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bittremieux / spectrum_utils

Python package for efficient mass spectrometry data processing and visualization
https://spectrum-utils.readthedocs.io/
Apache License 2.0
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No keyword argument neutral_losses for annotate_peptide_fragments #21

Closed Trulsson closed 3 years ago

Trulsson commented 3 years ago

print(inspect.signature(spectrum.annotate_peptide_fragments))

Returns

(fragment_tol_mass: float, fragment_tol_mode: str, ion_types: str = 'by', max_ion_charge: Union[int, NoneType] = None, peak_assignment: str = 'most_intense') -> 'MsmsSpectrum'

Was this feature removed?

bittremieux commented 3 years ago

No, the opposite actually. Annotating neutral loss peaks is not included in the latest release on PyPI (v0.3.5) yet. It will be included in spectrum_utils version 0.4.0, but I want to add ProForma support as well before releasing a new version.

If you want to annotate neutral loss peaks, for the moment you can install the development spectrum_utils version directly from GitHub:

pip install git+https://github.com/bittremieux/spectrum_utils.git

Apologies for the inconvenience.

Trulsson commented 3 years ago

I see! Thanks for the quick reply, most appreciated.