Proteomics Sample submission and data analysis

Sample preparation
Tryptic digests should be provided for analysis: A minimum of 10uL is required in a Waters No Waste total recovery vial. No waste vials can be purchased directly from Waters http://www.waters.com/waters/partDetail.htm?partNumber=186000385C
(Please note we specifically require this type of vial and will not accept those from other manufacturers at the present time)

Sample concentrations
The protein standard we use is a bovine serum albumin (BSA) tryptic digest at a concentration of 100fmol/uL. Protein concentrations should be between 5 and 500fmol/uL. It is important not to exceed this concentration. If you are unsure about the concentration of proteins in your sample then please state this clearly on the sample submission form.

Vials must be labelled using a digital labelling system or a permanent marker or equivalent on a sticky label. Sample names made directly on glass are liable to rub off and all samples that are not clearly identifiable, will not be run. Please use your initials plus a maximum 5 letter code to label your vial.

Proteomics sample submission
To submit a sample for proteomics analysis you need to fill out a proteomics sample submission form whihc can be found here. Submit this in the ‘Proteomics Service box next to the Biomolecular service trays in picture below and are located in the basement mass spec room, next to the tall fridge freezer. Please ask a member of the MS staff is you cannot locate these trays.

Your sample vials should be placed in the orange "Proteomics samples" submission box which can be found in the fridge freezer on the lab bench next to the mass spectrometry office in the basement.

Data Analysis and return
Proteomics samples will be run overnight where possible using MSe MS/MS fragmentation analysis. The results will be tranferred to the instrument processing computer which is located to the right hand side of the SYNAPT instrument computer. You may use the reprocessor to 1) convert your data files to PKL fir MASCOT searches, 2) transfer your data via the network to another location. Do not leave your data on the reprocessor computer for more than 2 weeks. Data older than 2 weeks is regularly deleted to make space for new data.

Please see a member of the MS staff in the first instance if you are not sure how to process your data.

(Lingzhi.gong@chem.ox.ac.uk) is charge of running your samples, please see him in the first instance if you have specific questions about the running of your samples.