Missing "combined_protein.tsv" File in Results Directory

[FragpipeIssue]

Uploading log_2025-01-13_11-48-21.txt…
Uploading log_2025-01-13_11-48-21.txt…

I followed the tutorial provided for the application, which indicates that upon completing the analysis, one of the main output files should be named "combined_protein.tsv". However, in my results folder, this file is not present. Instead, I only found a file named "combined.prot.xml".

The .tsv file is essential for me to proceed with the analysis in Perseus. Could you please advise me on how to generate the "combined_protein.tsv" file?

Thank you for your assistance.

Best regards

[fcyu]

The log file is not available. Could you upload it again?

Thanks,

Fengchao

[FragpipeIssue]

log_2025-01-09_16-50-35.txt

[FragpipeIssue]

Here is the log file, I hope it's okay! Thank you!

[fcyu]

Thanks for sharing the log file.

First of all, the combined_*.tsv files are for the DDA data type, whiles yours are DIA.

Second, your configures don't make any sense to me. You have 8 Thermo raw files that seem to be from DIA

LCMS files:
  Experiment/Group: 
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-A1.raw	DIA
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-A2.raw	DIA
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-A3.raw	DIA
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-A4.raw	DIA
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-B1.raw	DIA
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-B2.raw	DIA
  - D:\Simona\ProvaMiscela_Fragpipe\PAC-SCX-10ug-B3.raw	DIA

But, then, you enabled almost all modules in FragPipe, some of which are not for your data

    Cmd: [START], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [CheckCentroid], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [UmpireSe], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [diaTracer], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [MSFragger], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [MSBooster], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [Percolator], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [ProteinProphet], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [PhilosopherFilter], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [PhilosopherReport], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [PTMShepherd], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [WorkspaceClean], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [SpecLibGen], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [DIA-NN], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]
    Cmd: [Skyline], Work dir: [D:\Simona\ProvaMiscela_Fragpipe]

Please load one of the built-in workflow that matches your sample the closest, and do not change the settings that you don't understand.

Best,

Fengchao

[FragpipeIssue]

Thank you for your assistance!
This is my first time using FragPipe, and I’m trying to learn it, so I might have enabled more modules than necessary while following a tutorial. I apologize for that. My goal was to process data acquired in DIA mode from a peptide mixture derived from different species.

PS: In the end, I used the report.pg_matrix file I found in the "diann-output" folder on Perseus; however, it doesn’t contain the protein.names. I read in another response that you plan to add them in the future—I hope so!

Thank you for your reply.

[fcyu]

My goal was to process data acquired in DIA mode from a peptide mixture derived from different species.

Then, you should use the DIA_SpecLib_Quant workflow. I suggest you load that one (remember to click "load" after selecting it), and reprocess the data. Some of your previous settings might results in suboptimal results.

PS: In the end, I used the report.pg_matrix file I found in the "diann-output" folder on Perseus; however, it doesn’t contain the protein.names. I read in another response that you plan to add them in the future—I hope so!

Yes, we will add such info in the future version.

Best,

Fengchao