When you import a transition list into Skyline, you have to use column names that Skyline recognizes.
I can rename/remove some of the columns in the sml_translist.csv that you attached, and then Skyline is willing to import it:
MoleculeGroup,PrecursorName,PrecursorMz,PrecursorCharge,ProductMz,ProductCharge,PrecursorCE,ConeVoltage,ProductName
Compound 1,Molecule [2240.401097/2240.401097].light,1120.2,2,366.2,1,35.7,4,Ion [366.200549/366.200549]
Compound 2,Molecule [2345.401097/2345.401097].light,1172.7,2,366.2,1,37.4,4,Ion [366.200549/366.200549]
Compound 3,Molecule [2491.601097/2491.601097].light,1245.8,2,366.2,1,39.6,4,Ion [366.200549/366.200549]
If you you want to change all of the peptides in a Skyline document into small molecules, you can do a pretty good job by exporting a report that looks like a transition list, and then importing that.
Unfortunately, the report that comes with Skyline called "Small Molecule Transition List" does not have quite the right columns to be able to do this.
I have attached a .skyr file which does have a report that works.
You can get that .skyr file into Skyline by doing:
File > Export > Report > Edit List > Import
and then if you have a peptide document, you can export the report called "PeptideSmMolTranList" and you will have a .csv file that you can import into Skyline and get a document that measures the same transitions, but that treats everything as a small molecule.
I am still not sure that I understand your question, but I hope this helps. |