Feature Request: A new column in .blib RefSpectra table (iRT method and value)

support
Feature Request: A new column in .blib RefSpectra table (iRT method and value) Chris Ashwood  2018-01-27 05:20
 
Dear Skyline Support,

First of all, thanks for the great software and recent new features.

I'm currently preparing a small molecule .blib library (~200 precursors) and have been considering criteria to achieve correct automatic peak picking in samples containing unknowns using the spectral matching feature.

It looks like I can improve the success rate of correct automated peak picking with ion mobility CCS or retention time values. Unfortunately molecule retention time can be variable between samples/batches/columns/labs and is difficult to pick the right peak when peaks are quite close together. Maybe implementing an iRT field into Skyline would improve the retention time filtering option?

Although iRT is not currently applicable using the Skyline small molecule feature, it would be nice to be able to give more information in a spectral library to make it more widely applicable for other labs. I'm interested if this is in the pipeline or a solution already exists for the proteomics side of Skyline that I'm not familiar with?

Cheers,
Chris
 
 
Brian Pratt responded:  2018-01-29 12:24
Hi Chris,

One of the most important features of the Skyline 4.1 release is the change to small molecule handling which brings the internal model into line with that already in use for peptides (neutral molecule with adducts, similar to neutral peptide with charge+modifications). It's perhaps subtle from the user perspective, but programmatically it's now much easier to extend small molecule support to things like spectral libraries (done) and, yes, iRT (not done, but now possible).

So, look for small molecule support in iRT, optimzation libraries, IMS libraries, and others in upcoming Skyline-Daily releases. I don't have a schedule to offer for that yet. But now that it can happen, it will.

Cheers

Brian
 
Chris Ashwood responded:  2018-01-29 14:23
Hi Brian,

Thanks for the reply. The fundamental backbone to Skyline is out of sight for me, therefore out of mind. Thanks for reminding me :).

Cheers,
Chris