Viewing the proteome: How to visualize proteomics data?

Proteomics has become one of the main approaches for analyzing and understanding biological systems. Yet similar to other high-throughput analysis methods, the presentation of the large amounts of obtained data in easily interpretable ways remains challenging. In this review, we present an overview of the different ways in which proteomics software supports the visualization and interpretation of proteomics data. The unique challenges and current solutions for visualizing the different aspects of proteomics data, from acquired spectra via protein identification and quantification to pathway analysis, are discussed, and examples of the most useful visualization approaches are highlighted. Finally, we offer our ideas about future directions for proteomics data visualization.acceptedVersio

Shotgun proteomics approaches for authentication, biological analyses, and allergen detection in feed and food-grade insect species

Untargeted proteomics can contribute to composition and authenticity analyses of highly processed mixed food and feed products. Here, we present the setup of an analytical flow tandem mass spectrometry method (AF-HPLC HR-MS) for analysis of insect meal from five different species. Data acquired were compared with previously published data employing spectra matching and standard bottom-up proteomics bioinformatics analyses. In addition, data were screened for insect species marker peptides and common allergens, respectively. The results obtained indicate that the performance of the newly established AF-HPLC HR-MS workflow is in line with previously published methods for insect species differentiation. Data obtained in the present study, also lead to the discovery of novel markers for the development of targeted MS analyses of insect species in food- and feed-mixes and highlighted that known allergen such as arginine kinase or tropomyosin were consistently detected across all five species tested.publishedVersio

Earlier or delayed seasonal broodstock spawning changes nutritional status and metabolic programming of growth for next-generation Atlantic salmon

Atlantic salmon (Salmo salar) breeding companies depend on changing light, temperature and feeding regimes to achieve new generations outside the natural spawning season. However, there have been few conducted trials reported that have studied whether this shift affects important traits. We test whether an induced shift of two months earlier or two months later than normal spawning season affects the nutritional status (folate, methionine, vitamin B12, vitamin B6, free amino acids, N-metabolites and lipids) in broodstock liver and muscle and whether this affects the levels of the same nutrients in the offspring. The results showed significant seasonal differences in the Cahill cycle (glucose-alanine cycle), 1C metabolism and for free amino acids catabolized in the citric acid cycle all which are important for embryonic growth The broodstock nutritional status was reflected in the eggs. Nutritional status of broodstock liver and muscle and newly fertilized eggs showed two general scenarios: Advanced spawning period did not obtain optimal deposition of nutrients in the eggs. Delayed spawning broodstock displayed a metabolic profile which indicated that it had enhanced catabolization of muscle protein which led to accumulation of aminogroups from muscle breakdown to such a degree that these amino groups were increased in the eggs. The total body weight at start-feeding stage revealed best growth for both the normal and late spawning compared to early spawning. We show here that environmental alterations in broodstock husbandry influence the nutrient status of the next generation via nutritional and metabolic programming. This is an important concept which needs more careful awareness as the metabolism compensate and regulate the energy between catabolism and anabolism through the early stages of cell divisions which give rise to changes in permanent traits for the next generation.publishedVersio

Out-of-season spawning affects the nutritional status and gene expression in both Atlantic salmon female broodstock and their offspring

The Atlantic salmon aquaculture industry relies on adjustments of female broodstock spawning season to meet the demand for delivery of embryos outside the natural spawning season. Earlier results from zebrafish have shown that parental micronutrient status program offspring metabolism. Therefore, the main hypothesis of this study was to investigate if out-of-season (off-season) broodstock (spawning in June, in land-based recirculation systems) and their offspring deviate in micronutrient status when compared to broodstock and offspring from normal spawning season. Both seasons of female Atlantic salmon broodstock were fed the same diet and starved for approximately the same time interval prior to spawning. We compared nutrients related to the 1C metabolism (vitamin B12, folate, vitamin B6, methionine), free amino acids (FAAs) and lipid classes in broodstock muscle and liver tissues, and during offspring ontogeny. In general, the off-season broodstock showed higher levels of folate, vitamin B6 and selected FAAs in muscle tissue, and higher levels of folate and lipids (cholesterol and sphingomyelin) in liver tissue compared to normal-season. Furthermore, embryos from off-season had reduced amounts of all the measured lipid classes, like cholesterol and sphingomyelin, and lower levels of one type of folate and changes in FAAs and N-metabolites. We discovered significant differences between the seasons in mRNA levels of genes controlling fatty acid synthesis and 1C metabolism in both broodstock liver and offspring. Moreover, for genes controlling the methylation of DNA; both maintenance and de novo DNA methyltransferases (DNMTs) were expressed at higher levels in off-season compared to normal-season offspring. Our results show, in general that normal spawning season broodstock allocated more nutrients to eggs than off-season. Our results indicate a potential for improved maturation for off-season group to obtain a higher offspring growth potential, and this argues for a reassessment of the nutritional influence from broodstock to offspring and the consequences through nutritional programming.publishedVersio

Proteoglycans contribute to the functional integrity of the glomerular endothelial cell surface layer and are regulated in diabetic kidney disease

All capillary endothelia, including those of the glomeruli, have a luminal cell surface layer (ESL) consisting of glycoproteins, glycolipids, proteoglycans (PGs) and glycosaminoglycans. Previous results have demonstrated that an intact ESL is necessary for a normal filtration barrier and damage to the ESL coupled to proteinuria is seen for example in diabetic kidney disease (DKD). We used the principles of ion exchange chromatography in vivo to elute the highly negatively charged components of the ESL with a 1 M NaCl solution in rats. Ultrastructural morphology and renal function were analyzed and 17 PGs and hyaluronan were identified in the ESL. The high salt solution reduced the glomerular ESL thickness, led to albuminuria and reduced GFR. To assess the relevance of ESL in renal disease the expression of PGs in glomeruli from DKD patients in a next generation sequencing cohort was investigated. We found that seven of the homologues of the PGs identified in the ESL from rats were differently regulated in patients with DKD compared to healthy subjects. The results show that proteoglycans and glycosaminoglycans are essential components of the ESL, maintaining the permselective properties of the glomerular barrier and thus preventing proteinuria.publishedVersio

In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)

In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF proteome, and hydrazide-based glycopeptide capture for mapping glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) was identified, of which 520 were identified as glycoproteins from the glycopeptide enrichment strategy, including 1121 glycopeptides and their glycosylation sites. To our knowledge, this is the largest number of identified proteins and glycopeptides reported for CSF, including 417 glycosylation sites not previously reported. From parallel plasma samples, we identified 1050 proteins (9739 peptide sequences). An overlap of 877 proteins was found between the two body fluids, whereas 2204 proteins were identified only in CSF and 173 only in plasma. All mapping results are freely available via the new CSF Proteome Resource (http://probe.uib.no/csf-pr), which can be used to navigate the CSF proteome and help guide the selection of signature peptides in targeted quantitative proteomics.publishedVersio

Oksidativt stress, vårdropp i pigmentering og produksjonslidelser hos laks

I lakseoppdrett opplever man noen ganger en reduksjon i pigmentering av fileten i forbindelse med økt vekst i vårsesongen når temperatur og daglengde øker. I EU-prosjektet ARRAINA fant vi økt oksidativ status i fisk samplet i juni, bl.a. med redusert innhold av vitamin C i hel fisk, sammenlignet med fisk i ferskvann. Hypotesen i dette prosjektet er at økt vekst i sjø om våren er forbundet med oksidativt stress og at dette fører til nedbrytning av astaxanthin og gir den såkalte vårdroppen i pigmentering. Dette er vist tidligere med bruk av et fôr som inneholdt mye marine ingredienser, men vi ønsker å bekrefte disse resultatene under fôr- og fôringsbetingelser som er relevante for dagens oppdrett. Hvis fisken har økt oksidativt stress om våren, kan dette også føre til utvikling av katarakt og pigmentflekker i muskel. Disse hypotesene ble delvis bekreftet av resultatene i dette studiet.publishedVersio

A New Method for Isolation of Interstitial Fluid from Human Solid Tumors Applied to Proteomic Analysis of Ovarian Carcinoma Tissue

Major efforts have been invested in the identification of cancer biomarkers in plasma, but the extraordinary dynamic range in protein composition, and the dilution of disease specific proteins make discovery in plasma challenging. Focus is shifting towards using proximal fluids for biomarker discovery, but methods to verify the isolated sample's origin are missing. We therefore aimed to develop a technique to search for potential candidate proteins in the proximal proteome, i.e. in the tumor interstitial fluid, since the biomarkers are likely to be excreted or derive from the tumor microenvironment. Since tumor interstitial fluid is not readily accessible, we applied a centrifugation method developed in experimental animals and asked whether interstitial fluid from human tissue could be isolated, using ovarian carcinoma as a model. Exposure of extirpated tissue to 106 g enabled tumor fluid isolation. The fluid was verified as interstitial by an isolated fluid:plasma ratio not significantly different from 1.0 for both creatinine and Na+, two substances predominantly present in interstitial fluid. The isolated fluid had a colloid osmotic pressure 79% of that in plasma, suggesting that there was some sieving of proteins at the capillary wall. Using a proteomic approach we detected 769 proteins in the isolated interstitial fluid, sixfold higher than in patient plasma. We conclude that the isolated fluid represents undiluted interstitial fluid and thus a subproteome with high concentration of locally secreted proteins that may be detected in plasma for diagnostic, therapeutic and prognostic monitoring by targeted methods