NIST mps phosphopeptide library issue

NIST mps phosphopeptide library issue anne-christine uldry  2019-04-03

Dear Skyline developers,

We've just had a little issue with one of the NIST msp libraries, the human phosphopeptide spectral library human_hcd_labelfree_phospho_selected_passed.msp, which is deposited for instance here:

When we loaded it into Skyline via Peptide settings/Library, we noted that no phosphorylation (or any other usual modifications) was marked anywhere upon inspection of the library in View/Spectral Library, although the msp file loaded without warnings or error messages.

Upon inspection of the msp file, I noted that the format of the modifications in the phospho peptide msp was different to that, say, of hsa20140422.msp, which I found here
and which seems to exhibit modifications as expected when viewed as spectral library inside Skyline.

In the former the mods are marked thus


while in the latter they are marked as, for instance,


So I managed to solve my problem of reading the NIST phospho msp in Skyline simply by changing all the "(" of Mods into "/" and the ")" to nothing; that seems to work, in the sense that I now do see the relevant modifications in the spectral library, what I see in the file appears on the spectra, and there were no warnings or error messages while loading.

I am not familiar with the msp format, and cannot tell which of the two Mods formats I saw is the standard.

My questions to you however are

  1. Do you see any issues with my simple "sed" solution, or could they be other surprises with this (perhaps not very standard) human_hcd_labelfree_phospho_selected_passed.msp file ?

  2. Will Skyline be able in some future version to read this kind of msp format?

Many thanks in advance for your reply.

Kind regards,
Anne-Christine Uldry

Brendan MacLean responded:  2019-04-13

Hi Anne-Christine,
Nice work figuring all this out on your own. That sounds like a reasonable solution. We are always interested in improving Skyline to do a better job of recognizing the formats produced by other tools to help our users avoid having to do this kind of work, but we appreciate the people like you who lead the way and then give us clear descriptions and examples of what we should fix.

I have posted this to our issues list with you in the notification list. So, you should be notified when it is fixed.

Thanks again for the very clear bug report, and even coming up with the workaround.