I was contacted by a user who noted that mzIdentML input from MS-GF+ was not working. Looking into the code, I determined that this line is the problem:
I have been doing my testing with Comet, which outputs spectrumIDs that look like scan=25465, but MS-GF+ outputs a lot more info: controllerType=0 controllerNumber=1 scan=25465.
I was contacted by a user who noted that mzIdentML input from MS-GF+ was not working. Looking into the code, I determined that this line is the problem:
https://github.com/AnthonyOfSeattle/pyAscore/blob/c6d0146fcdcf6b5e7aba5f9700a7bc103e24b411/pyascore/parsing/id_parsers.py#L308
I have been doing my testing with Comet, which outputs spectrumIDs that look like
scan=25465, but MS-GF+ outputs a lot more info:controllerType=0 controllerNumber=1 scan=25465.