mass2chem 0.1.0

Common utilities for interpreting mass spectrometry data

mass2chem - common utilities in interpreting mass spectrometry data

Annotation and Inferrence

Included or work in progress

• Handling chemical formula

• A list of common mass values, including contaminants

• A list of common adducts, rules, while they are more directly ready in future Azimuth

to include

• Chemical similary computing

• Reaction inference, including mass diff corresponding to common reactions

• Annotation via in-house libraries

• hook/adaptor to other tools

Added basic formula based calculations

Note: RE based formula parsing is still limited.

Pychemy isn't good fit, as

1. high-resolution calculation needs update
2. 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.