AB 4700/4800

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

The 4700 and 4800 AB instruments use an Oracle database to store the MS spectra and extracting the data into a readable file format is required for use with PEAKS. Fortunately, there is a free tool that can convert T2D files from AB 4700/4800 instruments into a PKL file that PEAKS can read directly.

Extraction of the data for PEAKS requires our homegrown software that we call simply "ABI 4700 Data Extractor". This exractor does work for both 4700 and 4800 instruments. Contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it for the download link.

System Requirements:
This extractor can be installed on the same machine as AB 4700 Explorer and the Oracle database or another machine that has direct network access to the 4700 SERVER. There cannot be a firewall or proxy between the computers. This tool is recommneded to be used with either Windows 2000 or Windows XP.

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

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

Data Extraction Procedure:

  • 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.
  • 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.
  • 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.
  • Choose a filename to save: After clicking the 'Convert' button, the user needs to input a file name and the peak lists of the selected job run will be exported.

    • After the extractor, load it up!

  • Once all of that is complete, start PEAKS and select 'New Project' from the 'File' menu.
  • Give the new project a name and select the "Add data files..." button.
  • Browse to the location of the desired file and select it.
  • Multiple files can be loaded in as one sample by using the SHIFT or CTRL keys as multiple files are selected.
  • Press Open.
  • Complete the fields marked Instrument Vendor and Instrument Type.
  • Select whole sample or whole project, as most likely all files were produced by the same instrument.
  • Press OK to have the file loaded into PEAKS.
  • In the top left panel, marked Project View, a number of icons will appear.
  • First the Project node, then the Sample node and lastly the file node.
  • As the project loads, the file node will appear as a green outlined icon .
  • Wait until this icon turns solid green , this represents the file is completely loaded into PEAKS and is ready for processing.
  • For small files, users may not even notice the outlined icon, but larger files may take a short period of time to load.

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