Missing retention time when importing MSP file

Missing retention time when importing MSP file bart van puyvelde  2019-02-04

Dear Skyline team,

Is it possible to include retention time in an .msp file? In Progenesis QI for proteomics, we have the possibility to export our spectral library as an .msp file (with RT in mins included), after importing mascot search results. However, when I try to add an .msp library into Skyline, RT's are missing. Is it possible for Skyline to read the RT's as well?

At last, I would like to thank you for the amazing work on the new features (Audit log, Waters lock mass correction).

Kind regards,
Bart Van Puyvelde

Brian Pratt responded:  2019-02-04

Hi Bart,

In your example file (thanks for that!), if the line
RetentionTimeMins: 86.874
was written as
RetentionTime: 86.874
then Skyline would already handle it.

We can certainly add support for this variant, but for your immediate purposes you can run that file through a search and replace and it should work fine for you.

Thanks for using the Skyline support board!

Brian Pratt

Brian Pratt responded:  2019-02-04

I'm afraid I spoke too soon. It appears that we parse that RT information but don't currently pass it through. So no immediate quick fix, but still not a big deal to get that working in the next Skyline-Daily.


bart van puyvelde responded:  2019-02-04

Hi Brian,

Thank you very much for the quick answer !!!

It would be awesome if this could be fixed in the next Skyline-Daily edition. It would save me a lot of time !!

Kind regards,

Brian Pratt responded:  2019-02-05

Pretty simple change, it's in code review now.

MSP is yet another format that is only very loosely standardized. Was including RT an option you had to select when you exported the MSP? If so, were there other options we should be anticipating, such as ion mobility etc?



bart van puyvelde responded:  2019-02-07

Hi Brian,

Thank you very much!

Indeed, standardization could be very helpful. Still a lot of companies tend to come up with new formats or product specific names.

I have checked the exported .msp with HDMSE data, but no ion mobility parameters are incorporated.