Bruker Data

How do I load data from my Ion Trap instrument?

PEAKS can load data from Bruker mass spectrometers provided that the CompassXport software is installed on the same computer. When selecting a file to load, make sure you select the file with a .yep or .baf extension (i.e. Analysis.yep).
Be sure that CompassXport can be reached by PEAKS. To do this, go to:

  • Preferences -> Instrument -> Bruker
  • The path under 'Default Compass File Location' should contain a compass export file.
  • For example, for CompassXport 3, click Browse and follow the path: C:\Program Files\Bruker Daltonik\CompassXport\CompassXport.exe
  • In the Raw File Converter Options select 'raw data'.
  • Also, select 'no' to merging into one data set.

    • How do I load data from my TOF-TOF instrument?

    For AutoFlex and UltraFlex TOF-TOF instruments, in addition to CompassXtract, we have a converter that can be used outside of PEAKS. Contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it to obtain the download link. Once you have downloaded the folder, extract it. There are some .txt and .ppt slides contained in the folder with instructions on how to use it.
    CompassXtract freely available on the Bruker Daltonics web site.

    An Alternate Method for TOF-TOFs
    Loading .LIFT files into PEAKS requires a little bit of work. We offer a command line converter, which uses CompassXtract. For those with command line experience, this is the easiest method. Contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it to obtain the download link. To load data without this tool you will need CompassXport 1.3. This is available through a Bruker representative.

    The main steps are:

  • Within PEAKS -> Preferences -> Instrument -> Bruker, configure the path of CompassXport with the browse button to c:\program files\common files\Bruker Daltonik\AIDA\export\compassxport.exe
  • Select ‘raw data’ for data type to export and ‘yes’ to merge data.
  • Cick on the new project button and add the .LIFT files to it.
  • This will convert the files to mzxml but will not load them.
  • Repeat this step and add the Analysis.mzxml files by clicking into the deepest folder in the .LIFT file.
  • Repeat for each .LIFT file

    • Then load it up!

  • Once the data is in a format ready for PEAKS, 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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