Ideally, we would find a way to access the file names of the FASTA databases that were used by Sequest HT in the processing step and use the same databases for the LFQProfiler consensus step, instead of asking the user to select the same FASTA databases again.
This is a bit less straightforward than one might think at first glance:
At the moment, our only officially supported processing workflow is the one that includes Sequest HT. But in principle, the search engine is interchangeable. We would thus have to find out which node of the processing workflow was the search engine node that produced the PSMs.
If the consensus step is a multi consensus step combining the results of several processing workflows, these processing workflows could (in theory) have used different fasta databases. Although there is probably no scenario in which it would make sense to combine processing results that were searched against different sequence databases, we would have to deal with it. In this case we would probably want to use the union of all FASTA files used in any of the processing workflows.
Ideally, we would find a way to access the file names of the FASTA databases that were used by Sequest HT in the processing step and use the same databases for the LFQProfiler consensus step, instead of asking the user to select the same FASTA databases again.
This is a bit less straightforward than one might think at first glance: