Applied Biosystems Data Explorer
Data Explorer is used to view and process data files from Applied Biosystems Voyager instruments.
Recent versions, (4.2 and later), also support the 4700 and 4800 TOF/TOF instruments by opening
the *.T2D files exported from a 4000 Series database.
Interactive Searching
A Visual Basic Macro is available to export a peak list to the Mascot search form. This macro is not part of the
standard Data Explorer installation. It can be downloaded from the "unofficial" Applied Biosystems
Data Explorer support site.
Unless you have already created new macros, or modified existing ones, the toolbox can be installed very simply:
- Exit Data Explorer
- In Windows Explorer, change to the Data Explorer application directory, (e.g. C:\Program Files\Applied
Biosystems\Data Explorer)
- Rename DataExplorer.vb6 to (say) DataExplorer.vb6.bak
- Copy DataExplorer.vb6 from the downloaded archive into the application directory, (e.g. drag and drop
this file from Winzip)
To use the toolbox, open a data file in Data Explorer and perform peak detection. From the Tools menu,
choose Macros ..., then modToolBoxPalette.Toolbox_Palette
Choose Mascot Toolbox, and a dialog will be displayed to choose the Mascot server and the type of peak list.
For MS/MS (PSD) data, you also need to type in the precursor m/z
Choose Copy Peaks to invoke a Mascot search form and paste the peak data into the form
Mascot Distiller
It can be tricky to get the peak detection settings just right in Data Explorer. Mascot Distiller
is an alternative that does not require constant tweaking of the settings to get high
quality, de-isotoped peak lists. (Note: Mascot Distiller uses Data Explorer to access the
data file, so Data Explorer must still be installed and working on the same PC as Mascot Distiller).
For more information about Mascot Distiller, refer to the
Product Page.
Mascot Wizard
Mascot Wizard is a free desktop tool that provides a drag and drop interface
for submitting peptide mass fingerprint searches to a Mascot server. Internally, Mascot Wizard uses the
Mascot Distiller libraries to process Data Explorer files into high quality peak lists. However, note that
Mascot Wizard is only for peptide mass fingerprints. If your file contains MS/MS (PSD) data, you have
to use Mascot Distiller to process it.
Automation using Mascot Daemon
Mascot Daemon can use Data Explorer or Mascot Distiller as a data import filter, eliminating the need to
create peak lists manually. Step one is to create a suitable parameter
set and save it. If the parameter set is for searching MS/MS data, the file format should be specified as
Mascot Generic.
In the Task editor, if you want to use Data Explorer as the data import filter, select the parameter
set and then choose the 'Data Explorer (Voyager) MS data' option from the data import filters. This
will be listed if Data Explorer is installed and registered on the PC running Mascot Daemon.
Clicking on the Options button will invoke the dialog shown below. Most of these parameters refer
to Data Explorer settings, and full details can be found in the Mascot Daemon on-line help, (Reference;
Data Import Filter Options Dialog).
The intensity filter is a Daemon function, not a Data Explorer function. For MS/MS (PSD) data,
you should choose 'All peaks' because Mascot includes a peak selection algorithm. For peptide mass
fingerprint data, you will normally obtain best results by setting the value of % Base Peak Intensity
in the SET file to a low value, such as 0.25, and using the intensity filter to select (say) the 5 to
10 most intense peaks per 100 Da. This will allow sparse, weak high mass peaks through while limiting
the number of intense, low mass peaks.
Press OK to save the options, and then continue to set up either a batch or real-time monitor task.
Note that when the task is run, the options settings are saved as defaults for next time, but each task can
have different options settings.
To use Mascot Distiller as the data import filter, choose 'Mascot Distiller' from the list
of data import filters. This
will be listed if Mascot Distiller is installed and registered on the PC running Mascot Daemon.
Clicking on the Options button will invoke the dialog shown below. In most cases, you only need to
specify the file format as 'Applied Biosystems Data Explorer' and choose a file containing suitable set of
processing options. More details can be found in the Mascot Daemon on-line help, (Reference;
Data Import Filter Options Dialog).
Mascot Daemon tasks can be batch tasks, where a list of files is searched immediately, or at some pre-set
time, or can be real-time monitor tasks. These monitor a specified path for new data files. The advantage of
a real-time monitor task is that data files can be submitted to Mascot immediately after acquisition and
without any user intervention.
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