Proteomics and Metabolomics Services offered by the Cores of Weill Cornell Medicine – Qatar December 7, 2016 Weill Cornell Medicine – Qatar operates several core facilities that are supported by the Biomedical Research Program of Qatar Foundation. These WCM‐Q core facilities can support projects from PIs located in WCM – New York. Here we propose to add the services of two high‐throughput capable proteomics and metabolomics platforms, Somalogic and Metabolon, to the portfolio of the newly created WCM proteomics and metabolomics core. The Somalogic and the Metabolon platforms are representing the leading technologies in their respective fields. WCM‐Q PIs have published key paper with both technologies. The Somalogic platform is physically located in Qatar and runs kits that need to be purchased from Somalogic Inc. (Boulder, CO); the Metabolon platform is “virtual” in the sense that samples have to be shipped to Metabolon Inc. (Durham, NC) under an advantageous blanket agreement. WCM‐Q PIs have longstanding collaborations with both companies and an excellent knowledge of their capabilities, protocols, data types, and their respective strengths and limitations. Proteomics analyses are presently limited to EDTA blood samples; metabolomics analyses can be performed on any biological sample, including all bodily fluids, cell culture, and tissue extracts. The WCM‐Q Bioinformatics Core can effectively support users in the down‐stream data analysis, as it has extensive experience performing genome‐wide association and clinical studies using both platforms. It can support users in project proposal writing. For grant applications, the core can also provide reference data sets from human and mouse studies that can potentially serve as preliminary data. It should be emphasized that the technologies proposed here are particularly suited for high throughput analyses with at least 80 samples per study. However, small scale functional studies are not well accommodated. The two platforms proposed here are therefore complementary to the offers of the WCM Proteomics and Metabolomics core in New York. Contact: Karsten Suhre, Director of the WCM‐Q Bioinformatics and Virtual Metabolomics Core, Doha, Qatar, email: kas2049@qatar‐med.cornell.edu, phone: +974.33541843
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Proteomics Platform: Somalogic Platform reference: [1] Platform website: http://www.somalogic.com/ Executive summary: Somalogic provides readouts for presently 1300 blood circulating proteins that cover a wide range of protein functions and that are involved in many disease relevant pathways, taking a multiplexed aptamer‐based approach. Technical Summary: The SOMAscan™ assay is a highly multiplexed, sensitive, quantitative and reproducible proteomic tool for discovering previously undetected biomarkers for drug discovery, preclinical and clinical drug development, and clinical diagnostics, across a wide range of important diseases and conditions. The SOMAscan assay currently determines over 1300 protein analytes in only 65 µl of serum, plasma or cerebrospinal fluid, or equally small amounts of a variety of other biological matrices. The assay offers exceptional dynamic range, quantifying proteins that span over 8 logs in abundance (from femtomolar to micromolar), with low limits of detection (38 fM median LOD) and excellent reproducibility (5.1% median %CV). The SOMAscan proteomic assay is enabled by a new generation of protein‐capture SOMAmer™ (Slow Off‐rate Modified Aptamer) reagents. SOMAmer reagents are constructed with chemically modified nucleotides that greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the SOMAmer reagents are selected. The SOMAscan assay measures native proteins in complex matrices by transforming each individual protein concentration into a corresponding SOMAmer concentration, which is then quantified by standard DNA techniques such as microarrays or qPCR. The assay takes advantage of SOMAmers’ dual nature as both protein affinity‐binding reagents with defined three‐dimensional structures, and unique nucleotide sequences recognizable by specific DNA hybridization probes. Scientific Applications: To date, the SOMAscan assay has been applied successfully to biomarker discovery and validation in many pharmaceutical research and development projects, diagnostics discovery and development projects, and academic research projects, including Alzheimer’s disease [2,3], Duchenne muscular dystrophy [4], aging [5], cancer [6,7], cardiovascular disease [8], and genetic association [9]. Researchers at WCM‐Q recently conducted a genome‐wide association study with Somalogic [10] and compared the readouts to mRNA sequencing [11]. Availability: At least 80 samples of EDTA blood plasma, other matrices can be considered, costs are currently ~$450/sample, depending on the Somalogic kit price.
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Metabolomics Platform: Metabolon Platform reference: [12] Platform website: http://www.metabolon.com/ Executive summary: Metabolon provides readouts for about 700‐1200 small molecules (metabolites) that cover all relevant metabolic pathways, taking a semi‐quantitative non‐targeted mass‐spectroscopy based approach. Technical Summary: The current Discovery HD4TM platforms comprises four different injections and runs on a Waters ACQUITY ultra‐performance liquid chromatography (UPLC) and a Thermo Scientific Q‐ Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI‐II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. Sample extracts are dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contains a series of standards at fixed concentrations to ensure injection and chromatographic consistency. The scan range varies slighted between the fours methods but covers 70‐1000 m/z. Method 1: One aliquot is analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract is gradient eluted from a C18 column (Waters UPLC BEH C18‐2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Method 2: One aliquot is analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract is gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and is operated at an overall higher organic content. Method 3: One aliquot is analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts are gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. Method 4: One aliquot is analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternates between MS and data‐dependent MSn scans using dynamic exclusion Scientific Applications: Metabolon data has been used in several hundred studies word‐wide. PIs at WCM‐ Q participated among others in studies on diabetes [13], kidney function [14], kidney graft rejection [15], cancer [16], genome‐wide association with metabolomics [17,18], long term conservation of metabolic profiles [19], pharmacometabolomics [20], epigenetic regulation of metabolite levels [21], telomere length [22], arthritis [23], vitamin D [24], serum IGF‐1 levels [25], coffee consumption [26], and the relationship between gene expression and metabolomics [27]. Availability: At least 50 samples to be shipped, costs ~$350/sample, lower for larger sample numbers
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