Read MS data

This function is implemented in the MSData class to read the raw MS data.

mzML and mzXML files are supported. This function is achieved by using the pyopenms module.

readRawData(self, fileName)

Function to read the raw LCMS data to Function to read the raw LCMS data to MSExperiment object (supported by pyopenms).

Parameters:

fileName – str. The name of the file to be read (end with .mzML or .mzXML).

The loaded data is stored in the MSData object as MSExperiment object. Two more functions are implemented to get the MS1 and MS2 spectra from the MSExperiment object.

extractMS1(self, rtRange=None)

Function to extract all MS1 scans and convert them to ms1Spectrum objects (supported by bago).

Parameters:

rtRange – list. The retention time range to be extracted (in minute). If None, all MS1 scans will be extracted.

It generate an attribute ms1Data in the MSData object to store the extracted MS1 spectra.

extractMS2(self, rtRange=None)

Function to extract all MS2 scans and convert them to ms2Spectrum objects (supported by bago).

Parameters:

rtRange – list. The retention time range to be extracted (in minute). If None, all MS2 scans will be extracted.

It generate an attribute ms1Data in the MSData object to store the extracted MS1 spectra.

To load the raw data and extract the MS1 and MS2 spectra, you can use the following code:

from bago import rawDataHelper

fileName = 'data.mzML'

msData = rawDataHelper.MSData()
msData.readRawData(fileName)
msData.extractMS1()
msData.extractMS2()