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Glycopeptide analysis and NIST library import

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Glycopeptide analysis and NIST library import tschilp1  2025-07-14 02:03
 

Hi,

I am running into issues trying to import an exisiting IgG glycan library from NIST:
Glycopeptide Mass Spectral Library (HCD) of Human IgG1 mAb Drugs

Is it possible to use this library without any additional DDA result files?

Do you have additional tips for glycopeptide analysis in DIA data? I have seen some support topics about this but I'm fairly new to this and trying to figure things out with the neutral loss and modification settings.

Thank you in advance.

Best,
Tom Schilperoord
 
 
Nick Shulman responded:  2025-07-14 16:04
The way to use a .msp file in Skyline is to add it as a library.
That is, you go to the "Library" tab at "Settings > Molecule Settings" and push the "Edit List" button and then "Add".

Unfortunately, when I do that with the "IgG_Glycopeptide _HCD_V1.msp", I see a bunch of messages in the Immediate Window that say things like:
Missing details for TKPREEQYNSTYR_G33100/4/E12 at line 4, this entry will be ignored

It appears that every entry ends up getting ignored because when I go to:
View > Libraries > Library Explorer I do not see anything in that library.

Is that the same sort of issue that you are running into?
I am not the expert on .msp files in Skyline but I could try to find someone to investigate this.
-- Nick