Question about library intensity for small molecule transition list

Question about library intensity for small molecule transition list stefanie  2021-06-24


I am investigating Skyline's small molecule interface for our metabolomics data processing workflow. I am new to Skyline, so I apologize if this question has been asked and answered.

I am interested in importing an assay library (or transition list) with retention times and relative fragment intensities. So far, I can successfully import a transition list with these fields: PrecursorName, PrecursorFormula, PrecursorMz, ProductMz, ProductCharge, PrecursorAdduct, PrecursorRT, PrecursorRTWindow, PrecursorCE.

What is the best way for me to import this component of our spectrum data for my metabolites to Skyline? Is there a field name that would allow me to attach relative intensities to these entries as well? I noticed the LibraryIntensity field was present in the "Skyline format.tsv" import file for Webinar 10 (proteomics) but not present in the list of column names for small molecule transition lists in a previous support ticket (2018, see link below). If I'm trying to use the wrong tool, could you suggest an appropriate alternative for me in creating a Skyline-friendly library?

Thank you for your time and your assistance,
~Stefanie Kairs

Reference links:
Webinar 10
2018 Support Ticket "small molecule transition list error"

Brian Pratt responded:  2021-06-25

Hi Stefanie,

We have not yet implemented Assay Libraries for small molecules - yours is the first request. If you can provide an example we will see how much work it would be to adapt what we have to give you what you are looking for.

Thanks for using the Skyline support board!

Brian Pratt

stefanie responded:  2021-06-30

Hi Brian,

Thank you for the quick reply. It took me a bit to respond because I've been working with our mass spec scientists on the best example to offer.

We would like to be able to bring in spectrum information about our metabolite targets and have Skyline match these compounds on fragmentation in the experimental results files we import, but I'm not sure how to get there. Thanks for helping us figure it out!

I've attached a .csv file that has a transition list for a few example metabolites, with one additional field to capture their relative abundance information. (Without this field, I was successfully able to bring in these transitions via copy/paste to insert transitions or using import>transition list).

Our team would like to know:

  • Is importing/inserting transitions the right way to bring in spectrum information for metabolomics (small molecules)?
  • If not, what Skyline tools would you suggest that we use?
  • If we are able to bring in spectrum information via attaching relative abundance values to our transition list import, will Skyline match these compounds on fragmentation in our experimental data and provide dotp values for those matches?