TMT Integrator output files are only generating column headers with no data

[jessmajka]

Hello,

I am writing regarding an issue I encountered with TMT Integrator within a FragPipe search.

In previous analyses, I ran a TMT18 workflow with specified PTMs in MSFragger and obtained files in the tmt-report directory that reported the sample/channel names along with my modified peptides/proteins of interest.

However, when re-running this same workflow on a new dataset, the search completes, but all the files generated in the tmt-report folder contain only the column headers and no data. I even did a trial run with a file from the dataset I've successfully analyzed with this workflow and experienced the same issue. I have confirmed that the modified peptides of interest are present in the combined_modified_peptdie.tsv output files, so the modifications appear to be identified during the search. My goal is to map which of these peptides are present in each TMT sample/channel, but the TMT integrator outputs are currently empty.

I've attached the relevant log information for reference. Thank you for your time and help.

log_2026-03-10_11-52-51.txt

[fcyu]

Could you share the psm.tsv files with us?

Thanks,

Fengchao

[jessmajka]

Yes, here are those files.

These are the files in my experiment folder:
psm.tsv
ion.tsv
peptide.tsv
protein.tsv
combined_modified_peptide.tsv

These are the files in my tmt-report folder:
abundance_gene_None.tsv
abundance_multi-site_None.tsv
abundance_peptide_None.tsv
abundance_protein_None.tsv
abundance_single-site_None.tsv
ratio_gene_None.tsv
ratio_multi-site_None.tsv
ratio_peptide_None.tsv
ratio_protein_None.tsv
ratio_single-site_None.tsv

[fcyu]

Thanks for sharing the files. All PSMs were filtered out due to resolution and SNR filtering. Basically, if there is a channel with resolution < 45000 (the parameter "min resolution" in the "Quant (Isobraic)" table) and SNR >= 1, the PSM will be discarded.

The filtering is for the Astral mass spectrometer. If your data don't have that level of resolution, you could adjust the settings.

Best,

Fengchao