Provide a `combined_psm.tsv` when using LFQ-MBR workflow

[GianArauz]

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_SpeclibQuant do generates a unified psm.tsv.

What I tried?

I can follow two alternatives to get this unified PSM file:

1. Programmatically collect-and-append individual psm.tsv from each output folder (one folder by spectrum file) and export a home-made combined_psm.tsv (not sure if this is recommended...).
2. 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.

[fcyu]

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