MSFraggerGlyco to Skyline document

[juank1892]

- Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.) log_2024-08-29_17-44-58.txt

- Describe the issue or question: Hi there,

(Beforehand apologies! I have not played with FragPipe in quite a while!)

I downloaded the dataset of this publication https://pubs.acs.org/doi/10.1021/acs.analchem.3c05874 with PXD047898. I was able to re-run the search of some of the files and could identify some glycopeptides although not comparable number to those reported. I also tried using the new Skyline document creation option, but noticed that no glycopeptides made it to the document.

I have attached the log file to see if you can point me out to some settings that are not optimal.

When creating a spectral library for Skyline, which score should be used to filter the output?

Please let me know what other information would you need me to share to solve this concerns.

Looking forward to your response. JC