I am having consistent problems with mass accuracy on the Orbitrap Fusion (see attached powerpoint). The LC is fine and so is the standard. There is some sensitivity issues but that does not explain the +10 ppm mass drift (ppm centered at 15 ~ppm) nor does it explain why this is not a problem for anyone else in the lab (they all get within +/- 10 ppm). The instrument is tuned and calibrated ~ every 3wks so this plus the fact that others are getting good mass accuracy does not explain my problem. I have also rebuilt my methods from scratch in case they were corrupted, but the results are still the same.
Help.
Hi Norelle,
Do people running samples after you get good mass accuracy? i've seen this problem in the past - it occured due to corruption of the calibration file or data corruption. it would be helpful to know when others are getting good data.
besides that, my experience with the fusion led to calibration twice a week (though every instrument is different...), often going back to old calibration files and these tended to corrupt.
David.
Yes people running before or after me get good mass accuracy. This is why I though my method file was corrupt and I rebuilt a replica of it from scratch, yet that did not seem to help.
Also how would the data get corrupted right after or during acquisition?
Hi Norelle,
Data corruption can occur several ways - Data transfer into large data servers may be sometimes compressed, but this usually led to loss of information. data transfer on a slow bus can lead to partial acquisition and loss of communications.
what usually gets corrupted is the calibration file, but then the corruption is paramount - all samples should be affected. I would begin using someone else's methods file and go on from there.
out of curiosity why do you use intact protein mode? HCD cell pressure lowers and you've got difficulty trapping and fragmenting.
Hi David,
I have use another lab members method (there's an attached ppt in the original question). With this method, the error is centered ~9ppm. However, when other people are doing tMS2 or the Fusion equivalent to PRM. They are only looking at a few peptides and use Xcalibur to get XIC within their specified ppm (ie., 10) and it is not an issue for them. I am doing DDA peptidomics and so I use PEAKS.
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