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Target small molecule

a das

2025-03-16 00:48

Dear Skyline support,

I have done targeted MRM assay with peptides. Now I want to do the same targeted MRM with small molecule named Lactobionic acid.

My queries (total 3) related to:

How can I add this molecule to Skyline file?
I want to export the isolation list and use it as acquisition MRM method. After acquiring the MRM results, I want to check the presence of lactobionic acid in different samples.

I have followed the attached document which helps me to have an idea.
But I am unable to know the precursor and product charge of Lactobionic acid.

Please help me how I can proceed with Lactobionic acid. If you can share a skyline file with all the settings, it would be a great help.

Instrument: Xevo G2 XS qTOF

Thank you
Arpita

Nick Shulman responded:	2025-03-16 18:18
This web page has some information about what sort of transitions to expect from Lactobionic acid: https://pubchem.ncbi.nlm.nih.gov/compound/Lactobionic-Acid#section=LC-MS The set of transitions to expect seem to depend on whether you are starting with a precursor which is [M-H]- or [M+Na]+. In Skyline, "PRM" is the term that we use for the type of experiment where the mass spectrometer takes a list of precursor m/z values to isolate and collects MS2 spectra. Hope this helps, -- Nick