The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here, we present a draft map of the human proteome using high resolution Fourier transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells resulted in identification of proteins encoded by 17,294 genes accounting for ~84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream ORFs. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

Predictive computing tools are increasingly being used and have demonstrated successfulness in providing insights that can lead to better health policy and management. However, as these technologies are still in their infancy stages, slow progress is being made in their adoption for serious consideration at national and international policy levels. However, a recent case evidences that the precision of Artificial Intelligence (AI) driven algorithms are gaining in accuracy. AI modelling driven by companies such as BlueDot and Metabiota anticipated the Coronavirus (COVID-19) in China before it caught the world by surprise in late 2019 by both scouting its impact and its spread. From a survey of past viral outbreaks over the last 20 years, this paper explores how early viral detection will reduce in time as computing technology is enhanced and as more data communication and libraries are ensured between varying data information systems. For this enhanced data sharing activity to take place, it is noted that efficient data protocols have to be enforced to ensure that data is shared across networks and systems while ensuring privacy and preventing oversight, especially in the case of medical data. This will render enhanced AI predictive tools which will influence future urban health policy internationally.

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.

Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ϳ69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes. Molecular & Cellular Proteomics 13: 10.1074/mcp.M114.038299, 3184-3198, 2014. Zebrafish (Danio rerio)is an important vertebrate model organism that has been widely used in biomedical research in several areas, including developmental biology, disease biology, toxicology, and behavior. The latest genome assembly, Zv9, which was released in October 2011, combines the advantages of clone-by-clone sequencing and shotgun sequencing technologies. In this assembly, 83% of sequences were generated from capillary sequencing of clones, with the

The aqueous humor is a colorless, transparent fluid that fills the anterior chamber of the eye. It plays an important role in maintaining the intraocular pressure and providing nourishment to the lens and cornea. The constitution of the aqueous humor is controlled by the blood-aqueous barrier. Though this ocular fluid has been extensively studied, its role in ocular physiology is still not completely understood. In this study, aqueous humor samples were collected from 250 patients undergoing cataract surgery, subjected to multiple fractionation strategies and analyzed on a Fourier transform LTQ-Orbitrap Velos mass spectrometer. In all, we identified 763 proteins, of which 386 have been identified for the first time in this study. Sorbitol dehydrogenase (SORD), filensin (BFSP1), and phakinin (BFSP2) are some of the proteins that have not been previously reported in the aqueous humor. Gene Ontology analysis revealed 35% of the identified proteins to be extracellular, with a majority of them involved in cell communication and signal transduction. This study comprehensively reports 386 novel proteins that have important potential as biomarker candidates for future research into personalized medicine and diagnostics aimed towards improving visual health.

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Hypothalamic enzymatic activities capable of degrading LHRH may play a physiological role in the neuroendocrine control of LHRH. There is increasing evidence, however, that these enzymes are not peptide specific. The present study in the ewe analyzed the possibility that the specificity of LHRH-degrading activity (LHRH-DA) could be conferred by the relative location of LHRH-DA with respect to that of the LHRH peptide itself. LHRH content was correlated with LHRH-DA in discrete hypothalamic samples containing LHRH-positive cell bodies and axons and in immediately adjacent areas apparently devoid of LHRH immunoreactivity. LHRH content was assessed by RIA, and LHRH-DA was determined by HPLC of the LHRH decapeptide and its degradation fragments. The sampling of discrete hypothalamic areas was designed after immunocytochemical localization of LHRH. LHRH-containing cell bodies were observed in the medial preoptic area, projecting LHRH-positive fibers to the infundibular region. At all hypothalamic levels, there was a tight correlation (r greater than 0.95; P less than 0.01) among the regional distribution of LHRH-DA, LHRH content, and the presence of LHRH-like immunoreactivity. LHRH-DA, in addition, was present in areas of low (e.g. lateral hypothalamus) or undetectable (e.g. cerebral cortex) LHRH content that were devoid of LHRH-like immunoreactivity. The appearance of LHRH degradation fragments suggests that the initial cleavage of LHRH by LHRH-DA occurs at the Tyr5-Gly6 bond at all hypothalamic levels studied. These findings indicate that part of the total hypothalamic LHRH-DA may be located within the LHRH hypophysiotropic pathway. This suggests an anatomical locus for a possible physiological interaction between LHRH and LHRH-DA.

Mycobacterium tuberculosis, the causative agent of tuberculosis, accounts for 1.5 million human deaths annually worldwide. Despite efforts to eradicate tuberculosis, it still remains a deadly disease. The two best characterized strains of M. tuberculosis, virulent H37Rv and avirulent H37Ra, provide a unique platform to investigate biochemical and signaling pathways associated with pathogenicity. To delineate the biomolecular dynamics that may account for pathogenicity and attenuation of virulence in M. tuberculosis, we compared the proteome and phosphoproteome profiles of H37Rv and H37Ra strains. Quantitative phosphoproteomic analysis was performed using high-resolution Fourier transform mass spectrometry. Analysis of exponential and stationary phases of these strains resulted in identification and quantitation of 2709 proteins along with 512 phosphorylation sites derived from 257 proteins. In addition to confirming the presence of previously described M. tuberculosis phosphorylated proteins, we identified 265 novel phosphorylation sites. Quantitative proteomic analysis revealed more than five-fold upregulation of proteins belonging to virulence associated type VII bacterial secretion system in H37Rv when compared to those in H37Ra. We also identified 84 proteins, which exhibited changes in phosphorylation levels between the virulent and avirulent strains. Bioinformatics analysis of the proteins altered in their level of expression or phosphorylation revealed enrichment of pathways involved in fatty acid biosynthesis and two-component regulatory system. Our data provides a resource for further exploration of functional differences at molecular level between H37Rv and H37Ra, which will ultimately explain the molecular underpinnings that determine virulence in tuberculosis.