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compomics / moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Apache License 2.0
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Raw to mgf conversion in moFF? #46

Closed CarlosHorro closed 5 years ago

CarlosHorro commented 5 years ago

Hi,

I just wanted to ask if, at some point, it is planned to include the conversion from Raw to MGF in moFF (as it's already using the RawFileReader).

Greetings, Carlos

Maux82 commented 5 years ago

hi, I suppose you mean the conversion between raw to mzml because the mgf format is not used in moff. there is no plan to include the conversion from raw to mzml.

CarlosHorro commented 5 years ago

Um... well, I though moFF is prepared for running in a unique workflow together with PeptideShaker, I've already seen that moFF accepts PS's PSM report, but PS still needs mgfs files (it cannot manage directly raw files). So, in order to run them both together, do you use an external conversion tool to get mgfs files and give them to PeptideShaker?

bgruening commented 5 years ago

@CarlosHorro can you not use: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1 ?

CarlosHorro commented 5 years ago

@CarlosHorro can you not use: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1 ?

Well, maybe, I have not tried that tool yet (although it still seems to be in beta version), we just wondered about how moFF managed this scenario...

Maux82 commented 5 years ago

@CarlosHorro in this scenario , moFF works fine because does not need any mgf file in input. if you integrate Thermo_raw_file_converter in PS-searchgui and then you run moFF on PS report (PSM report) and its original raw file/mzml works.

CarlosHorro commented 5 years ago

Thank you for the info :-)