We are attempting a shotgun proteomics experiment using LC ESI-MS/MS with an Orbitrap LTQ XL, but are suddenly encountering a problem with excessive background noise. The noise level is fairly constant at ~4E6 intensity for the entire gradient, obscuring many peaks. The peaks that are above the noise are sharp and we still obtain several hundred identifications, but total IDs have dropped by 50-75% and comparison with previous, much more successful, runs shows that the noise in those runs was 0.5-1xE6. The difference between ~5E5 and ~5E6 is enough to obscure most of the sample peaks. The ESI spray appears to be good, and the Orbitrap was recently tuned and serviced by a ThermoFisher technician. Running samples that previously were of high quality shows the same problem, indicating a problem with the instrument, not the sample preparation. Any advice would be greatly appreciated.
Thanks for the response. I should note that the servicing was the annual scheduled service and the instrument was working adequately before and for a while afterwards, so I can't fault the technician, as you say it may well be a problem with the solvents. Buffers used are 0.1% formic acid in LC-MS grade water and 80% acetonitrile, .1% formic acid in LC-MS grade water. Flow rate is 0.3uL/minute, 35C column oven temperature, all unchanged, as is the C18 column. What I know to have changed since the last good run is the batch of solvents and the ESI tip (though again the spray looks pretty good at the moment). I will make a fresh batch of the buffers and see if that resolves the issue.
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