Nonlinear Dynamics: A Waters Company

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Progenesis QI for proteomics

The next generation in LC-MS proteomics data analysis software.
Discover the significantly changing proteins in your samples.

Support for Waters (.raw)

Support for this data file format is provided as standard.

About this plug-in

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

To select runs 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 each run 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 run 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