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Example Workflows

Example Workflows

Example workflows that can be used in Proteome Discoverer:

Proteome Discoverer 3.0 / 3.1 / 3.2 / 3.3

Proteome Discoverer 2.5

General Remarks

The provided workflows also require the installation of MS Amanda  which can be downloaded here .

The general processing workflow for almost any crosslink search is depicted here .

For MS2 searches (CID, ETD, HCD, stepped HCD) it can also be beneficial to employ the IMP MS2 Spectrum Processor  node, an example workflow for Proteome Discoverer 3.0 is given here:

This workflow additionally requires the installation of the IMP MS2 Spectrum Processor  node beforehand, which can be directly downloaded from here (Proteome Discoverer 3.0)  or here (Proteome Discoverer 3.3) .

Note

When starting these workflows you might get a warning in Proteome Discoverer that certain parameters do not exist, even though all parameters are set in the workflow. This is because of different MS Annika versions that have different parameter sets. You can safely ignore these warnings!

Thermo Fisher Scientific Workflows

We have also tested some workflows together with researchers from Thermo Fisher Scientific specifically (but not exclusively) for Astral and Astral Zoom instruments (please also refer to the sections for Astral data). You can find the workflows that we came up with and that yielded the best results for our test setup at this directory here .

The workflows require that you have a licensed version of Proteome Discoverer and access to the Spectrum Files RC node. We found recalibration to improve results significantly!

Important

Please set crosslink and linear peptide modifications accordingly in these workflows, they are not preset!

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Example DataAstral Data