Small Molecule Untargeted Exploration of MS2

Small Molecule Untargeted Exploration of MS2 bwidner  2019-04-09


I am new to Skyline and interested in using it for small molecules for targeted and untargeted analysis. Is there a way to click on a MS1 scan and see the MS2s that were collected for that scan? I looked through the tutorials, and I couldn't find this. I only found mention of MS2s for targeted analysis.


Brendan MacLean responded:  2019-04-09

Hi Brittany,
That's just not what we do. You need to choose some targets of interest and Skyline will help you measure them consistently or explore their presence in your data, but we don't do much untargeted data exploration.

You might have a look at the tool SeeMS in the ProteoWizard tools suite. Just install ProteoWizard from here:

And it should install an "Open with SeeMS" menu item on the Windows Explorer right-click menu. Then just right-click on your raw data file of interest, click Open with SeeMS and you should be able to explore the spectra in your raw data file. Though, you can also do this with many instrument vendor-supplied tools, like Xcalibur and Analyst.