Closed animesh closed 3 weeks ago
Hi @animesh apologies if the documentation was unclear. Since you are working with LC-MS data, the data is converted to an mzML file. The --imzml_mode parameter is meant for mass spectrometry imaging datasets from the MALDI source on the timsTOF fleX which produces imzML files instead of mzML. Therefore, for your datasets, it makes no difference what you set this parameter to. I will work on updating the documentation to explicitly mention this.
my bad, i though "i" was for ion-mobility 🤪 how is timsconvert dealing with that BTW?
TIMSCONVERT handles ion mobility data by essentially adding a third binary data array for the 1/K0 values. In these mzML/imzML files, the 3 binary data arrays are derived from a long dataframe containing the m/z array, intensity array, and 1/K0 array that are pulled using the TDF-SDK.
I have tried with and without
--imzml_mode continuous
but no difference in output it seemsis
continuous
the default modeeven if specified otherwise
or based on input, it gets fixed?