The Aberdeen Proteome Facility is housed in the recently completed Institute of Medical Sciences at the Foresterhill site of University's Medical Campus. The building houses a number of research groups covering microbiology, biomedical sciences, immunology and medicine. The building also houses the many core facilities that provide analytical services to researchers at the University of Aberdeen and other Academics. The Proteome Facility forms one of these core laboratories
The Aberdeen Proteome Facility was established in 1997 and is staffed by researchers specialising in the analysis of protein mixtures by high resolution 2DE together with identification and characterisation of proteins using peptide mass mapping and automated N-terminal sequencing. A wide variety of samples are analysed at the Aberdeen Proteome Facility including tissue samples, bodily fluids, plant material and bacterial proteins.
High resolution 2D gel electrophoresis remains a key technology in proteomics for the separation of complex protein mixtures. Proteins are separated according to charge in the first dimension and molecular mass in the second dimension. The Aberdeen Proteome Facility uses standard immobilised pH gradient technology for the first dimension separation coupled with SDS-PAGE for the second dimension. The latter separations are carried out in vertical electrophoresis systems. The Facility processes 2D gels using both large and small format gel systems. Proteins resolved by 2DE are detected using standard protocols of staining with either CBB G250 of silver. In many cases these detection methods are compatible protein identification by peptide mass mapping. Proteins can also be transferred to PVDF membranes for later immune detection in the researcher's laboratory. The gels produced by 2DE are imaged using a laser densitometer and the images generated are compatible with most analytical software.
	Peptide mass mapping is one of the most widely used approaches for the post-electrophoretic identification of proteins extracted from 1D or 2D electrophoresis gels. With the continued progress in whole genome sequencing reliable identifications can now be achieved for proteins from many different sources. Peptide profiles from proteins subjected to in-gel trypsin digestion are determined using an Applied BioSystems Voyager DE-STR MALDI-TOF instrument to achieve mass accuracies of between 10-100 ppm for individual peptides. The current capacity of the Facility for peptide mass mapping is up to 100 samples per day with optional full databases search and identification report. Intact protein mass spectra can also be determined with a mass accuracy of between 500-1000 ppm for proteins of masses up to 300kDa.
The Aberdeen Proteome Facility is equipped for the semi-automated processing of samples for peptide mass mapping using robots from Genomic Solutions for excising spots from gels, protein digestion, peptide extraction and purification and subsequent sample plate spotting for mass spectrometry. This equipment minimises the risks from keratin contamination of the samples.
	The Aberdeen Proteome Facility has recently installed an Applied BioSystems Procise automated sequencer to determine N-terminal amino acid sequences of proteins and peptides by Edman degradation chemistry. The machine handles both liquid samples and samples which have been blotted onto PVDF membrane. Internal sequences can be determined by first digesting the sample with an appropriate enzyme or reagent, separating the digested fragments by HPLC and applying the fragments of choice to the sequencer.The capacity is up to 10 samples per week and sequences of between 5-30 amino acids can be achieved from 0.1-20 pmols of proteins or peptide depending on the sample quality. Optional database searching can be performed from the sequences obtained for protein identification.
For further information on the services offered by the Aberdeen Proteome Facility as well as the option of arranging a visit to the Facility please contact Dr Phil Cash (p.cash@abdn.ac.uk)