mzML file format?

[Samuel Miller]

Hi DeNovoGUI devs,

Have you considered modifying DeNovoGUI to allow input files in mzML format?  I have encountered problems with mgf files generated by different tools, as there is no single specification for mgf.  A file format with a standard specification would ease the incorporation of DeNovoGUI into programmatic pipelines.

Thanks for your consideration,

Sam Miller

[Marc Vaudel]

Hi Sam,

Yes, we are working towards supporting more formats in our tools. However, to run the sequencing engines, we still need to convert the files into a format they support so there is no way around a conversion step. If you use mzML or raw files in your pipeline you can use ProteoWizard as intermediate step to generate mgf files supported by most software.

Hope this helps,

Marc

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