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.