Prepec modification error: Multiple modifications per site not supported in Peptide Record format. #108
Description
Hi,
I am trying to use ms2Rescore to rescore the output i get from a searchGUi / peptideshaker analysis
here is the log of ms2rescore in debug mode
Running DeepLC for PSMs from run (1/1): `586APMS_FLAG_alt1`...
Calibrating DeepLC...
Using 5135 PSMs for calibration
Multiple modifications per site not supported in Peptide Record format.
Traceback (most recent call last):
File "ms2rescore\gui\function2ctk.py", line 301, in run
self.fn(*self.fn_args, **self.fn_kwargs)
File "ms2rescore\gui\app.py", line 637, in function
rescore(configuration=config)
File "ms2rescore\core.py", line 76, in rescore
fgen.add_features(psm_list)
File "ms2rescore\feature_generators\deeplc.py", line 163, in add_features
seq_df=self._psm_list_to_deeplc_peprec(psm_list_calibration)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "ms2rescore\feature_generators\deeplc.py", line 210, in _psm_list_to_deeplc_peprec
peprec = peptide_record.to_dataframe(psm_list)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "psm_utils\io\peptide_record.py", line 505, in to_dataframe
return pd.DataFrame([PeptideRecordWriter._psm_to_entry(psm) for psm in psm_list])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "psm_utils\io\peptide_record.py", line 505, in <listcomp>
return pd.DataFrame([PeptideRecordWriter._psm_to_entry(psm) for psm in psm_list])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "psm_utils\io\peptide_record.py", line 285, in _psm_to_entry
sequence, modifications, charge = proforma_to_peprec(psm.peptidoform)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "psm_utils\io\peptide_record.py", line 443, in proforma_to_peprec
ms2pip_mods.append(_mod_to_ms2pip(mod, i + 1))
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "psm_utils\io\peptide_record.py", line 433, in _mod_to_ms2pip
raise InvalidPeprecModificationError(
psm_utils.io.peptide_record.InvalidPeprecModificationError: Multiple modifications per site not supported in Peptide Record format.
On searchGUI i used the thermofisherrawparser to parse my raw file, X!Tandem and MS-GF+ as search algorithms and used peptideshaker
In peptideshaker, i used the export->peptideshaker project as -> mzldentML to produce the mzid im using in ms2rescore (including protein sequences)
modification used are Carbomidomethyl of C as fixed, and Oxidation , Acetylation for variables
percolator was used but i dont think it got to its step
I parsed the peptides in the mzid file to make sure that for the same peptide, all the modification had a different location
here is a link to a google drive folder containing the mzid and mzml and the fasta i used
https://drive.google.com/drive/folders/1DUUn7fyeJR2rgIze2dQQ3r4ikcyfwiLI?usp=sharing
here is the line in the config.json file generated by ms2rescore
`{
"$schema": "./config_schema.json",
"ms2rescore": {
"feature_generators": {
"basic": {},
"ms2pip": {
"model": "HCD2021",
"ms2_tolerance": 0.02
},
"deeplc": {
"deeplc_retrain": false,
"n_epochs": 20,
"calibration_set_size": 0.15
}
},
"rescoring_engine": {
"percolator": {
"write_weights": true,
"write_txt": true,
"write_flashlfq": false,
"protein_kwargs": {}
}
},
"config_file": null,
"psm_file": [
"C:/Users/pron2107/Desktop/mspipeline/test1/report/test1.mzid"
],
"psm_file_type": "mzid",
"psm_reader_kwargs": {},
"spectrum_path": "C:/Users/pron2107/Desktop/mspipeline/test1/586APMS_FLAG_alt1.mzML",
"output_path": "C:/Users/pron2107/Desktop/mspipeline/test1/ms2rescore/test1",
"log_level": "info",
"id_decoy_pattern": "_REVERSED",
"psm_id_pattern": ".*scan=(\\d+)$",
"spectrum_id_pattern": ".*scan=(\\d+)$",
"lower_score_is_better": false,
"modification_mapping": {
"Oxidation": "U:Oxidation",
"Acetyl": "U:Acetylation"
},
"fixed_modifications": {
"U:Carbamidomethyl": [
"C"
]
},
"processes": 12,
"rename_to_usi": false,
"fasta_file": "C:/Users/pron2107/Desktop/mspipeline/test1/human-openprot-2_0-refprots+altprots+isoforms-min_2_pep-uniprot2022_06_011_concatenated_target_decoy.fasta",
"write_report": true
}
}`
after all that i am wondering if I am doing anything wrong, with my settings
Thanks in advance
Nicolas