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|
|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.