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This is the conversion for Agilent.

MSConvert and GNPS2

One of the key issues with Agilent software converted with MSConvert, is that the MSConvert makes the scans non-sequential. Molecular Networking does not like this, so we have created a workflow in GNPS2 that renumbers the MS scans so that it is sequential. The general process involves this:

  1. Convert the Agilent data with MSConvert
  2. Upload the data to GNPS2
  3. Run the Agilent Conversion workflow
  4. Run the Classical Molecular Networking workflow in GNPS2.

Agilent Software - Qual

We can also do export directly from Agilent software.

TODO: Finish this