discovery rate estimations are inaccurate and how to spot instances. J. Proteome Res. 12, 1062-1064
40. Su, C., Peregrin-Alvarez, J. M., Butland, G., Phanse, S., Fong, V., Emili, A., and Parkinson, J. (2008) Bacteriome.org - an integrated protein interaction database for E. coli. Nucleic Acids Res. 36, D632-D636
41. Trnka, M. J., and Burlingame, A. L. (2010) Topographic studies of the GroEL-GroES chaperonin complex by chemical cross-linking using diformyl ethynylbenzene. Mol. Cell. Proteomics 9, 2306-2317