MS2rescore for PeptideShaker ouput

[trinhxt]

Hi,

I am trying to use MS2rescore to reanalyze MS data processed by SearchGUI & PeptideShaker.
For the input files of MS2rescore: Identification file is Extended PSM report from PeptideShaker; and Spectrum file is the mgf file produced by ThermoRawFileParser.

I could not make MS2rescore run properly; it produced the below error.
Could you please give me hints about how to run MS2rescore properly?

Thank you!

Traceback (most recent call last):
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\runpy.py", line 194, in _run_module_as_main
return run_code(code, main_globals, None,
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\Scripts\ms2rescore-gui.exe_main.py", line 7, in
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\site-packages\gooey\python_bindings\gooey_decorator.py", line 134, in
return lambda *args, **kwargs: func(*args, **kwargs)
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\site-packages\ms2rescore\gui.py", line 54, in main
rescore.run()
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\site-packages\ms2rescore_init.py", line 238, in run
search_engine_features = self.pipeline.get_search_engine_features()
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\site-packages\ms2rescore\id_file_parser.py", line 449, in get_search_engine_features
return self.extended_psm_report.ext_psm_report.get_search_engine_features()
File "C:\Portable\ms2rescore-gui-windows\Miniconda3\envs\ms2rescore\lib\site-packages\ms2rescore\peptideshaker.py", line 187, in get_search_engine_features
raise NotImplementedError
NotImplementedError

[RalfG]

Hi @trinhxt,

Thanks for posting your question. With MS²Rescore 3.0, we now directly support rescoring PeptideShaker PSMs from exported mzIdentML files.

Let us know how it works out for you!

Ralf