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Provide a `combined_psm.tsv` when using LFQ-MBR workflow
Context
I'm making my first steps with the LFQ-MBR workflow in order to compare its performance with other search soft. Since I like to have Proteins and PSMs information explicitly for each spectrum file searched, I use to set the "Experiment" from the Workflow tab with the "By file name" button.
Problem
However, I noticed that the LFQ-MBR workflow doesn't generates a combined_psm.tsv
. Is this the expected behavior of FPv18.0? For example, the DIA_Speclib_Quant do generates a unified psm.tsv
.
What I tried?
I can follow two alternatives to get this unified PSM file:
- Programmatically collect-and-append individual
psm.tsv
from each output folder (one folder by spectrum file) and export a home-madecombined_psm.tsv
(not sure if this is recommended...). - Re-launch the search specifying a common "Experiment" name on the Workflow tab, and get the unified
psm.tsv
generated this way.
Request
In any case, it is possible to implement the exporting of this combined_psm.tsv
within FPv18.0 by default? Or alternatively, can I specify some FPv18.0 search parameter to get this unified PSM file?
As usual, thank you so much for developing FPv18.0 and for devoting your time dealing with our issues.
However, I noticed that the LFQ-MBR workflow doesn't generates a combined_psm.tsv. Is this the expected behavior of FPv18.0?
Yes, it is expected.
In any case, it is possible to implement the exporting of this combined_psm.tsv within FPv18.0 by default? Or alternatively, can I specify some FPv18.0 search parameter to get this unified PSM file?
Thanks for your suggestion. We will discuss it internally.
Best,
Fengchao