spectrum_utils

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While using annotate_proforma(), we noticed that several fragments have isotopic peaks, which are currently not annotated.

issararab

Include code examples in the documentation on how to read spectra from peak files using various software packages (Pyteomics) and initializing `MsmsSpectrum` objects.

bittremieux

Cross-link spectra annotation

1

Hi, I was looking to annotate spectra containing cross-linked peptides (using DSS; XLMOD:02001). I can't seem to get the peaks of the cross-linked ions in the plot. Is there an...

jstrobaek

Investigate [Lark-Cython](https://github.com/lark-parser/lark_cython) for faster parsing of the ProForma grammar.

bittremieux

When given a proforma like: `[+56.026215]-K[+70.041865]SAPSIGGVK[-28.0313]K[+56.026215]PHR/3` the masses returned do not contain the sign if they are positive, the returned proforma is: `[56.026215]-K[70.041865]SAPSIGGVK[-28.0313]K[56.026215]PHR/3` Regards Yasset

ypriverol