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

Volumn 7, Issue 6, 2012, Pages

  Söderberg, Christopher A G ^a   Lambert, Wietske ^a   Kjellström, Sven ^a   Wiegandt, Alena ^a   Wulff, Ragna Peterson ^a   Månsson, Cecilia ^a   Rutsdottir, Gudrun ^a   Emanuelsson, Cecilia ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; NITROGEN; NITROGEN 15; PROTEIN HSP21; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER PROGRAM; DATA PROCESSING; ISOTOPE LABELING; LC MALDI TOFTOF MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; TANDEM MASS SPECTROMETRY; VALIDITY; WORKFLOW;

ISOTOPE LABELING; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PEPTIDES; PROTEIN CONFORMATION; PROTEIN SUBUNITS; PROTEINS; REPRODUCIBILITY OF RESULTS; SOFTWARE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84862499676     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038927     Document Type: Article

References (27)

1. Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, et al. (2010) Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics 9: 1634-1649.
2. Singh P, Panchaud A, Goodlett DR, (2010) Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique. Anal Chem 82: 2636-2642.
3. Sinz A, (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom Rev 25: 663-682.
4. Stengel F, Aebersold R, Robinson CV, (2012) Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 11: R111 014027.
5. Schilling B, Row RH, Gibson BW, Guo X, Young MM, (2003) MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J Am Soc Mass Spectrom 14: 834-850.
6. Nooren IM, Thornton JM, (2003) Diversity of protein-protein interactions. Embo J 22: 3486-3492.
7. Vaynberg J, Qin J, (2006) Weak protein-protein interactions as probed by NMR spectroscopy. Trends Biotechnol 24: 22-27.
8. Muller DR, Schindler P, Towbin H, Wirth U, Voshol H, et al. (2001) Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal Chem 73: 1927-1934.
9. Petrotchenko E, Borchers C, (2010) Crosslinking combined with mass spectrometry for structural proteomics. Mass Spectrom Reviews 29: 862-876.
10. Mayne SL, Patterton HG, (2011) Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links. Brief Bioinform 12: 660-671.
11. Rasmussen MI, Refsgaard JC, Peng L, Houen G, Hojrup P, (2011) CrossWork: software-assisted identification of cross-linked peptides. J Proteomics 74: 1871-1883.
12. Gotze M, Pettelkau J, Schaks S, Bosse K, Ihling CH, et al. (2012) StavroX- a software for analyzing crosslinked products in protein interaction studies. J Am Soc Mass Spectrom 23: 76-87.
13. Lambert W, Soderberg CA, Rutsdottir G, Boelens WC, Emanuelsson C, (2011) Thiol-exchange in DTSSP crosslinked peptides is proportional to cysteine content and precisely controlled in crosslink detection by two-step LC-MALDI MSMS. Protein Sci 20: 1682-1691.
14. Nagaraj N, Alexander Kulak N, Cox J, Neuhauser N, Mayr K, et al. (2011) System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap. Mol Cell Proteomics 11: M111 013722.
15. Zhang R, Sioma CS, Wang S, Regnier FE, (2001) Fractionation of isotopically labeled peptides in quantitative proteomics. Anal Chem 73: 5142-5149.
16. Ahrman E, Lambert W, Aquilina JA, Robinson CV, Emanuelsson CS, (2007) Chemical cross-linking of the chloroplast localized small heat-shock protein, Hsp21, and the model substrate citrate synthase. Protein Sci 16: 1464-1478.
17. Baldwin AJ, Lioe H, Hilton GR, Baker LA, Rubinstein JL, et al. (2011) The polydispersity of alphaB-crystallin is rationalized by an interconverting polyhedral architecture. Structure 19: 1855-1863.
18. Taverner T, Hall NE, O'Hair RA, Simpson RJ, (2002) Characterization of an antagonist interleukin-6 dimer by stable isotope labeling, cross-linking, and mass spectrometry. J Biol Chem 277: 46487-46492.
19. Lambert W, Koeck PJ, Ahrman E, Purhonen P, Cheng K, et al. (2011) Subunit arrangement in the dodecameric chloroplast small heat shock protein Hsp21. Protein Sci 20: 291-301.
20. Andersson FI, Tryggvesson A, Sharon M, Diemand AV, Classen M, et al. (2009) Structure and function of a novel type of ATP-dependent Clp protease. J Biol Chem 284: 13519-13532.
21. Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, et al. (2008) Identification of cross-linked peptides from large sequence databases. Nat Methods 5: 315-318.
22. Stoscheck CM, (1990) Quantitation of protein. Methods Enzymol 182: 50-68.
23. Peri S, Steen H, Pandey A, (2001) GPMAW-a software tool for analyzing proteins and peptides. Trends Biochem Sci 26: 687-689.
24. Basha E, O'Neill H, Vierling E, (2012) Small heat shock proteins and alpha-crystallins: dynamic proteins with flexible functions. Trends Biochem Sci 37: 106-117.
25. Painter AJ, Jaya N, Basha E, Vierling E, Robinson CV, et al. (2008) Real-time monitoring of protein complexes reveals their quaternary organization and dynamics. Chem Biol 15: 246-253.
26. Van Montfort R, Slingsby C, Vierling E, (2001) Structure and function of the small heat shock protein/alpha-crystallin family of molecular chaperones. Adv Protein Chem 59: 105-156.
27. Guex N, Peitsch MC, (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723.