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mobiusklein / ms_peak_picker

A small library to provide peak picking for software processing mass spectrometry data
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lorenztian typo #5

Closed Kawue closed 5 years ago

Kawue commented 5 years ago

Thanks for this nice piece of code. There is a small typo in your peak_picker class. Its consistently wrong, so it does not matter but your documentations states it as "lorentzian". Would be nice to adjust either the code or the comments.

mobiusklein commented 5 years ago

Thank you for catching that.

I'll fix the spelling in the code itself, but the old misspelling will still work when selecting fit type in pick_peaks.

I've found the Lorentzian fit didn't find the centroid very well when dealing with clipped peaks, which happen fairly frequently when operating the mass spectrometer for throughput.

mobiusklein commented 5 years ago

I've made the name changes. Both "lorentzian" and "lorenztian" will work with fit_type. I noticed I've disabled the C implementation of the Lorentzian least squares, and it appears to be a long standing setting. I've re-enabled them after some manual testing on some "clean" data sets. If I remember correctly, there were intermittent issues with the full width at half max calculation it required early in this library's development, and I couldn't demonstrate it was objectively better than the simpler quadratic fit.

Theoretically, an FTICR's peak shape should be closer to Lorentzian.

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But my experience has been that Orbitrap peaks tend to be more Gaussian.

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