Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome

The Concept of an Epilepsy Brain Bank

Epilepsy comprises more than 40 clinical syndromes affecting millions of patients and families worldwide. To decode the molecular and pathological framework of epilepsy researchers, need reliable human epilepsy and control brain samples. Brain bank organizations collecting and supplying well-documented clinically and pathophysiologically tissue specimens are important for high-quality neurophysiology and neuropharmacology studies for epilepsy and other neurological diseases. New development in molecular mechanism and new treatment methods for neurological disorders have evoked increased demands for human brain tissue. An epilepsy brain bank is a storage source for both the frozen samples as well as the formaldehyde fixed paraffin embedded (FFPE) tissue from epilepsy surgery resections. In 2014, the University of Saskatchewan have started collecting human epilepsy brain tissues for the first time in Canada. This review highlights the necessity and importance of Epilepsy Brain bank that provides unique access for research to valuable source of brain tissue and blood samples from epilepsy patients.

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

BACKGROUND

Daphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.

RESULTS

A comprehensive set of 701,274 peptide tandem-mass-spectra, derived from Daphnia pulex, was generated, which lead to the identification of 531 proteins. To measure the impact of the Daphnia pulex filtered models database for mass spectrometry based Daphnia protein identification, this result was compared with results obtained with the Swiss-Prot and the Drosophila melanogaster database. To further validate the utility of the Daphnia pulex database for research on other Daphnia species, additional 407,778 peptide tandem-mass-spectra, obtained from Daphnia longicephala, were generated and evaluated, leading to the identification of 317 proteins.

CONCLUSION

Peptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the Daphnia genome. Furthermore it could be demonstrated that identification of Daphnia longicephala proteins using the Daphnia pulex protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the Daphnia genome database is the key for mass spectrometry based high throughput proteomics in Daphnia.