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
| Vendor | Instrument | Data Type | Converter & Set Up |
|---|---|---|---|
| Thermo | Ion Trap / Orbitrap | raw | MSFileReader |
| Agilent | Ion Trap / Q-TOF | yep / d | CompassXtract / MassHunter |
| Bruker | Q-TOF / Ion Trap / timsTOF Pro / TOF TOF | baf / yep / tdf / lift | CompassXtract |
| SCIEX | TripleTOF / QSTAR / QTRAP TOF TOF |
wiff2 / wiff t2d |
ProteoWizard-MSConvert Extractor |
| Shimadzu | AXIMA-CFR | run | Kratos Converter |
| Varian | FTICR / Ion Trap | sms / xms | VarianMS |
| Waters | Q-TOF | raw | MassLynx |
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)