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Approaching Clinical Proteomics: Current State and Future Fields of Application in Cellular Proteomics Ghent University
Abstract: Recent developments in proteomics technology offer new opportunities for clinical applications in hospital or specialized laboratories including the identification of novel biomarkers, monitoring of disease, detecting adverse effects of drugs, and environmental hazards. Advanced spectrometry technologies and the development of new protein array formats have brought these analyses to a standard, which now has the potential to be used in ...
Tissue Based Proteomics and Biomarker Discovery - Multivariate Data Mining Strategies for Mass Spectral Imaging (Weefsel-gebaseerde proteomica en biomerkeranalyse - Multivariate data-analysestrategieën voor massaspectrale beeldvorming) KU Leuven
Het wordt alsmaar duidelijker dat de moleculaire mechanismen die ten gro ndslag liggen aan vele van 's werelds meest invloedrijke ziekten, e en veel grotere complexiteit vertonen dan oorspronkelijk gedacht. Aan di agnostische zijde kent de zoektocht naar ziekte-rapporterende biomerkers in makkelijk toegankelijke vloeistoffen, zoals bloed, slechts gemengd s ucces. De biomerkers in dergelijke vloeistoffen zijn vaak in zodanig lag e concentraties ...
ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics Ghent University Flanders Institute for Biotechnology
Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, due to the high levels of data reduction that occur between raw data and machine learning-ready data. Since predictive proteomics is an emerging field, when predicting peptide behavior in LC-MS setups, each lab ...
Getting a grip on proteomics data: Proteomics Data Collection (ProDaC) Ghent University
In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of ...
Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users. Flanders Institute for Biotechnology Ghent University
A guide to the Proteomics Identifications Database proteomics data repository Ghent University
Abstract: The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in ...
A pipeline for differential proteomics in unsequenced species Institute of Tropical Medicine KU Leuven Ghent University
Shotgun proteomics experiments often take the form of a differential analysis, where two or more samples are compared against each other. The objective is to identify proteins that are either unique to a specific sample or a set of samples (qualitative differential proteomics), or that are significantly differentially expressed in one or more samples (quantitative differential proteomics). However, the success depends on the availability of a ...
Cleavable Linkers in Chemical Proteomics Applications KU Leuven
The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their ...