Christie Hunter

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Current proteomics software compatibility for ZenoTOF 7600 system

Below is a summary of various other software packages that are useful for processing proteomics data from the ZenoTOF 7600 system.  Note this list is not comprehensive and only covers the tools we have lightly tested to date.

Acquisition Type Software Files needed Notes
DDA/IDA ProteinPilot app (OneOmics suite) Wiff Processes CID DDA data only
DDA/IDA
EAD DDA
Mascot mgf Convert wiff to mgf using AB SCIEX Data converter (Win10) – use ProteinPilot peak detectors for best results
DDA/IDA MaxQuant 2.1 Wiff Processes CID DDA data only
DDA/IDA Peaks Wiff Processes both CID and EAD data (use EThCD
DDA/IDA MSFragger mzML Convert wiff to mzML using AB SCIEX Data converter (Win10) – use ProteinPilot peak detectors for best results
Processes CID DDA data only
SWATH DIA Proteomics (OneOmics) Wiff Will process DIA CID data.
SWATH DIA DIA-NN 1.8.1 Wiff Processes CID DDA data only
SWATH DIA Spectronaut Wiff Spectronaut 16 will be competitive with DIA-NN
MRMHR Skyline wiff or wiff2 files Direct method building not yet supported, use text export/import

Note the wiff.scan file is the same for wiff and wiff2 files.

RUO-MKT-18-14816-A

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