This study, which performs an extensive mass spectrometry-based analysis of 19 brain regions from both left and right hemispheres, presents the first draft of the human brain interhemispheric proteome. This high-resolution proteomics data provides comprehensive coverage of 3300 experimentally measured (nonhypothetical) proteins across multiple regions, allowing the characterization of protein-centric interhemispheric differences and synapse biology, and portrays the regional mapping of specific regions for brain disorder biomarkers. In the context of the Human Proteome Project (HPP), the interhemispheric proteome data reveal specific markers like chimerin 2 (CHN2) in the cerebellar vermis, olfactory marker protein (OMP) in the olfactory bulb, and ankyrin repeat domain 63 (ANKRD63) in basal ganglia, in line with regional brain transcriptomes mapped in the Human Protein Atlas (HPA). In addition, an in silico analysis pipeline was used to predict the structure and function of the uncharacterized uPE1 protein ANKRD63, and parallel reaction monitoring (PRM) was applied to validate its region-specific expression. Finally, we have built the Interhemispheric Brain Proteome Map (IBPM) Portal () to stimulate the scientific community’s interest in the brain molecular landscape and accelerate and support research in neuroproteomics. Data are available via ProteomeXchange with identifier PXD019936.

Proteomics has enormous applications in human and animal research. However, proteomic studies in fisheries science are quite scanty particularly for economically important species. Few proteomic studies have been carried out in model fish species, but comprehensive proteomics of aquaculture species are still scarce. This study aimed to perform a comprehensive organ-based protein profiling of important tissue samples for one of the most important aquaculture species,Labeo rohita.Deep proteomic profiling of 17 histologically normal tissues, blood plasma, and embryo provided mass-spectrometric evidence for 8498 proteins at 1% false discovery rate that make up about 26% of the total annotated protein-coding sequences in Rohu. Tissue-wise expression analysis was performed, and the presence of several biologically important proteins was also verified using a targeted proteomic approach. We identified the global post-translational modifications (PTMs) in terms of acetylation (N-terminus and lysine), methylation (N-terminus, lysine, and arginine), and phosphorylation (serine, threonine, and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal has been developed for an overall landscape of protein expression across the studied tissues of Labeo rohita (www.fishprot.org). This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.

Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal () for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.

With the global consumption of fish outpacing population growth, aquaculture sector is facing challenges to address the rising demand of food and nutritional security. Integrative omics research provides a strong platform to understand the basic biology and translate this knowledge into sustainable solutions in tackling disease outbreak, increasing productivity thus ensuring food security. To further understand the complex biology of host-pathogen response and support the aquaculture effort, genome and proteome reference maps moving beyond simple sequence information of cultivated fish species will accelerate research and translation of quality products for food industries. Towards this end, we have performed an extensive proteomics-based investigation of Labeo rohita, one of the economically important fish species produced in world aquaculture. Deep proteomic profiling of 17 histologically normal tissues, plasma and embryo provided mass-spectrometric evidence for 6015 high confident canonical proteins at 1% false discovery rate. Tissue enriched expression of several biologically important proteins was validated using targeted proteomics with high quantitative accuracy. We characterised the global post translational modifications (PTMs) in terms of acetylation (n-terminus and lysine), methylation (n-terminus, lysine and arginine) and phosphorylation (serine, threonine and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal was developed to support the Labeo rohita PeptideAtlas, (www.peptideatlas.org), a unique community resource for mass spectrometry-based peptide/protein evidence in fish. This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.

The human brain has always been a black box full of mysteries. Here we present one of the most comprehensive proteomics investigation of the brain, focusing on inter-hemispheric differences. An extensive mass spectrometry-based analysis of 19 brain regions from both left and right hemispheres measured more than 3300 proteins and 38700 peptides. This high-resolution data provides a comprehensive coverage of experimentally measured (non-hypothetical) proteins across various regions to characterize inter-hemispheric differences. We also tried to understand the brain proteins in terms of synapse analysis. The study has attempted to investigate the expression of neuroanatomical allied region and brain disorder protein markers in 19 region and sub-region of brain. Furthermore, we have developed the most comprehensive Brain Proteome Database, based on our, and publicly available curated data representing more than 9000 proteins (with isoforms) and around 90000 peptides at www.brainprot.org, which can aid in understanding the human brain’s complexity.