Bio-Rad EXQuest Spot Cutter - Manual (Page 324)

10-1
10. Mass Spectrometry
Analysis
After you have cut spots from a gel using the Integrated Excision Tool and digested
them, you can select the parameters for processing them using Micromass’s MALDI
or MS/MS mass spec instruments. You can then import the mass spec data back into
PDQuest in the form of annotations.
10.1 Creating a MassLynx Batch File
After you have cut spots from a gel using the Integrated Excision Tool and digested
them, you can select the parameters for processing them using Micromass’s MALDI
or MS/MS mass spec instruments.
First you set up a project file using MassLynx software, then you export the
processing parameters from PDQuest into the project file. After you have identified
the proteins, you can import the results back into PDQuest.
Note: See Micromass’s MassLynx documentation for information on project files and
how to use them.
Before you can generate a MassLynx batch file, you must map the directories where
your Micromass projects and parameters are stored. Go the Edit menu, select
Preferences, and click the Paths tab. Map the directory where your MassLynx projects
are stored using the Micromass Projects path. Map the directory where the mass spec
parameters are stored using the Micromass Install path. See Path Preferences for more
information.
Note: These paths must be mapped correctly, or you will not be able to access the
proper batch file parameters.
With the MatchSet containing your cut spots open, select Generate MassLynx Batch
File from the Identification menu to set up the batch file.