Common utilities for interpreting mass spectrometry data
Project description
mass2chem - common utilities in interpreting mass spectrometry data
Annotation and Inferrence
Included or work in progress
-
Handling chemical formula
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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
to include
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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/rounding 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. It may be removed completely in future versions.
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
Third party:
https://github.com/domdfcoding/chemistry_tools
Dev note
The organization of this repo will change, after compatibility check on application packages.
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