Request: Consistency between note importing and exporting Chris Ashwood  2024-06-06 23:14
 

Dear Skyline Team,

I hope you've had a great ASMS. I've been working on my reports, and noticed that when I import a transition list, only one form of note is available, "Note". However, when I try to export the same note from the document, there are four different note types (transition, precursor, molecule, molecule list). Skyline seems to default that "Note" in the transition list import is a "Transition Note", and this cannot be changed in the transition list import stage. This becomes problematic when exporting MS1 data with isotopes because only the monoisotopic line in the export features the imported note.

Could the transition list import feature please be updated to include all existing note forms? I would like to say that a note is a precursor note, ensuring the note is specified across different isotopes coming from the same precursor.

Cheers,
Chris
 
 
Brian Pratt responded:  2024-06-12 08:23

Hi Chris,

That's a good idea, and not terribly difficult to implement. I'll add it to our development queue.

Cheers
Brian
 
Chris Ashwood responded:  2024-06-12 19:15

Hi Brian,

Sounds great, thank you!

Cheers,
Chris
 
Brian Pratt responded:  2024-08-14 13:45

Hi Chris,

Do you have an example report that you can share?

Thanks

Brian
 
Chris Ashwood responded:  2024-08-15 05:34

Hi Brian,

Thanks for looking into this, please find attached. It would essentially report the "Molecule Note" instead of the "Transition Note" that is currently populated based on the "Note" field from the transition list import. By "Transition Note" being the only note transferable across import of transition list to export of the report, you'll see that we essentially have a duplicated row for every transition but since we're only monitoring idotp and MS1 peak area, there's no need to export each transition as a row, rather "Molecule Note" would be the desired level of notation. That way, we would only get one row per molecule per file.

In our specific case, we have a "search engine" that assigns chemical formulae/molecules to observed precursor m/z values from a series of files. The filename in which the match is observed is written as the Note on the transition list import.

Cheers,
Chris
 
Brian Pratt responded:  2024-08-15 11:24
So if I understand you properly, you'd like this list to import properly if the header line was this

Molecule List Name,Molecule Name,Molecule Formula,Precursor Adduct,Total Area MS1,Isotope Dot Product,Transition Note,Replicate Name,Molecule Note
Glucose Polymers,(Hex)3,C18H32O16,[M-H],1299522,0.9961,,20240705_CA_Poly_PotatoStarch.mzML,Dextran
Glucose Polymers,(Hex)3,C18H32O16,[M-H],1299522,0.9961,,,Dextran
Glucose Polymers,(Hex)3,C18H32O16,[M-H],1299522,0.9961,,,Dextran
Glucose Polymers,(Hex)4,C24H42O21,[M-H],995043,0.9913,,20240705_CA_Poly_PotatoStarch.mzML,Dextran
Glucose Polymers,(Hex)4,C24H42O21,[M-H],995043,0.9913,,,Dextran
Glucose Polymers,(Hex)4,C24H42O21,[M-H],995043,0.9913,,,Dextran
etc

but you'd also like to not have all those redundant lines, so your report could just be

Molecule List Name,Molecule Name,Molecule Formula,Precursor Adduct,Total Area MS1,Isotope Dot Product,Replicate Name,Molecule Note
Glucose Polymers,(Hex)3,C18H32O16,[M-H],1299522,0.9961,20240705_CA_Poly_PotatoStarch.mzML,Dextran
Glucose Polymers,(Hex)4,C24H42O21,[M-H],995043,0.9913,20240705_CA_Poly_PotatoStarch.mzML,Dextran
Glucose Polymers,(Hex)5,C30H52O26,[M-H],2301748,0.9939,20240705_CA_Poly_PotatoStarch.mzML,Dextran
etc.

If possible, it would also be handy to have an example Skyline document that uses the report format (Files > Share > Store Everything).

Thanks
Brian