Maybe look into Mass++ that was first posted here on spctools-discuss
back in 2008::

https://groups.google.com/forum/?hl=en&fromgroups#!forum/massplusplus
http://www.first-ms3d.jp/english/mass2

On Tue, Oct 23, 2012 at 4:15 PM, Gautam Saxena <gsaxena...@gmail.com> wrote:
> Does anyone know of a tool that can convert Shimazdu MS files to mzXML
> (preferred) or mgf/mzML etc.? Based on the website of ProteoWizard, it
> doesn't look like the Shimazdu files are supported....

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