mspire

Mspire is a full featured library for working with mass spectrometry data, particularly proteomic, metabolomic and lipidomic data sets. It aims to be fast, robust, and beautiful.

Cite

Prince JT, Marcotte EM. mspire: mass spectrometry proteomics in Ruby. Bioinformatics. 2008 Dec 1;24(23):2796-7. (pubmed)

Features

mzml

  • Reading and writing
  • True random access to spectra or chromatograms
  • Complete object model with implicit object link resolution (even with random access)
  • Simplified creation of and full support for CV params and referenceable param groups

imzml

Mspire is the only converter from mzml into imzml.

  • handles both processed and continuous modes
  • gracefully handles SIM data

Other Feature Highlights

  • isotope distribution prediction: uses fastest method known (FFT convolution)
  • protein digestion: Support for 32 enzymes/variants by name
  • pepxml: full object model and complete write support
  • fasta files: complete programmatic access to description lines (via bio-ruby)
  • peak lists: merging/summing and splitting algorithms
  • obo: ontology hash access
  • molecular formulas: can do arithmetic with formulas
  • calculates q-values

Examples

mzml

require 'ms/mzml'

MS::Mzml.open("somefile.mzml") do |mzml|
  spectrum = mzml[0]   # the first spectrum ( same as mzml.spectrum(0) )
  spectrum = mzml["controllerType=0 controllerNumber=1 scan=2"]  # query by id string
  mzml.spectrum_from_scan_num(23) # raises ScanNumbersNotFound or ScanNumbersNotUnique errors if problems
end

require 'ms/mass/aa'

MS::Mass::AA::MONO['A'] # or access by symbol

Acronym

Mass SPectrometry In Ruby. Mspire originally stood for Mass Spectrometry Proteomics In Ruby but the library has since proven useful for all kinds of mass spectrometry projects, hence the more inclusive form. The e was originally included for aesthetic reasons, but it also provides the user/developer the ability to attach whatever Exclamation or Epithet they choose to the acronym (the best ones will begin with e of course).

MIT license. See LICENSE for details.