mzML¶ ↑

MzML is a standard data format for encoding mass spectrometry data. For more information see mzML the specification at psidev.info/index.php?q=node/257

This library is a non-validating, read-only mzML parser for mzML version 1.1.x

It is built on top of the nokogiri gem for XML parsing, which itself relies on the libxml2 C library. The library It is relatively fast

require 'mzml'
mzml =  MzML::Doc.open("test.mzXML")
# to iterate through spectra
mzml.each do |spectrum|
  # ... do something interesting
end
# to get an Array of spectrum IDs
mzml.spectrum_list
# to fetch a specific spectrum, whose ID you already know
mzml.spectrum("controllerType=0 controllerNumber=1 scan=1")

You can also get chromatograms

mzml.each_chromatogram
mzml.chromatogram("TIC")

• Fork the project. It is hosted @ github.com/delagoya/mzml

• Make your feature addition or bug fix.

• Add tests for it. This is important so I don’t break it in a future version unintentionally.

• Commit, do not mess with rakefile, version, or history. (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)

• Send me a pull request. Bonus points for topic branches.

Copyright © 2009 Angel Pizarro. See LICENSE for details.