Christie Hunter

Member

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 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
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 (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 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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3 Comments

  1. Heather Eastwood

    Hi Christie,
    Any experience using the newest build of MaxQuant (v 2.1.3.0) for Zeno TOF 7600 SWATH files?
    Thanks,
    Heather

  2. Eric Chan

    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!

    • Christie Hunter

      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!

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