Bio-Rad EXQuest Spot Cutter - Manual (Page 326)

Mass Spectrometry Analysis
10-3
Select the processing parameters using the Processing Parameters pulldown list.
You can specify a mass spec run number in the MS Run Sequence Number field.
The format for use with Mascot check box allows you to include the matchset name
in the sample identifier string so that results from the specific matchset can be filtered
out of the master search log.
When you have made all your selections, click Done.
10.2 Importing MassLynx Results
After you have completed a mass spec analysis and processed the data using
MassLynx, you can import the results back into PDQuest and include them in
annotations for the spots you have analyzed.
Note: Before importing MassLynx results, you must select the Bio-Rad output
checkbox in the MassLynx project settings. To access this checkbox, go to the
ProteinLynx menu in MassLynx and select Setup ProteinLynx. One of the setup
steps is called Select Output. In this step, under Database Searching, select the
Bio-Rad (full text output) checkbox.
With the appropriate MatchSet open, select Import MassLynx Results from the
Identification menu.
In Step 1, the MatchSet name will appear in the MatchSet field. Select the instrument
used in the analysis by selecting the MALDI or MS/MS button.
The Required Project Name is based on the MatchSet name. Use the MassLynx
Project pulldown list to select the project with this name from the appropriate
directory.
Note: If you have mapped the path to the Micromass project directory using the
Preferences dialog (Edit > Preferences), the correct MassLynx project will be
automatically selected. See Path Preferences.
In Step 2, the mass spec runs that have been performed in this project are listed. Click
on a run name to select it.