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small molecule transition list error dspiciarich  2018-04-25 15:31
 
I've generated a small molecule library that I'm able to manually inport into skyline (see attachment #1). Everything seems to load correctly and I can export the transition list. However if I close the window and then try to re-import the transition list into the gui, I get an error (see 2nd attachment).

When I try to use skylinerunner I get the following error:

Error: Failed importing the file c:\skyline_test\exported_sml_molecule_translist.csv. Failed to find peptide column., line 1.

I think my .sky file is expecting proteomic data and that I need to tell it that it should expect small molecule data. Is this correct? How do you recommend proceeding?

These are actually peptides but that I want skyline to treat the transitions as small molecules because the transitions wouldn't be predicted by the molecular weight or the molecular formula.

Thank you.
 
 
Nick Shulman responded:  2018-04-25 15:53
Can you attach that file "exported_sml_molecule_translist.csv"?

I believe SkylineRunner expects the same sort of file as doing:
File > Import > Transition List

The first row of a small molecule transition list should be the column names ("PrecursorFormula", etc).

It's only if the first row does not have the column names that Skyline then tries to guess which column is the peptide sequence.

This is the complete list of column names that you can use in small molecule transition lists:
MoleculeGroup
PrecursorName
ProductName
PrecursorFormula
ProductFormula
PrecursorMz
ProductMz
PrecursorCharge
ProductCharge
PrecursorRT
PrecursorRTWindow
PrecursorCE
PrecursorDT
HighEnergyDTOffset
PrecursorIM
HighEnergyIMOffset
IMUnits
PrecursorCCS
SLens
ConeVoltage
CompensationVoltage
DeclusteringPotential
Note
LabelType
PrecursorAdduct
ProductAdduct
CAS
InChiKey
InChi
HMDB
SMILES

You can also put a space in the middle of some of those names, so that they look the column names that you see when you do:
Edit > Insert > Transition List
 
dspiciarich responded:  2018-04-25 17:22
Maybe I'm misunderstanding but what I'm trying to do is look for peptides that won't be predicted by the peptide sequence so I'm trying to use the small molecule feature. I can do this in the gui but when try to do this with skylinerunner it is looking for peptides.

Also when I export my transition list and then try to reimport my transition list it throws an error that my transitions are for peptides. Any thoughts on how to resolve this?

Thanks,
David
 
Nick Shulman responded:  2018-04-25 18:15
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.
 
dspiciarich responded:  2018-04-25 18:21
Thank you Nick, I really appreciate it.

-David