Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

AB Sciex Data Explorer

Data Explorer is used to view and process data files from AB Sciex Voyager instruments. Versions 4.2 and later also support the 4×00 and 5×00 series TOF/TOF instruments by opening the *.T2D files exported from the Oracle database. But, if you want to search and quantitate TOF/TOF data, the AB Sciex MS Data Converter is a more convenient option that can also be automated using Mascot Daemon 2.5.

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).


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 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 Mascot Daemon, 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 ‘AB Data Explorer’ and choose a file containing suitable set of processing options. More details can be found in the Mascot Daemon and Mascot Distiller on-line help files.

Data Explorer 8

Mascot Daemon tasks can be batch tasks, where a list of files is searched either 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