v0.5.0a0

0.5.0a0 - 2024-09-03

Added

• Bubble plot for mass errors by @RalfG.
• Speedup of peptide parsing and annotation by @jspaezp.
• Generate theoretical fragments for non-monoisotopic peaks.

Fixed

• Support Python 3.11.
• Ensure proper version number is set when installed using Conda.
• XLMOD location changed from the mzIdentML repository to a dedicated repository.
• Metabolomics USI resolver moved from GNPS to GNPS2.
• Replace deprecated appdirs dependency by platformdirs.

v0.4.2

0.4.2 - 2023-04-26

Added

• Verify that the given mass tolerance unit is always "Da" or "ppm".

Changed

• Update to matplotlib version 3.5 and above.

v0.4.1

0.4.1 - 2022-10-10

Fixed

• Plot spectra without a ProForma peptide annotation.

v0.4.0

0.4.0 - 2022-10-06

Added

• Load spectra directly from online resources (ProteomeXchange members, metabolomics resources through GNPS) using the Universal Spectrum Identifier mechanism.
• Full support of the ProForma 2.0 standard based on a formal context-free grammar.
• Retrieve controlled vocabularies used by ProForma from their online sources and (cross-platform) cache locally.
• Annotate different ion types: peptide fragments, internal fragment ions, immonium ions, intact precursor ions.
• Annotate spectrum peaks that include a neutral loss.
• Recommend installing pyteomics.cythonize for faster mass calculations.
• Automatic code style enforcement using black.
• Added contributing guidelines.
• Added code of conduct.
• Added .gitignore.
• Minimum supported Python version bumped to Python 3.8.
• Maximum supported Python version extended to Python 3.10.

Changed

• Annotate spectrum peaks based on the ProForma 2.0 specification to described (modified) peptides.
• Use jitclass instead of multiple jit functions to group the Numba spectrum processing functionality.
• Use MyST instead of recommonmark to generate the documentation from MarkDown files.
• Update runtime benchmark to the latest versions of all libraries.

Removed

• annotate_molecule_fragment function to annotate peaks with a molecule string.
• annotate_mz_fragment function to annotate peaks with their m/z values. Use the ProForma interface instead.
• Global interface to set a static modification; specify modifications using ProForma directly instead.

Fixed

• Don't crash when plotting empty spectra.
• Use the correct 13C mass difference for isotope precursor removal.

v0.3.5

• Remove RDKit as a dependency.

v0.3.4

Including changes for version 0.3.3:

• Python 3.8 support
• Bugfix when the input m/z and intensity NumPy arrays are read-only
• Bugfix for annotating peptide fragments with precursor charge 1

v0.3.2

Update version number

v0.3.1

• Mirror plot bugfixes for y-labels and peak annotations

v0.3.0

• Interface to set static amino acid modifications
• Molecule structure peak annotations
• Custom peak annotations
• Minor plotting improvements

v0.2.1

• FIX: Correctly calculate the mass of multiply charged fragments of modified peptides