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VPBrowse, genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins

ABSTRACT: SWATH is a mass spectrometry data acquisition strategy that relies on peptide spectral libraries to perform quantitatively accurate and consistent measurement of proteins across multiple samples. Public libraries have been developed for humans and several laboratory species that have accelerated biomarker discovery, and similarly comprehensive resources would be useful for other species. The Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), is an on-line platform developed for genome-based representation of the Bos taurus proteome and is equipped with an interactive database and tools for visualization and building quantitative mass spectrometry assays. VPBrowse contains high quality tandem mass spectrometry (MS/MS) spectra acquired on QToF instrument for over 36,000 proteotypic peptides corresponding to over 10,000 bovine proteins. Data can be downloaded in different formats to enable analysis using popular software packages for SWATH data processing whilst normalization to iRT scale ensures compatibility with diverse chromatography systems. When applied to 25 different tissues and body fluids, the resource supported label-free quantification of nearly 30% of the protein-coding genes annotated in bovine section of UniprotKB.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Bos Taurus (bovine)

SUBMITTER: Pawel Sadowski

LAB HEAD: Pawel Sadowski

PROVIDER: PXD044768 | Pride | 2024-03-07

REPOSITORIES: Pride

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Project description:Rodents are commonly housed below thermoneutrality (~20°C) 1. Under these conditions there is a substantial effect on rodent physiology including the hyperactivation of brown (BAT) and beige adipose tissue 2. Here, we raised animals from weaning, on an obesogenic diet at thermoneutrality (28°C) to closer mimic human physiology and determine the impact of a) moderate cold exposure (i.e. 20°C, a temperature reduction of ~8°C) or b) treatment with YM-178, a highly-selective, clinically used β3-adrenoreceptor agonist on classical BAT or subcutaneous inguinal (IWAT) beige depots. Under these conditions, uncoupling protein 1 mRNA was undetectable in IWAT in all groups. Maintenance at 20°C drove weight gain and a 125% increase in subcutaneous fat, an effect not seen with YM-178 administration thus suggesting a direct effect of ambient temperature in promoting weight gain and adiposity in obese rats. Using exploratory adipose tissue proteomics we reveal novel processes and pathways associated with cold-induced weight gain in BAT (i.e. histone deacetylation and glycosphingolipid biosynthesis) and IWAT (i.e. NAD+ binding and retinol metabolism). Conversely, YM-178 had minimal metabolic-related effects on BAT and drove a pro-inflammatory phenotype in IWAT. Exercise training elicits diverse effects on brown (BAT) and white adipose tissue (WAT) physiology in rodents housed below their thermoneutral zone (i.e. 28-32°C). In these conditions, BAT is chronically hyperactive and, unlike human residence, closer to thermoneutrality. Therefore, we set out to determine the effects of exercise training in obese animals at 28°C (i.e. thermoneutrality) on BAT and WAT in its basal (i.e. inactive) state. Sprague-Dawley rats (n=12) were housed at thermoneutrality from 3 weeks of age and fed a high-fat diet. At 12 weeks of age half these animals were randomised to 4-weeks of swim-training (1 hour/day, 5 days per week). Following a metabolic assessment interscapular and perivascular BAT and inguinal (I)WAT were taken for analysis of thermogenic genes and the proteome. Exercise attenuated weight gain but did not affect total fat mass or thermogenic gene expression. Proteomics revealed an impact of exercise training on2-oxoglutarate metabolic process, mitochondrial respiratory chain complex IV, carbon metabolism and oxidative phosphorylation. This was accompanied by an upregulation of multiple proteins involved in skeletal muscle physiology suggesting an adipocyte to myocyte switch in BAT. UCP1 mRNA was undetectable in IWAT with proteomics highlighting changes to DNA binding, the positive regulation of apoptosis, HIF-1 signalling and cytokine-cytokine receptor interaction.

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VPBrowse, genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins

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