Nonlinear Dynamics: A Waters Company

UK: +44 191 230 2121
USA: +1 919 806 4401
info@nonlinear.com

Progenesis LC-MS

A unique approach for label-free LC-MS data analysis
Quantify and identify the significant proteins in your experiment…

Support for Waters (MassLynx 4.0-4.1) .RAW folders

Support for this data file format is provided as standard.

About this plug-in

Note: You need to have MassLynx installed to use this reader.

This is the standard format produced by Waters mass spectrometers. When using MassLynx Raw data, each sample run is contained within a separate .RAW folder.

To select samples to import, first click Browse to select the parent folder containing your .RAW folders:

Selecting the Waters .RAW folders

The .RAW folders within the parent will then be shown in the Import Waters .RAW Data wizard's list box, allowing you to select those you wish to import.

Click Next and the each sample will be examined to determine which pre-processing steps may be applied. If either lock mass calibration or dead time correction are appropriate, then you will be asked whether or not these steps should be performed.

Lock mass calibration

Some Waters systems allow you to periodically inject a calibration compound with a known m/z peak into the mass spectrometer. The variation between the expected and measured m/z peak value is measured over time so it can then be used to calibrate the m/z values in the sample data.

For .RAW folders that contain lock mass information, you can make the software perform this calibration by ticking the “Perform lock mass calibration” box and entering the expected value in the “lock mass m/z” control. The scan data will then be calibrated as it is imported.

Dead time correction

In Waters TDC ToF mass spectrometers, the dead time effect can result in the detector underestimating the abundance and m/z of higher intensity ions. This import method allows you to apply a dead time correction algorithm to correct for these effects.

See also