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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 SCIEX Data converter 1.3.1 (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 mode) |
| DDA/IDA | MSFragger | mzML | Convert wiff to mzML using SCIEX Data converter 1.3.1 (Win10) – use ProteinPilot peak detectors for best results Processes CID DDA data only |
| SWATH DIA | Proteomics app (OneOmics suite) | Wiff | Will process DIA CID data. |
| SWATH DIA | DIA-NN 1.8.1 | Wiff | Processes CID DIA data only |
| SWATH DIA | Spectronaut | Wiff | Spectronaut 16 or later |
| 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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Hi Christie,
Any experience using the newest build of MaxQuant (v 2.1.3.0) for Zeno TOF 7600 SWATH files?
Thanks,
Heather
On a related note, I want to say it’s great that MSConvert can now write out individual mzML files when there are multiple “samples” within a single wiff2 file!
That is great news!!!! Have made that mistake a few times! 🙂 Does this happen automatically when MSConvert detects this or is there a UI element that we need to know about to ask it to split the files? Thanks for sharing!
is there any way to open/convert zeno files to MZML on Linux? i.e. are there mono versions of the latest DLLs (Clearcore2) or is it just windows 10?