Agilent Data

How do I load data from my Ion Trap instrument?

Agilent Ion Traps produce a .D folder, which contains all data associated with that data set. The spectral data is contained in the .yep file. CompassXport can be used to read the .yep file and convert it to an mzXML file inside the .d folder. This file is then loaded into PEAKS. CompassXport must be installed on the same computer as PEAKS to perform this conversion automatically.

To load .yep files, 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. Then press Open. Complete the fields marked Instrument Vendor and Instrument Type. Then 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.

How do I load data from my QTOF instrument?

The Agilent QTOF produces .d files which can be read by PEAKS, provided that the MassHunter software is installed on the same computer.

To load .d files, 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. Then press Open. Complete the fields marked Instrument Vendor and Instrument Type. Then 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.

After the data has been converted, 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 .yep (from Ion Trap) or .d (from QTOF) 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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