Hello,

I'm currently trying to preprocess my GC-MS data. Initially my files are in a XMS format and I converted them in netCDF using OpenChrom. When using readMSData function on it, only the TIC en rtime are being extracted, but not the single ions' mz nor their intensity.

Is it an issue with netCDF files or is there a way to get those informations ?

Best regards, Julien

If you read the data with readMSData and the mode = "onDisk" then indeed only the retention time, tic and other information are imported. You can access the m/z and intensity values then by calling mz or intensity on the object returned by readMSData (i.e. the OnDiskMSnExp object).