How would one go about deserialising custom binary formats?

I use a bunch of scientific instruments that initially output their data in binary formats and which require the instrument software to output as a Ascii, csv, xml (etc.) File.

Is there a way to deserialise the data without the software? How would one go about it? Any links to get me started?

Data is GCMS data (shimadzu), isothermal nitrogen adsorption data amongst others.