Database searchingPKL Micromass File?

Question

[rh5118]

Hi BioStars-

Anyone have a good way of doing a database search on a PKL file? I need to search the mass spec data against a supplied proteome. I'd like to use Galaxy but I need to convert PKL to MGF, which I also don't know how to do. Many thanks!

• A mass spec newbie

Answer 1

[mobiusklein]

To convert most mass spectrometry data format into one of the open standard formats or popular plain text formats, you can use msconvert, part of ProteoWizard. Reading vendor binary files requires that you use a Windows machine, but the open XML based formats and those text formats are usable on all platforms the program can build on.

MSGF+ can read from PKL files directly according to the documentation, and it has a few Galaxy wrappers.