Skip to main content

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

  • 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 (they are using average molecular weight, not mass spec oriented)

Third party:

Dev note

The organization of this repo will change, after compatibility check on application packages.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for mass2chem, version 0.1.9
Filename, size File type Python version Upload date Hashes
Filename, size mass2chem-0.1.9-py3-none-any.whl (6.0 MB) File type Wheel Python version py3 Upload date Hashes View
Filename, size mass2chem-0.1.9.tar.gz (5.8 MB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page