Common utilities for interpreting mass spectrometry data
Project description
mass2chem - common utilities in interpreting mass spectrometry data
Annotation and Inferrence
to include
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Handling chemical formula via pychemy (which needs update to high res data)
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A list of common mass values, including contaminants
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A list of common adducts, rules, while they are more directly ready in future Azimuth
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Chemical similary computing
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Reaction inference, including mass diff corresponding to common reactions
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Annotation via in-house libraries
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hook/adaptor to other tools
Added basic formula based calculations
Note: RE based formula parsing is still limited.
Pychemy isn't good fit, as
- high-resolution calculation needs update
- Open babel binding is not worthy the trouble
E.g. in pychemy.adducts, it's wrong to use ('M+3H', 0.33, 1.0073), because the computing error in 0.33 (correct is 1/3) is far too large for mass precision.
Pychemy is included as stripped version in "mass2chem.chem" for now, but only used for formula handling.
For high-resolution measurements, electrons should be considered too.
Related
https://github.com/shuzhao-li/pychemy
https://github.com/opencobra/cobrapy/blob/devel/cobra/core/formula.py (they are using average molecular weight, not mass spec oriented)
https://github.com/shuzhao-li/Azimuth
Dev note
The organization of this repo will change, after compatibility check on application packages.
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