Brain Proteome of Drosophila melanogaster Is Enriched with Nuclear Proteins.

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.

The study of the proteome of healthy human blood plasma under conditions of long-term confinement in an isolation chamber.

We identified changes in the proteome of healthy human blood plasma caused by exposure to 105-day confinement in an isolation chamber. After removal of major proteins and concentration of minor proteins, plasma fractions were analyzed by two-dimensional electrophoresis followed by identification of significantly different protein spots by mass spectrometric analysis of the peptide fragments. The levels of α- and ß-chains of fibrinogen, a fragment of complement factor C4, apolipoproteins AI and E, plasminogen factor C1 complement, and immunoglobulin M changed in participants during the isolation period. These changes probably reflect the adaptive response to altered conditions of life.

[Selection of the peptide mass tolerance value for the protein identification with peptide mass fingerprinting].

Peptide mass-fingerprint is widely used for protein identification while studying proteome with the use of 1D or 2D electrophoresis. Peptide mass tolerance indicates the fit of theoretical peptide mass with the experimental measurements, and choice of this parameter sufficiently influences the protein identification. The role of peptide mass tolerance was estimated by counting the number of identified proteins for the reference set of mass-spectra. The reference set of 400 Ultraflex (Bruker Daltonics, Germany) mass-spectra was obtained for the slices of 1D gel of liver microsomes. Using Mascot server for protein identification, the peptide mass tolerance value was varied in the range from 0.02 to 0.40 Da with a step 0.01 Da. Depending on the tolerance the number of identified protein changes up to 10 times. Maximal number of identified proteins was reported for the tolerance value of 0.15 Da (120 ppm), which is 1.5 - 2 times higher than the recommended values for such type of mass-spectrometers. The software program PMFScan was developed to obtain the dependence of number of identified proteins of the tolerance values.