Sage with TimsTOF Data Rescoring

[jonathan-krieger-bruker]

Hello,

I am trying to run a rescore with Sage results and timsTOF data.

My configuration for Rescore and the error I receive is as follows.

oktoberfest -c ./oktoberfest_rescore_config.json
2025-02-21 16:19:23,837 - INFO - oktoberfest.utils.config::read Reading configuration from ./oktoberfest_rescore_config.json
2025-02-21 16:19:23,837 - INFO - oktoberfest.runner::run_job Oktoberfest version 0.8.3
Copyright 2025, Wilhelmlab at Technical University of Munich
2025-02-21 16:19:23,837 - INFO - oktoberfest.runner::run_job Job executed with the following config:
2025-02-21 16:19:23,837 - INFO - oktoberfest.runner::run_job {
"type": "Rescoring",
"tag": "",
"output": "./out",
"inputs": {
"search_results": "./results.sage.tsv",
"search_results_type": "Sage",
"spectra": "../",
"spectra_type": "d",
"instrument_type": "TIMSTOF"
},
"models": {
"intensity": "AlphaPept_ms2_generic",
"irt": "AlphaPept_rt_generic"
},
"prediction_server": "koina.wilhelmlab.org:443",
"numThreads": 30,
"fdr_estimation_method": "mokapot",
"add_feature_cols": "none",
"regressionMethod": "spline",
"ssl": true,
"thermoExe": "ThermoRawFileParser.exe",
"massTolerance": 20,
"unitMassTolerance": "ppm",
"ce_alignment_options": {
"ce_range": [
19,
50
],
"use_ransac_model": false
}
}
2025-02-21 16:19:23,837 - INFO - oktoberfest.utils.config::read Reading configuration from ./oktoberfest_rescore_config.json
2025-02-21 16:19:23,838 - INFO - oktoberfest.preprocessing.preprocessing::list_spectra Found 3 d directories in the spectra input directory.
2025-02-21 16:19:23,838 - INFO - oktoberfest.runner::_preprocess Converting search results from results.sage.tsv to internal search result.
2025-02-21 16:19:23,838 - INFO - spectrum_io.search_result.search_results::generate_internal Found search results in internal format at out/msms/msms.prosit, skipping conversion
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/oktoberfest/bin/oktoberfest", line 8, in
sys.exit(main())
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/main.py", line 40, in main
runner.run_job(args.config_path)
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/runner.py", line 1378, in run_job
run_rescoring(config_path)
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/runner.py", line 1249, in run_rescoring
spectra_files = _preprocess(spectra_files, config)
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/runner.py", line 77, in _preprocess
timstof_metadata = pp.convert_timstof_metadata(
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/preprocessing/preprocessing.py", line 592, in convert_timstof_metadata
raise ValueError(f"Unsupported search engine provided for reading timstof metadata: {search_engine}")
ValueError: Unsupported search engine provided for reading timstof metadata: sage

Thank you for your help!
Jonathan

[picciama]

Hi @jonathan-krieger-bruker, this is unfortunately not supported. When integrating the timsTOF support, we did so for MaxQuant, specifically accumulatedMsmsScans.txt and PasefMsmsScans.txt, since it provides the required metadata on how individual scans are summed up so that we can do the same thing for correct rescoring. This is search engine specific as it seems. I am not sure, if Sage provides all that information, but if it does, we can add support for it.