lazear
commented
1 year ago Couple different options I use:
- You can use PeptideShaker to visualize Sage search results (https://github.com/compomics/searchgui/issues/334 - find the links for downloads in this thread, or direct link to https://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/2.2.18-beta/PeptideShaker-2.2.18-beta.zip).
- You can map Sage results onto mzml spectra using https://github.com/bittremieux/spectrum_utils
- If you want to put in the effort to do something more advanced, I have python bindings for Sage (that enable interactivity with the search engine) on Github as well: https://github.com/lazear/sage-pyo3
How do you check the hits? A visual display of the spectra and ion assignments is very useful. Did you use something in development? I see a high number of chimeric spectra returned. I would like to look at these spectra assignments to think about the appropriate scoring thresholds.