Wout Bittremieux
Wout Bittremieux
The [nnDescent constructor docstring](https://github.com/lmcinnes/pynndescent/blob/master/pynndescent/pynndescent_.py#L657) states that `compressed` is False by default, by the [default value is actually `True`](https://github.com/lmcinnes/pynndescent/blob/master/pynndescent/pynndescent_.py#L685). I would have created a PR to fix this small inconsistency, but...
The documentation for `n_jobs` says that the default value is `-1`, whereas it's actually `1`. I think the default got changed recently, but this isn't appropriately reflected in the documentation.
Spectrum deisotoping based on the theoretical isotope intensity ratios by [Valkenborg et al. (2008)](http://link.springer.com/10.1016/j.jasms.2008.01.009). First, sequences of peaks at isotopic mass differences are identified. Next, the intensity ratios are compared...
The [`GnpsBackend` should use](https://github.com/bittremieux/spectrum_utils/blob/main/spectrum_utils/spectrum.py#L15) `"https://metabolomics-usi.gnps2.org/proxi/v{version}/spectra?usi={usi}"` now.
Include code examples in the documentation on how to read spectra from peak files using various software packages (Pyteomics) and initializing `MsmsSpectrum` objects.
To try: - [ ] Intensity correspondence for first three prefix/suffix ions. (Rationale: these are more reproducible than ions further away from the termini.)
Read library spectra from various library formats: - [X] Full SpectraST support (sptxt). - [X] Mascot Generic support (MGF). - [ ] BiblioSpec support (blib). See #2. - [ ]...
[ANN-SoLo is now included in the PSI-MS-CV.](https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L22124) We can use the correct CV term in the mzTab output now instead of the more general one.
As spectrum prediction tools are becoming increasingly more accurate, in case a spectral library for a specific proteome is not available, we can accurately simulate a spectral library instead. Implement...
Currently we use feature hashing to convert spectra to vectors. Instead, [Gaussian random projections](https://github.com/bittremieux/falcon/issues/10) might give a similar performance at lower dimensionalities, which would speed up searching and reduce the...