ABF converter in CMD

July 14, 2022, 05:50:04 PM

Hi there,

I am trying to automate a workflow using compMS where I need to convert my input files to .ABF before running compms for LCMSDDA. We noticed some missing peaks when using MZML files as inputs. Is there any way to use ABF convert as part of a batch script? I have not been able to make the .exe files in the ABF convert download work on the command line.

Thanks,
Jonah

Re: ABF converter in CMD

Reply #1 – July 21, 2022, 08:48:52 PM

In addition to drop in signal intensity (to be expected apparently), I have also noticed some missing peaks when using centroided *.mzML files as input for the ABF converter. For me, my processing steps were:
profile Sciex *.wiff files --[msConvert peak picking 1- ]--> centroid *.mzML --[ABF converter]--> *.abf

I find the best results I get, however, are obtained by simply loading *.wiff files directly into MS-DIAL, or going straight from *.wiff to *.abf without centroiding if using the MsdialConsoleApp.

PS - These were SWATH DIA files

Cheers,
Triston