Expanding the zebrafish embryo proteome using multiple fractionation approaches and tandem mass spectrometry

Proteomics

Volumn 12, Issue 11, 2012, Pages 1879-1882

  Lößner, Christopher ^a   Wee, Sheena ^a   Ler, Siok Ghee ^a   Li, Rachel H X ^a   Carney, Tom ^a   Blackstock, Walter ^a   Gunaratne, Jayantha ^a  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

Animal proteomics; Deyolking; Fractionation; Gene ontology; Whole proteome; Zebrafish embryo

Indexed keywords

NUCLEOCYTOPLASMIC TRANSPORT PROTEIN; RIBOSOME PROTEIN; YOLK PROTEIN; ZEBRAFISH PROTEIN;

ANIMAL EXPERIMENT; ANION EXCHANGE; ARTICLE; BIOINFORMATICS; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; EMBRYO; EXTRACELLULAR SPACE; INTRACELLULAR SIGNALING; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TANDEM MASS SPECTROMETRY; ZEBRA FISH;

ANIMALIA; DANIO RERIO;

EID: 84862866916     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100576     Document Type: Article

References (16)

1. Grunwald, D. J., Eisen, J. S., Headwaters of the zebrafish-emergence of a new model vertebrate. Nat. Rev. Genet. 2002, 3, 717-724.
2. Flicek, P., Amode, M. R., Barrell, D., Beal, K. et al., Ensembl 2011. Nucleic Acids Res. 2011, 39, D800-D806.
3. Lucitt, M. B., Price, T. S., Pizarro, A., Wu, W. et al., Analysis of the zebrafish proteome during embryonic development. Mol. Cell Proteomics 2008, 7, 981-994.
4. Groh, K., Nesatyy, V., Segner, H., Eggen, R. et al., Global proteomics analysis of testis and ovary in adult zebrafish (Danio rerio). Fish Physiol. Biochem. 2011, 37, 619-647.
5. De Souza, A. G., MacCormack, T. J., Wang, N., Li, L. et al., Large-scale proteome profile of the zebrafish (Danio rerio) gill for physiological and biomarker discovery studies. Zebrafish 2009, 6, 229-238.
6. Singh, S. K., Sundaram, C. S., Shanbhag, S., Idris, M. M., Proteomic profile of zebrafish brain based on two-dimensional gel electrophoresis matrix-assisted laser desorption/ionization MS/MS analysis. Zebrafish 2010, 7, 169-177.
7. Zhang, J., Lanham, K. A., Peterson, R. E., Heideman, W., Li, L., Characterization of the adult zebrafish cardiac proteome using online pH gradient strong cation exchange-RP 2D LC coupled with ESI MS/MS. J. Sep. Sci. 2010, 33, 1462-1471.
8. Link, V., Shevchenko, A., Heisenberg, C.-P., Proteomics of early zebrafish embryos. BMC Dev. Biol. 2006, 6, 1.
9. Fang, Y., Robinson, D. P., Foster, L. J., Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. J. Proteome Res. 2010, 9, 1902-1912.
10. Wang, H., Chang-Wong, T., Tang, H.-Y., Speicher, D. W., Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes. J. Proteome Res. 2010, 9, 1032-1040.
11. Wisniewski, J. R., Zougman, A., Nagaraj, N., Mann, M., Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-362.
12. Hubner, N. C., Ren, S., Mann, M., Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008, 8, 4862-4872.
13. Wiśniewski, J. R., Zougman, A., Mann, M., Combination of FASP and stagetip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 2009, 8, 5674-5678.
14. McQuade, L. R., Schmidt, U., Pascovici, D., Stojanov, T. et al., Improved membrane proteomics coverage of human embryonic stem cells by peptide IPG-IEF. J. Proteome Res. 2009, 8, 5642-5649.
15. Cordwell, S. J., Thingholm, T. E., Technologies for plasma membrane proteomics. Proteomics 2010, 10, 611-627.
16. Vizcaíno, J. A., Côté, R., Reisinger, F., Barsnes, H. et al., The proteomics identifications database: 2010 update. Nucleic Acids Res. 2010, 38, D736-D742.