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)

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

$ python setup.py install

or

$ pip install .

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.

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.