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The Metabolomics Core Facility focuses on targeted metabolomics (quantitation and validation) and untargeted metabolomics (discovery of metabolites).

General Limitations MS proteomics is a powerful tool for the analysis of protein samples, but there are some limits to the techniques we employ in the Proteomics Core. Knowing the limitations of the services we provide can help to ensure your experiment is a success, and you do not incur costs for unsuccessful analyses. Detection Limits & Protein Requirement For Protein Identification Generally the instrumentation we use for service work can easily identify Coomassie-stained bands, will identify

TMT Quantitation Introduction Tandem Mass Tag (TMT) technology is a powerful technique for comparing protein (and peptide) amounts between six to eighteen conditions. This technique involves labeling samples after digestion, meaning this technique can be used on in vivo samples, unlike SILAC. TMT or TMTpro samples are to be submitted in solution or on-bead, not in gel. It is the responsibility of the customer to ensure that similar amounts of protein is present in each sample and that the

Cutting Gels Introduction Many proteomics samples are well suited for SDS-PAGE, including protein identification and PTM identification. We recognize that a gel approach may not be compatible with all samples, so please contact us if you have concerns about running your sample into a gel. We require that: Precast SDS-PAGE gels are used whenever possible to reduce contamination. The advice on this page must be followed to avoid keratin and detergent/polymer contamination. All gels should be

Charging Policy What is our policy for charging users? The Proteomics Core has a simple charging policy: No samples will be prepared or run until the information has been entered into our sample submission site. We charge for every sample run , regardless of whether an expected result is obtained. The only exception to this rule is where processing or instrument problems in the core have caused the lack of result. Why do I have to pay for samples that deliver no useful result? Many users are

Intact Mass What do we use to measure the mass of intact proteins? We do LC/MS analysis of intact proteins using a Q-TOF mass spectrometer with electrospray ionization. This means that samples must be free of detergents. An ideal solvent is 5% acetonitrile in water containing 1-5% formic acid or acetic acid, though many standard biological buffers and salts are acceptable (see below). What are some limitations of your intact mass analysis? We are not able to look at native or non-covalent

Gel Band ID Introduction Identification of proteins from visible bands excised from Coomassie or silver-stained gels using mass-spectrometry is generally very successful. Almost all visible Coomassie bands contain enough protein for MS identification. Most silver-stain bands can be identified on our instruments. Sequence coverage achieved is dependent on the sequence of the unknown protein (does it produce observable tryptic peptides), and the amount of protein in the band. Silver stained bands

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