How to process a file using MaxEnt in OpenLynx - WKB3138

OBJECTIVE or GOAL

Immediately after acquisition or in a post-processing analysis, automatically process a sample using OpenLynx, applying the maximum entropy program to deconvolute the spectrum.

ENVIRONMENT

• MassLynx
• OpenLynx, OALogin OA Manager
• MaxEnt I, MaxEnt II, MaxEnt III

PROCEDURE

1. Ensure that MaxEnt is enabled on the processing PC (see the article How can I tell if MaxEnt is enabled in MassLynx? - WKB3140).
2. Open the OpenLynx method in OpenLynx > SetUp.
3. Go to View > Options and select the processing option Max Ent to display this option.
4. Click the MS Process tab, and then click MaxEnt.
5. Ensure that the Do MaxEnt box is selected.
6. Edit the available parameters as appropriate:
   Mass Range: specifies the range of data in the acquired spectrum that will be processed.
   Output Mass: defines the mass range where the software will look for the deconvoluted mass.
   Range Around Specified Mass: There must be a mass specified in the log in process (sample list or OALogin). This enables OpenLynx to give an HIT or MISS result.
   Output Mass Resolution: The spectral resolution the software will aim to achieve on the deconvoluted spectrum after processing.
   Output Mass Range: Use this range if you do not know the mass of the target compound. Separate the masses with a colon (for example, 3000:9000). Using this value will not give a hit or miss result but a "not searched" color.
   Damage Model: the default setting is to use Uniform Gaussian and set the Width at Half Height to the approximate peak width of the spectral peaks (remember, peaks MUST be acquired in continuum mode).
   Completion Options: Maximum iterations - twenty is usually enough to get a reasonable spectrum without a long processing time.
   Minimum Intensity Ratios: The minimum height an adjacent peak within a series needs to be in order to be included in the deconvolution calculation. An appropriate value is normally 33%.
7. Save the OLP file.
8. Processing a data file with this method results in an automatically generated deconvoluted spectrum.
9. To see the deconvoluted spectra in the OpenLynx browser, go to View > Options and, on the Spectrum page, select the “Default range to Data” box. Without this selection, only the acquired data will be shown, not the processed data.

ADDITIONAL INFORMATION

From MassLynx Help:

The MaxEnt algorithm uses the maximum entropy method to produce true molecular mass spectra from multiply charged ElectroSpray spectra.

MaxEnt automatically finds the molecular weights of the components in a protein mixture without any knowledge other than that they lie within a specified mass range. This range can be large (for example, 5 to 100 kDa). To reduce processing time, the technique currently involves a preliminary survey run, producing a coarse output to find the approximate masses of the components present.