If you are referring to the library available at https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:lib:phoshopept_labelfree_20190214, I don't see anything unusual about it - indeed, the description says "It is also directly readable by some software applications, including Skyline, after unzipping."

I didn't encounter any difficulty importing it into Skyline - perhaps you can supply some screenshots to describe the problem you are experiencing.

Thanks for using the Skyline support board,

Brian Pratt

Yes, I could import it into Skyline. However, it does not show any spectra for our phosphopeptides. I was wondering if this is related to the file format or if this library does not contain spectra for our targets.

I'm still not understanding the nature of the issue. If you can provide a screenshot, or better yet a Skyline document (use File | Share in Skyline, include at least one of your mass spec data files) we will be able to better assist you.

I shared the file in file sharing.
Name: Unscheduled_PRM.sky.zip
We need MS2 peak intensity predictions for our phosphopeptides. I imported the msp file as a spectral library, but there are no spectra for our phosphopeptides in this library.

Thank you for uploading your Skyline document including the .msp file.
The syntax used for describing modifications is different from what Skyline is expecting.

Skyline expects modifications to be described with something containing "/" characters, for example:
Mods=2/13,C,Carbamidomethyl/15,C,Carbamidomethyl

The modifications in your .msp file look different, and seem to be using parentheses instead of slashes:
Mods=2(10,S,Phospho)(14,C,CAM)

When I look at other .msp files that have been uploaded to the support board, I see a lot of files that use this syntax that Skyline does not understand.
I imagine that we will need to add support for this to Skyline.
I am not the expert on .msp files in Skyline so I will ask my coworkers what we should do.
-- Nick

Thanks for looking at this, Nick.

I'm not surprised at this diagnosis. The .msp format is very loosely specified: we encounter all kinds of novel implementations. Keywords may vary, or may appear within a "comment" line (or "comments" line!) alongside other key-value pairs instead of on individual lines, and the representation of the value itself may vary - as is the case here.

I'll add handling for this variant.

Brian