Can I visualize my LCMS data acquired with Shimadzu (.lcd files)? dimitris korovesis  2022-09-01
 

Hello,

I just download the Skyline beta, based on a thread for reading .lcd files so that I can open my LCMS data. These data concern assessing the purity (e.g. in the UV trace) of samples from organic reactions and checking whether small molecules I synthesised in the lab have the expected mass. Is Skyline beta the right software to use for looking at my data?
After installing and running the software, I chose "molecule interface" and clicked on "Blank Document". Then I tried opening my data, either by dragging it in the Skyline or through "Open" but doesn't open it. Probably I'm doing something wrong so any help on how to easily open my data would be greatly appreciated. For convenience in case someone wants to test it, I have attached the lcd file.

Thanks a lot.

Best,
Dimitris

 
 
Nick Shulman responded:  2022-09-01
I believe that Skyline cannot do anything with this data.

We have a different program called "SeeMS.exe" which you get when you install ProteoWizard:
https://proteowizard.sourceforge.io/download.html

SeeMS.exe will let you look at the spectra in that file. I do not understand what kind of spectra they are.
SeeMS says that their MS Level is zero, which means that Skyline will not be able to do anything with them.

Typically what you need to do with Skyline is first tell Skyline which molecules you are interested in looking at. For small molecules you usually have to do "File > Import > Transition List" and import a CSV file containing a list of your molecules and transitions. If you wanted Skyline to extract data from MS1 or MS2 spectra you would then have to go to "Settings > Transition Settings > Full Scan" and tell Skyline what to do with those spectra.
After you have told Skyline which transitions to extract chromatograms for you can usually use the "File > Import > Results" menu item to extract chromatograms.

The small molecule tutorial is a great place to start:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule

However, Skyline is not the right software for your data file.
-- Nick