Re: Lockmass gap correction
Reply #4 –
Hey guys,
just saw this thread. For some reason the forum has stopped sending me alerts when new messages are posted.
Anyways, I just wanted to let you know that there is a new version of the lock mass gap correction that I put in the last version of xcms, ie its in the current stable release. With this version xcms will read the lock mass function files to get the scan times directly from the files. This is a good alternative if for some reason the scans weren't regular or something odd happened. To run it you need to have your lock mass function CDF files in the same folder as your analysis files. The naming schema that I found to happen was that the lock mass files were always called myFileName02.CDF. If this is different on your conversion then you need to change the 0x.CDF to 02.CDF. Then use the lockMassFreq=TRUE and everything should be good. The peak detection will only happen on the 01.CDF files and keep the 02.CDF (lock mass files) for correction.
I hope that this is going to clean up a lot of the issues with the lock mass correction. There's always a lot that happens with the lock mass correction, we always find interesting things happening with our data.
Let me know how you get on.
Paul
EDIT: Asun - In the paper for the lock mass gap correction we looked at the integrated intensity of the peaks but not really peak picking detection. We did find that most of the same peaks were detected along with some peaks that were not detected previously. This was using the mzData format. I would be very interested to know what results you get and if it makes a difference to the peak detection quality.