mscheck 0.1.7b0

Auto MS mass checker

MScheck for locating target compound masses in mass spectra

MScheck is a python package that hunts for a target compound mass + given ion mass (eg. H+, Na+). MScheck was created to assist with the automated mass spectrum analysis of target compounds synthesised using a high throughput approach.

MScheck installation

MScheck relies on rdkit for generating molecule SVG images and for calculating molecular weights
Installing rdkit using conda works best followed by a pip install of MScheck

1. Create a conda environment with rdkit

   conda create -c conda-forge -n MScheck rdkit

2. Activate the MScheck conda environment created

   conda activate MScheck

3. Pip install MScheck

   pip install mscheck

MScheck use

MScheck has been tested on using Agilent LCMS files (.D) as the starting file format. One challenge is to convert vendor file formats into a format with the binary decoded.

1. Convert .D Agilent folder to a .d MassHunter format using Agilent's ChemStation to MassHunter Translator (B.04.00)
2. Convert .d format into .mzML format using ProteoWizard's MSConvert tool
3. Finally - we have an file format that we can use!
4. In your favourite IDE or Jupyter notebook - as basic example of using MSCheck is prvided below:
   

from mscheck.analyse import AnalyseSpectrum

# Create MS scptrum object and find peaks
test = AnalyseSpectrum("<path to .mzML file>", mode="Positive")

# Analyse test spectrum
test.analyse(compoundsmiles=target_compound,
             ionstoadd=["[H]", "[Na]", "[K]", "[NH4+]"],
             tolerance=1)test.analyse

# Create a SVG report - if you do not give a compound_name
# the ending leaf of the file name will be used
test.create_report(compound_name="Test")

Example of report output:

The .SVG report will be in a folder called Reports