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kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
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MGF compatibility with MS-Amanda #17

Closed verheytb closed 5 years ago

verheytb commented 5 years ago

Hi,

I've been using MGF files generated from RawTools successfully with several search engines. However, with MS Amanda, I get the following error:

Searching file 'filename.raw.mgf'...
Error parsing mgf file at or after spectrum 'Spectrum_3'.
Input string was not in a correct format.
Search failed.

Parsing of the MGF files is likely the issue. When I look at the MGF file specifications here it looks like the issue is the CHARGE line, which should be CHARGE=2+ instead of CHARGE=2.

kevinkovalchik commented 5 years ago

Hello,

Thanks for bringing this to our attention. We've tried to follow the specifications you mention, but since a lot of search engines try to correct any errors I sometimes don't know if something is wrong! I'll get this fixed soon.

Thanks, Kevin

verheytb commented 5 years ago

I appreciate it, thanks!

Ted

kevinkovalchik commented 5 years ago

Hi Ted,

Try this out:

RawTools_FixMgf_20181220.zip

Its based on the beta.4 version, so if you are using an earlier version it will look a little different on the console. There are some detail here.

Kevin

verheytb commented 5 years ago

Hi Kevin, MS-Amanda seems to be working fine now. Thanks!

kevinkovalchik commented 5 years ago

Thanks for letting me know!

Kevin

On Wed, Jan 2, 2019, 8:22 AM Ted Verhey <notifications@github.com wrote:

Closed #17 https://github.com/kevinkovalchik/RawTools/issues/17.

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