Example Workflows
Example workflows that can be used in Proteome Discoverer:
Proteome Discoverer 3.0 / 3.1 / 3.2
- DSS/BS3 MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
- DSS/BS3 MS2 search (for large datasets and proteome-wide searches, CID, ETD, HCD, stepped HCD): pdAnalysis / zip
- DSSO MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
- DSSO MS2-MS3 search (MS3 recorded in the orbitrap): pdAnalysis / zip
- DSSO MS2-MS3 search (MS3 recorded in the ion trap): pdAnalysis / zip
- DSBSO MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
- DSBSO MS2-MS3 search (MS3 recorded in the orbitrap): pdAnalysis / zip
- DSBSO MS2-MS3 search (MS3 recorded in the ion trap): pdAnalysis / zip
Proteome Discoverer 2.5
- DSSO MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
- DSSO MS2-MS3 search (MS3 recorded in the orbitrap): pdAnalysis / zip
- DSSO MS2-MS3 search (MS3 recorded in the ion trap): pdAnalysis / zip
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:
- DSSO MS2 search with IMP MS2 Spectrum Processor: pdAnalysis / zip
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) .
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!