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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 4x00 and 5x00 series TOF/TOF instruments by opening the *.T2D files exported from the Oracle database.

Interactive Searching

A Visual Basic Macro is available to load a peak list directly into the Mascot search form. Another can be used to save the peak list to an MGF file. These macros are not part of the standard Data Explorer installation, but can be downloaded here.

If you have already created new macros for Data Explorer, or modified existing ones, unpack the zip archive and import the individual *.bas, *.frm, and *.frx files. Otherwise, the complete set of macros can be installed by copying a single file:

  • 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 zip archive into the application directory, (e.g. drag and drop this file from Winzip)
  • Make sure the new file is not read only

To use the toolbox, open a data file in Data Explorer and, if necessary, perform peak detection. From the Tools menu, choose Macros ..., modToolBoxPalette.MASCOT, Run.

Data Explorer 1

If you have an in-house Mascot Server, enter the URL (e.g. http://mslab/mascot) and test the connection by choosing Navigate to. This setting will be remembered. The precursor m/z may not be displayed automatically for Voyager PSD data. If missing, type the value into the field. Choose Copy Peaks to invoke a Mascot search form and automatically paste the peak data into the form. The Sequence Query form will be used whether the spectrum is MS or MS/MS.

Data Explorer 3

To save a peak list as an MGF file, choose Export_to_MGF_file. There are no controls. The peak list is saved to the same directory as the data file with the extension TXT.

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 is stand-alone for *.T2D files. For earlier, Voyager *.DAT files, Data Explorer must be installed and working on the same PC as Mascot Distiller).

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.

Data Explorer 4

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.

Data Explorer 5

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.

Data Explorer 6

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).

Data Explorer 8

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.

Data Explorer 7
 
 
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