MSRead

The MSRead module enables a simple reading of popular Mass Spectrometry data formats including: mzData, mzXML, mzML, MGF, ASCII XY and Thermo Raw files.

import msread

# open file
with msread.read("myfile.mzML") as reader:
    
    # show summary
    reader.summary(show=True)
    
    # read headers only
    for header in reader.headers(min_rt=5*60, max_rt=10*60, ms_level=1):
        print(header)
    
    # read scans
    for scan in reader.scans(min_rt=5*60, max_rt=10*60, ms_level=1):
        print(scan.header)
        print(scan.centroids)

Requirements:

• Python 3.7+
• Numpy 2.0+
• [comtypes] (To read Thermo Raw files. Windows only.)
• [MSFileReader] (To read Thermo Raw files. Windows only.)

Install from source:

$ python setup.py install

or simply use pip

$ pip install msread

Reading Thermo Raw files:

To enable Thermo Raw files reading you need to download and install the MSFileReader by creating an account at:

https://thermo.flexnetoperations.com/control/thmo/login

then logging in and choosing "Utility Software". Current version is developed using MSFileReader v3.1 SP2.

Disclaimer:

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For Research Use Only. Not for use in diagnostic procedures.