Data Types

We always encourage users to load unprocessed data (directly from the instrument) so that PEAKS can access the complete, unprocessed experimental data including the mass spectrometry survey scan and retention time information. This will ensure that the PEAKS analysis does not suffer from poor preprocessing. In order to load raw data from different vendors, PEAKS may require third-party software to be installed. As you will see in the chart below, many of the third-party software required are the native instrument software already installed on your system.

Instrument Formats

Vendor Name MS Type Data Type Converter
AB Sciex 4700/4800 wiff AB Extractor
  QSTAR wiff Analyst QS 2.0 + mzWiff
  QTRAP wiff Analyst 4.1 + mzWiff
Agilent Ion Trap D (yep) CompassXport
  Q-TOF d MassHunter
Bruker APEX/micrOTOF baf CompassXport
  HCT Ion Trap yep CompassXport
  TOF-TOF LIFT CompassXtract
Shimadzu AXIMA-CFR run Kratos Converter
Thermo LTQ/Orbitrap/FT raw XCalibur/MSFileReader
Varian 500 MS xms VarianMS
  900 MS sms VarianMS
Waters Q-TOF raw MassLynx

Standard/Other Data Formats

  • .ANZ (PEAKS 1.0-4.5)
  • .DAT (AB converter)
  • .DTA (Sequest)
  • .MGF (Mascot)
  • .mzData (HUPO format)
  • .mzML
  • .mzXML
  • .PepXML
  • .PKL (MassLynx)
  • .XML (mzData schema)
  • .XML (mzXML schema)

Load it Up!

  • Open 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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