Using Panorama .clib File to generate scheduled MRM methods

Using Panorama .clib File to generate scheduled MRM methods hogan  2019-11-06


I am wondering why you cannot generate a scheduled MRM transition list using just a .clib file from a Panorama Chromatography library. I have uploaded multiple proteins from multiple runs/documents into the library and can export one concatenated clib file that I thought would allow me to generate a scheduled method with all of the validated targets. I pull the .clib file into a new document and when I attempt to generate a scheduled method it throws an error that I need scheduling information from a data file to generate a scheduled method/transition list.

The clib file contains the RT, Precursor, and Y ion information for all the peptides in the library. Why can it not be used to generate a scheduled transition list without importing data.



Brendan MacLean responded:  2019-11-09

Hi Kyle,
Just as with a BLIB spectral library, which also has measured retention times in it, a CLIB is assumed to be a general library where absolute measured retention times on the instrument used to create the library are not necessarily directly applicable to your current instrument or chromatography. It is assumed that a certain chromatographic setup is a temporal thing that can't hope to last long enough to be used directly from library collection to library use.

Therefore, you would need to recalibrate the measured retention times to your own system or current chromatography, usually using iRT as supported by Skyline. CLIBs and BLIBs also support storing iRT values and using them to populate a "Retention Time Calculator" for a retention time predictor in Skyline. If you get that set up correctly, then all you need to do is measure your standards on your current set-up and use that measurement to calibrate predicted RTs for the rest of the peptides in your library.

If you are not familiar with iRT, then you should have a look at the iRT Retention Time Prediction tutorial:

Hope this helps. Thanks for exploring CLIBs on Panorama.