How do I load data from my SCIEX 4700/4800/5800 instrument?

BSI produces a free tool that can convert T2D files from SCIEX 4700/4800/5800 instruments into a PKL file that PEAKS can read directly. You can download this software from the PEAKS Configuration Wizard:

  1. Open PEAKS and go to Window -> Config Wizard
  2. Click Next
  3. Click the AB 4700/4800 button
  4. Go through the Config Wizard to the download screen, the converter will download automatically
  5. When the download is complete, click the install button
  6. Installation and running instructions are provided below


Start the SCIEX 4700 converter tool. Choose “Settings” from the “File” menu. Configuration requires the following:

  1. 4700 SERVER Name or IP Address: input “localhost” if the Extractor is running on the same computer as AB 4700 Explorer (this is the default value), otherwise enter the IP address of the 4700 SERVER.
  2. The socket used by the 4700 SERVER: this is the port that the Oracle database listens to (the default is 1521).
  3. Username to access the Oracle database: most likely we do not need to change this (the default is “tsquared”).
  4. Password to access the Oracle database: mostly likely you do not need to change this either.

Data Extraction Procedure:

  1. Load Spot Set List from the database: (Do this via menu File | Load Spot Set List). The extractor will export the peak list of a spot set into a PKL file.
  2. Open a Spot Set: (menu File | Open Spot Set) Spot Set Chooser will help the user to choose a spot set. After selecting a spot set, click ‘OK’ to open it. The job run information of a spot set will be shown.
  3. Select a job to run: There is a button to select before each run. Only the MS/MS job run can be selected for export, as the precursor information is needed. Select a job run and click ‘Convert’ to do the extraction.
  4. Choose a filename to save: After clicking the ‘Convert’ button, the user needs to input a file name with .pkl as the file extension and the peak lists of the selected job run will be exported. For example, spectra.pkl. You will only be able to load the files into PEAKS with the .pkl extension.

For instructions on how to load your data (after it has been extracted) into PEAKS click here or see the PEAKS User Manual.