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Brain Proteome of Drosophila melanogaster Is Enriched with Nuclear Proteins

K. G. Kuznetsova1, M. V. Ivanov2, M. A. Pyatnitskiy1,3, L. I. Levitsky2, I. Y. Ilina1, A. L. Chernobrovkin4, R. A. Zubarev4,5, M. V. Gorhskov2, and S. A. Moshkovskii1,6,a*

1Institute of Biomedical Chemistry, 119121 Moscow, Russia

2Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia

3Higher School of Economics, 101000 Moscow, Russia

4Karolinska Institutet, SE-171 77, Stockholm, Sweden

5Sechenov First Moscow State Medical University, 119991 Moscow, Russia

6Pirogov Russian National Research Medical University (RNRMU), 117997 Moscow, Russia

* To whom correspondence should be addressed.

Received August 30, 2018; Revised October 10, 2018; Accepted October 10, 2018
The brain proteome of Drosophila melanogaster was characterized by liquid chromatography/high-resolution mass spectrometry and compared to the earlier characterized Drosophila whole-body and head proteomes. Raw data for all the proteomes were processed in a similar manner. Approximately 4000 proteins were identified in the brain proteome that represented, as expected, the subsets of the head and body proteomes. However, after thorough data curation, we reliably identified 24 proteins unique for the brain proteome; 13 of them have never been detected before at the protein level. Fourteen of 24 identified proteins have been annotated as nuclear proteins. Comparison of three used datasets by label-free quantitation showed statistically significant enrichment of the brain proteome with nuclear proteins. Therefore, we recommend the use of isolated brain preparations in the studies of Drosophila nuclear proteins.
KEY WORDS: proteomics, mass spectrometry, Drosophila melanogaster, brain, nuclear protein

DOI: 10.1134/S0006297919010097