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levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
http://pyteomics.readthedocs.io
Apache License 2.0
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Addition of spectrum_utils backend #43

Closed levitsky closed 2 years ago

levitsky commented 3 years ago

@bittremieux I'm thinking of adding integration with spectrum_utils to pylab_aux.annotate_spectrum. What do you think?

The idea is to take the work of transforming the spectra from pyteomics format to spectrum_utils off the user. It can be tested with the following (based on spectrum_utils doc):

from pyteomics import pylab_aux as pa, usi
spectrum = usi.proxi('mzspec:PXD004732:01650b_BC2-TUM_first_pool_53_01_01-3xHCD-1h-R2:scan:41840', 'massive')
peptide = 'WNQLQAFWGTGK'

pa.annotate_spectrum(spectrum, peptide, precursor_charge=2, backend='spectrum_utils',
     scaling='root', min_intensity=0.05, ion_types='aby', remove_precursor_peak=True, colors={'a': 'yellow'})
bittremieux commented 3 years ago

Hi Lev, apologies for the slow reply. Integrating spectrum_utils in pyteomics would be very cool! I'm currently a bit overwhelmed with grant writing duties, but I'll try to have a look at the code asap.