Mascot MGF parsing error

[sureshhewabi]

While I was parsing an MGF file provided by Mascot itself(so which I can trust it is correct), I encountered with this error:

__main__ - ERROR - Pyteomics error, message: 'MGF format error: cannot parse PEPMASS = 352.1888 836632.25 2+'
Traceback (most recent call last):
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/pyteomics/mgf.py", line 207, in _read_spectrum_lines
    pepmass = tuple(map(float, params['pepmass'].split()))
ValueError: could not convert string to float: '2+'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/userpath/xiview-api/process_dataset.py", line 239, in <module>
    main(parser.parse_args())
  File "/userpath/xiview-api/process_dataset.py", line 50, in main
    convert_dir(local_dir, project_identifier, nopeaklist=args.nopeaklist)
  File "/userpath/xiview-api/process_dataset.py", line 213, in convert_dir
    raise e
  File "/userpath/xiview-api/process_dataset.py", line 208, in convert_dir
    id_parser.parse()
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/parser/MzIdParser.py", line 88, in parse
    self.main_loop()
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/parser/MzIdParser.py", line 598, in main_loop
    spectrum = peak_list_reader[sid_result["spectrumID"]]
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/parser/peaklistReader/PeakListWrapper.py", line 71, in __getitem__
    return self.reader[spec_id]
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/parser/peaklistReader/PeakListWrapper.py", line 188, in __getitem__
    spec = self._reader[spec_id]
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/pyteomics/auxiliary/file_helpers.py", line 285, in __getitem__
    return self.get_by_index(key)
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/pyteomics/auxiliary/file_helpers.py", line 263, in get_by_index
    return self.get_by_id(key)
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/pyteomics/auxiliary/file_helpers.py", line 253, in get_by_id
    return self._item_from_offsets(offsets)
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/pyteomics/mgf.py", line 359, in _item_from_offsets
    return self._read_spectrum_lines(lines)
  File "/Users/username/.local/share/virtualenvs/xi-mzidentml-converter-MB5dCI2Q/lib/python3.10/site-packages/pyteomics/mgf.py", line 209, in _read_spectrum_lines
    raise aux.PyteomicsError('MGF format error: cannot parse '
pyteomics.auxiliary.structures.PyteomicsError: Pyteomics error, message: 'MGF format error: cannot parse PEPMASS = 352.1888 836632.25 2+'

Please find the example mgf file in the following link:
https://drive.google.com/drive/folders/14wtAxOamqtf3A0BWQD_8_m5u0kpIRtQw?usp=sharing

[vrkosk]

It may help to refer to https://www.matrixscience.com/help/data_file_help.html#PARAMS:

PEPMASS is peptide mass "optionally followed by intensity and charge".

Positive and negative charge states are specified as "N- to N+ where N is an integer".

[sureshhewabi]

@vrkosk Yes So will you be able to correct this bug from pyteomics software?

[levitsky]

Thanks for reporting, I will try to implement support for this syntax shortly.

[ypriverol]

@levitsky we can try to do a PR with the changes needed if is needed.

[levitsky]

Thanks Yasset, I don't mind fixing this at all, just having a busy weekend celebrating my birthday :) I should be able to have a fix for this on Monday.

[ypriverol]

happy birthday my friend. All the best and I hope everything is going well for you. We probably will start contributing with some PRs in the future ;)