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Five years ago, the NCBI Probe database (ProbeDB) was established to provide a centralized archive of molecular probes used in biomedical applications. Currently ProbeDB contains around 10 million probes of 65 types including gene silencing agents, in situ hybridization probes, and probes for variation analysis and genome mapping. Presently, ProbeDB is the largest and most extensive database of this type available in public domain.

In the post acqusition analysis of comprehensive -omics data the pre-processing pipe-line is crucial to extract the maximum possible amount of information from the data. Here we show a processing pipe-line for (1D)H-NMR and (2D)X/MS data comprising; feature detection, inter-sample feature alignment and internal-standard free normalization that outperforms today’s state-of-the-art processing schemes.

In metabolic profiling, multivariate data analysis techniques are used to interpret 1D 1H–NMR data. Multivariate data analysis techniques require that peaks are located in the same variables in every spectrum – this requirement is not met in native NMR spectra. Current state-of-the-art alignment algorithms are unable to align peaks when the spatial order of the peaks changes. We present the Fuzzy Generalized Hough Transform alignment which solves the alignment problem.

A metabolomic approach was used to detect changes in urinary metabolic profile of rats treated orally with methylmercury (MeHg), a ubiquitous fish contaminant with well known neurotoxic properties. An aliquot of urine was collected on day 14, extracted and the extract successively methoxymated and trimethylsilylated prior to analysis by GC/TOF-MS. Results indicate that several metabolic pathways were altered by MeHg treatment, including urea cycle, glutathione metabolism and amino acid degradati

Metabolite profiling (HPLC-UV-MS) was performed for extracts from Tithonia diversifolia (Td) and Smallanthus sonchifolius (Ss) leaves [aqueous crude (ACE); leaf rinse (LRE); 70%MeOH rinsed leaves (GFE)]. LREs presented mainly sesquiterpene lactones (SLs) and flavonoids. FGEs and ACEs presented mainly chlorogenic acids. SLs were not detected in GFEs but traces were detected in ACEs. All extracts presented anti-inflammatory potential. LREs were highly toxic while GFEs did not presented significant

Small molecular compounds (PR-619 and P22077) was assessed for their abilities to inhibit DUB function in crude extracts and in cells. Activity-based profiling combined with quantitative mass spectrometry revealed the inhibitory capacity of a broad range of DUBs by the PR-619, whereas P22077 showed specificity towards subsets of DUBs including USP7 in cells. Our results demonstrate the usefulness of activity-based quantitative proteomics to monitor inhibition of endogenous DUBs in vivo.

Capture Compound Mass Spectrometry (CCMS) enables the enrichment of proteins based on their functionality. CCMS is commercialized as kits for research applications and in collaborations with pharmaceutical companies. The focus is on investigating mechanisms of drug action and avoidance of toxic effects of small molecule drugs.

Aberrant sialylation affects the metastatic behaviour of cancer cells.We have quantified the sialylated cell surface glycoproteins from cells with different metastatic behaviour.The membrane proteins from isogenic human cell lines were analyzed by a method based on TiO2-HILIC-MS.1200 sialylated glycosites, 116 enzymes involved in the glycoconjugate metabolism and for the first time 4 glycosylation sites of Her2 receptor were identified, showing the importance of this tool for discovery and thera

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an extremely toxic pollutant and regarded the most potent chemical carcinogen in experimental animals. Most of its biological effects are mediated by binding of TCDD to the cytosolic Ah receptor (AHR). In addition, TCDD cause AHR-dependent alterations in signal transduction that are independent of changes in gene expression. In this study, we have therefore conducted a quantitative phospho proteomic study on TCDD-induced alterations.

Using a standardized method to acquire MALDI-TOF proteome profile spectra of bronchoalveolar lavage fluid (BALF), we have shown the upregulation of histatin 3 and calgranulin C in a small pilot cohort of NSCLC patients. This pilot study serves to demonstrate that it is feasible to screen a larger NSCLC patient cohort for BALF proteome level biomarkers in a clinical setting.