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Problem with SCANS=0 in MGF files - MN and Library Search #787

Closed crisfbazz closed 2 years ago

crisfbazz commented 2 years ago

When running the Library Search with a MGF that have an ion with SCANS=0, this ion does not appear in the results. When running the Molecular Networking with the same MGF, in the clusterinfo output file the #Scan column is wrongly set to 1 instead of 0 for the ion with SCANS=0.

To Reproduce

  1. Create a MGF file with 3 identical ions, with SCANS number from 0 to 2 and with a MS/MS that is present in the GNPS Libraries
  2. Run the Molecular Networking and Library Search workflows using this MGF file
  3. Inspect the output, looking for the SCANS=0 library results and clusterinfo values

Expected behavior The ion with SCANS=0 should be present, but will be missing in the Library Search result and the other 2 identical ions will be present. And in the Molecular Networking result the #Scan column value for the ion with SCANS=0 will be set to 1 in the clusterinfo table instead of 0.

Below is a MGF file to reproduce this behavior. test_library_search_scans0.txt

mwang87 commented 2 years ago

a scan number of 0 is not really valid in GNPS. We expect scan numbers to start at 1 for MGF files.

crisfbazz commented 2 years ago

oh, good to know that. I'll close this issue then. Thank you