PyHRMS: Tools For working with High Resolution Mass Spectrometry (HRMS) data in Environmental Science

PyHRMS is a python package for processing high resolution Mass Spectrometry data coupled with gas chromatogram (GC) or liquid chromatogram (LC).

It aims to provide user friendly tool to read, process and visualize LC/GC-HRMS data for scientist.

Contributers: Rui Wang

Release date: Nov.15.2021

Update

JAN.6.2022: pyhrms 0.2.7 new features:

  • optimized identify_isotopes() function, add Na+, NH4+ adducts and 13C and Cl isotopes

  • add quantification function, support orbitrap data

  • debug some small issues

Installation & major dependencies pyhrms can be installed and import as following:

` pip install pyhrms `

If you just want to update a new version, please update as following:

` pip install pyhrms -U `

pyhrms requires major dependencies:

  • numpy>=1.19.2

  • pandas>1.3.3

  • matplotlib>=3.3.2

  • pymzml>=2.4.7

  • scipy>=1.6.2

  • numba>=0.53.1

  • molmass>=2021.6.18

  • tqdm >= 4.62.3

Features

PyHRMS provides following functions:

  • Read raw LC/GC-HRMS data in mzML format;

  • Powerful and accurate peak picking function for LC/GC HRMS;

  • retention time (rt) and mass over Z stands for charge number of ions (m/z) will be aligned based on user defined error range.

  • Accurate function for comparing response between/among two or more samples;

  • Covert profile data to centroid

  • Parallel computing to improve efficiency;

  • Interactive visualizations of raw mzML data;

  • Supporting searching for Local database and massbank;

  • MS quality evaluation for ms data in profile.

Licensing

The package is open source and can be utilized under MIT license. Please find the detail in licence file.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (1.0.9)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for wangrui from gravatar.com wangrui

Credits

Author: Wang Rui

License

MIT License

Requires

Python >=3.6

Classifiers

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