Does anyone have example instrument hardware settings for analysing proteomic samples from e.g. a HeLa digest. Also any "tips and tricks" that you have picked up would be most appreciated.
Can you please be more specific? What are your actual questions around this?
Thanks Christof - I should have been more specific. I will update the question now. Are you a Q-Exactive user currently?
Yes I am - we are running a Q Exactive for proteomics analysis in a core facility. If you are looking for tips on instrument settings on the QE then you are in a good position - the instrument has been a sort of "battlegrounds" for who can identify the most proteins. Look for e.g. Kelstrup et al., "Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer", J Proteome Res 2012. A large part of the story actually is the separations/chromatography setup you want to use. We use SDS-PAGE/23 Fractions/1h nLC setups to identify up to 7000 proteins in a day or two - I believe the hotshots of the field can do even better than that, but it is a nice stable setup to get started.Please feel free to contact me off-forum if you would like to discuss.
One really good place to find MS settings for many instruments (including at least 12 Q-Exactive datasets) is ProteomeXchange.
(http://proteomecentral.proteomexchange.org)
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