Annotating modified lysine Immonium NH3 neutral loss

[bittremieux]

Annotating modified lysine Immonium NH3 neutral loss

[mwang87]

Yes totally possible, for example in the interactive interface you can see it here:

http://metabolomics-usi.gnps2.org/dashinterface?usi1=mzspec%3AMSV000085444%3AHui_N3_fe%3Ascan%3A500&width=10.0&height=6.0&mz_min=None&mz_max=None&max_intensity=125&annotate_precision=4&annotation_rotation=90&cosine=standard&fragment_mz_tolerance=0.1&grid=True&annotate_peaks=%5B%5B%5D%2C%20%5B%5D%5D

[mwang87]

[HijaziHassan]

Thank you for this awesome tool.
I am working with an unpublished data so the usi help me now. Actually, I was using the pa.annotate_spectrum function with backend='spectrum_utils' from pyteomics library. There, I did not find any argument that allow me to annotate such kind of fragments.
Could you please point me at any?

[bittremieux]

If you directly use spectrum_utils itself, you can annotate spectra using MsmsSpectrum.annotate_proforma.

In your case, you'll want to do the following:

• For immonium ions, include "I" in the ion_types of annotate_proforma.
• For loss of ammonio, include {"NH3": -17.026549} as neutral_losses. (Or set neutral_losses=True to consider several common losses, as described in the API documentation.)
• By default, spectrum_utils will only display annotated peaks for standard b/y ions. See here how to customize the spectrum plotting.