Corrigendum: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry (Nature Methods (2015) 12 (1179-1184) DOI: 10.1038/nmeth.3603);Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

Nature Methods

Volumn 12, Issue 12, 2015, Pages 1179-1184

  Liu, Fan ^a,b   Rijkers, Dirk T S ^c   Post, Harm ^a,b   Heck, Albert J R ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CORE PROTEIN; ELONGATION FACTOR 2; LYSINE; PLASMINOGEN ACTIVATOR INHIBITOR 1; PROTEOME; RIBOSOME PROTEIN; RNA BINDING PROTEIN; CROSS LINKING REAGENT; MULTIPROTEIN COMPLEX;

AMINO ACID SEQUENCE; ARTICLE; CATION EXCHANGE; CELL LYSATE; CHROMATIN CONDENSATION; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRON MICROSCOPY; FEMALE; HELA CELL LINE; HUMAN; HUMAN CELL; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN CROSS LINKING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; RIBOSOME; RNA SPLICING; SIZE EXCLUSION CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY; CHEMICAL STRUCTURE; CHEMISTRY; DEVICES; PROCEDURES; PROTEIN DATABASE; REPRODUCIBILITY;

CROSS-LINKING REAGENTS; DATABASES, PROTEIN; HELA CELLS; HUMANS; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; RIBOSOMAL PROTEINS; TANDEM MASS SPECTROMETRY;

EID: 84949106630     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth0517-539     Document Type: Erratum

References (37)

1. Robinson, C.V., Sali, A., & Baumeister, W. The molecular sociology of the cell. Nature 450, 973-982 (2007
2. Bruce, J.E. In vivo protein complex topologies: sights through a cross-linking lens. Proteomics 12, 1565-1575 (2012
3. Rappsilber, J. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J. Struct. Biol. 173, 530-540 (2011
4. Sinz, A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682 (2006
5. Sinz, A. The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks. Expert Rev. Proteomics 11, 733-743 (2014
6. Chen, Z.A., et al. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 29, 717-726 (2010
7. Lauber, M.A., & Reilly, J.P. Structural analysis of a prokaryotic ribosome using a novel amidinating cross-linker and mass spectrometry. J. Proteome Res. 10, 3604-3616 (2011
8. Kao, A., et al. Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling. Mol. Cell. Proteomics 11, 1566-1577 (2012
9. Leitner, A., et al. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure 20, 814-825 (2012
10. Erzberger, J.P., et al. Molecular architecture of the 40S eIF1 eIF3 translation initiation complex. Cell 158, 1123-1135 (2014
11. Martinez-Rucobo, F.W., et al. Molecular basis of transcription-coupled pre-mRNA capping. Mol. Cell 58, 1079-1089 (2015
12. Arlt, C., Ihling, C.H., & Sinz, A. Structure of full-length p53 tumor suppressor probed by chemical cross-linking and mass spectrometry. Proteomics 15, 2746-2755 (2015
13. Plaschka, C., et al. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature 518, 376-380 (2015
14. Benda, C., et al. Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4. Mol. Cell 56, 43-54 (2014
15. Greber, B.J., et al. Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature 505, 515-519 (2014
16. Guerrero, C., Milenkovic, T., Przulj, N., Kaiser, P., & Huang, L. Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis. Proc. Natl. Acad. Sci. USA 105, 13333-13338 (2008
17. Herzog, F., et al. Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science 337, 1348-1352 (2012
18. Rinner, O., et al. Identification of cross-linked peptides from large sequence databases. Nat. Methods 5, 315-318 (2008
19. Yang, B., et al. Identification of cross-linked peptides from complex samples. Nat. Methods 9, 904-906 (2012
20. Trnka, M.J., Baker, P.R., Robinson, P.J.J., Burlingame, A.L., & Chalkley, R.J. Matching cross-linked peptide spectra: only as good as the worse identification. Mol. Cell. Proteomics 13, 420-434 (2014
21. Kao, A., et al. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol. Cell. Proteomics 10, M110.002212 (2011
22. Soderblom, E.J., & Goshe, M.B. Collision-induced dissociative chemical cross-linking reagents and methodology: applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 78, 8059-8068 (2006
23. Buncherd, H., Roseboom, W., de Koning, L.J., de Koster, C.G., & De Jong, L. A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database. J. Proteomics 108, 65-77 (2014
24. Müller, M.Q., Dreiocker, F., Ihling, C.H., Schäfer, M., & Sinz, A. Cleavable cross-linker for protein structure analysis: reliable identification of cross-linking products by tandem MS. Anal. Chem. 82, 6958-6968 (2010
25. Petrotchenko, E.V., Serpa, J.J., & Borchers, C.H. An isotopically coded CID-cleavable biotinylated cross-linker for structural proteomics. Mol. Cell. Proteomics 10, M110.001420 (2011
26. Weisbrod, C.R., et al. In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy. J. Proteome Res. 12, 1569-1579 (2013
27. Chavez, J.D., Weisbrod, C.R., Zheng, C., Eng, J.K., & Bruce, J.E. Protein interactions, post-translational modifications and topologies in human cells. Mol. Cell. Proteomics 12, 1451-1467 (2013
28. Navare, A.T., et al. Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry. Structure 23, 762-773 (2015
29. Götze, M., et al. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. J. Am. Soc. Mass Spectrom. 26, 83-97 (2015
30. Meng, F., et al. Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat. Biotechnol. 19, 952-957 (2001
31. Anger, A.M., et al. Structures of the human and Drosophila 80S ribosome. Nature 497, 80-85 (2013
32. Budkevich, T.V., et al. Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell 158, 121-131 (2014
33. Tange, T.Ø., Shibuya, T., Jurica, M.S., & Moore, M.J. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11, 1869-1883 (2005
34. Kulak, N.A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat. Methods 11, 319-324 (2014
35. Combe, C.W., Fischer, L., & Rappsilber, J. xiNET: cross-link network maps with residue resolution. Mol. Cell. Proteomics 14, 1137-1147 (2015
36. Liu, F., van Breukelen, B., & Heck, A.J. Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Mol. Cell. Proteomics 13, 2776-2786 (2014
37. Liu, F., & Goshe, M.B. Combinatorial electrostatic collision-induced dissociative chemical cross-linking reagents for probing protein surface topology. Anal. Chem. 82, 6215-6223 (2010