Tested Instruments
Instruments whose raw files have been converted and searched with Pioneer, using public data sets and in-house runs. Other instruments or acquisition methods from these vendors may work but have not been tested.
Thermo Fisher
.raw files, converted with ConvertRAW (pioneer convert-raw).
| Instrument | Mass analyzer (MS2) | Acquisition tested |
|---|---|---|
| Q Exactive | Orbitrap | DIA, including gas-phase fractionation |
| Q Exactive HF | Orbitrap | DIA |
| Q Exactive HF-X | Orbitrap | DIA |
| Orbitrap Exploris 480 | Orbitrap | DIA |
| Orbitrap Eclipse | Orbitrap | DIA |
| Orbitrap Astral | Astral | DIA, including 250 pg single-cell inputs |
Bruker
.d folders, converted with ConvertRAW (pioneer convert-bruker).
| Instrument | Mass analyzer (MS2) | Acquisition tested |
|---|---|---|
| timsTOF Pro | TIMS-QTOF | diaPASEF |
| timsTOF Pro 2 | TIMS-QTOF | diaPASEF |
| timsTOF SCP | TIMS-QTOF | diaPASEF |
| timsTOF HT | TIMS-QTOF | diaPASEF, Thin-diaPASEF |
| timsTOF Ultra | TIMS-QTOF | diaPASEF |
| timsTOF Ultra 2 | TIMS-QTOF | diaPASEF, including single-cell inputs |
| timsTOF Ultra AIP | TIMS-QTOF | diaPASEF |
Bruker data must be searched with a library built with the Bruker timsTOF library option, which adds ion mobility.
SCIEX
.wiff files with their .wiff.scan files, converted with ConvertRAW (pioneer convert-sciex).
| Instrument | Mass analyzer (MS2) | Acquisition tested |
|---|---|---|
| ZenoTOF 7600 | QTOF | SWATH |
| ZenoTOF 8600 | QTOF | ZT Scan DIA |
| TripleTOF 6600 | QTOF | SWATH |
| TripleTOF 5600+ | QTOF | SWATH |
| TripleTOF 5600 | QTOF | SWATH |
.wiff2 files are not supported; convert them to mzML with msConvert and use ConvertRAW with the mzML format.
Other Instruments
Centroided .mzML files from other instruments can be converted with ConvertRAW (pioneer convert-mzml).