readMSData to support lock mass

[zhijcao]

Hi there, I am trying to use XCMS analyze metabolomics data. The raw files were generated from Waters q-tof with three functions (MS1, MS2, Reference: see details at end of this email). I have converted raw files to CDF format, which each raw file became three CDF files related to three functions. I am using readMSData function to read the raw files, but I cannot find any option parameters to deal with lock mass. I appreciate it if you could provide a way to support the lock mass. Thank you, zhijun

[sneumann]

Hi, my preferred way would be to have the data already in calibrated form. The newer (all 2018 should support it IIRC) Proteowizard msconvert are supposed to write recalibrated mzML. Would that be an option ? Yours, Steffen

[zhijcao]

Yes, make sense. Yours, zhijun

[xiaodfeng]

@sneumann Thank you for the suggestion. I also come across the lock mass issue with waters q-tof data. We use only Leucine encephalin for lock mass with a a neutral Mass: 556.27724. The mass trace of the .raw data is shown as the following figure:

There are three clear line of lock mass around MZ 557. And I am sure the middle line (shown in the red dot) of the lock mass is from [M+H] with a MZ 557.2845. But the other two lines don't match any adducts of Leucine encephalin. Any ideas of these two lines?

The msconvert parameters for recalculating the lock mass are shown in the following figure with reference mz 557.2845 and tollerence: 0.003. Am I setting the right parameters?

[stanstrup]

You should use the scanEvent filter (I think commandline only) to remove the lockmass function. Getting calibrated data and removing the scans are separate issues. Many files don't require the lockmassRefiner filter so you should check without first.