|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
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
Many thanks in advance for your reply.