Explaining any terms likely to be unfamiliar to laymen or specialists in other fields (most of the Monks, for example, or, at least, to /me anyway) when raising a question here (rather than, making us search for explanations) is helpful or even prerequisite if you hope for quick, on-target help.

Starting with the most nearly obvious:

• mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for Systems Biology.
• shimadzu is a tech corp which uses .gcd as a format for some of its mass spectrometers (and other tools?)
• .gcd is a file format used as above, and for digital architectural drawings and for map files for the like of Garmin's mobile/portable gps devices.

See I know what I mean. Why don't you? and please also note that most SoPW should demonstrate that you've made some effort to answer your own question. If you're stuck whilst coding, please include your code, error messages and warnings, etc.. as well as sample data.

1. ) Look up documentation to understand the source file.
2. ) Convert the file by hand once to be sure you understand it.
3. ) Write function to do the same thing you just did by hand.
4. ) Upload it as a module to CPAN

1. ) Create a few of the simplest possible sets of data you can make, and save them.
2. ) Open the files in a hex editor and compare them in order to figure out how the data is arranged.
3. ) Repeat from Step 1 until you understand how all the features you care about are saved.
4. ) Convert the file by hand.
5. ) Write a function to do the same thing.
6. ) Upload it as a module to CPAN.