Supported Data Formats

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.

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

VendorInstrumentData TypeConverter & Set Up
ThermoIon Trap / OrbitraprawMSFileReader
AgilentIon Trap / Q-TOFyep / dCompassXtract / MassHunter
BrukerQ-TOF / Ion Trap / timsTOF Pro / TOF TOFbaf / yep / tdf / liftCompassXtract
SCIEXTripleTOF / QSTAR / QTRAP
TOF TOF
wiff2 / wiff
t2d
ProteoWizard-MSConvert
Extractor
ShimadzuAXIMA-CFRrunKratos Converter
VarianFTICR / Ion Trapsms / xmsVarianMS
WatersQ-TOFrawMassLynx

Additional Supported Standard Data Formats

  • .DAT (AB converter)
  • .DTA (Sequest)
  • .MGF (Mascot)
  • .mzData (HUPO format)
  • .mzML (including mzIdentML)
  • .mzXML
  • .PepXML
  • .PKL (MassLynx)
  • .XML (mzData schema)
  • .XML (mzXML schema)