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 commandline converter from mzml into imzml (also see imzMLConverter)
- 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
ruby
mzml_file = "yourfile.mzML"
mzml
See Mspire::Mzml, Mspire::CV::Paramable, Mspire::Mzml::Spectrum and other objects associated with Mzml files.
reading
```ruby require ‘mspire/mzml’
| Mspire::Mzml.open(mzml_file) do | mzml |
# random access by index or id (even if file wasn’t indexed) spectrum = mzml[0] spectrum = mzml[“controllerType=0 controllerNumber=1 scan=2”]
spectrum.mzs spectrum.intensities
# first 5 peaks spectrum.peaks[0,5].each do |mz, intensity| puts “#mz #intensity” end
# true if key exists and no value, the value if present, or false if spectrum.fetch_by_acc(‘MS:1000128’) puts “this is a profile spectrum!” end
if spectrum.ms_level == 2 low_mz = spectrum.scan_list.first.scan_windows.first.fetch_by_acc(“MS:1000501”).to_i puts “begin scan at #low_mz m/z” end end ```
normalize spectra and write new mzML
See Mspire::Mzml for complete example building all objects from scratch.
```ruby require ‘mspire/mzml’
| Mspire::Mzml.open(mzml_file) do | mzml |
# MS:1000584 -> an mzML file mzml.file_description.source_files « Mspire::Mzml::SourceFile[mzml_file].describe!(‘MS:1000584’) mspire = Mspire::Mzml::Software.new mzml.software_list.push(mspire).uniq_by(&:id) normalize_processing = Mspire::Mzml::DataProcessing.new(“ms1_normalization”) do |dp| # ‘MS:1001484’ -> intensity normalization dp.processing_methods « Mspire::Mzml::ProcessingMethod.new(mspire).describe!(‘MS:1001484’) end
mzml.data_processing_list « normalize_processing
spectra = mzml.map do |spectrum| normalizer = 100.0 / spectrum.intensities.max spectrum.intensities.map! {|i| i * normalizer } spectrum end mzml.run.spectrum_list = Mspire::Mzml::SpectrumList.new(normalize_processing, spectra) mzml.write(outfile) end ``` ### Masses
```ruby # very high precision NIST masses aa_to_mass = Mspire::Mass::AA::MONO # a hash with residue masses aa_to_mass[‘A’] # or access by symbol - Alanine
elements
Mspire::Mass::MONO[:c] # carbon Mspire::Mass::MONO[:e] # electron (includes other useful symbols) ```
Isotopes and molecular formulas
```ruby require ‘mspire/isotope’ isotopes = Mspire::Isotope::ISOTOPES # 288 isotopes hydrogen_isotopes = isotopes.select {|iso| iso.element == :h }
c12 = Mspire::Isotope::BY_ELEMENT[:c].first c12.atomic_number # also: mass_number atomic_mass relative_abundance average_mass c12.mono # => true (this is the monoisotopic isotope)
require ‘mspire/molecular_formula’ # requires fftw gem propane = Mspire::MolecularFormula[‘C3H8’] butane = propane + Mspire::MolecularFormula[‘CH2’] puts butane # => C4H10
require ‘mspire/isotope/distribution’ # requires fftw gem puts butane.isotope_distribution # :total, :max, :first as arg to normalize ```
Digestion
ruby
require 'mspire/digester'
trypsin = Mspire::Digester[:trypsin].
trypsin.digest("AACCKDDEERFFKPGG") # => ["AACCK", "DDEER", "FFKPGG"]
## TODO
- write the mzml index onto a file (along with correct SHA-1)
- implement spectrum unpack into an nmatrix or narray
- do a proper copy over of meta-data from mzml into imzml
- consider implementing params as a hash and formalizing more complete implementation agnostic params api
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).
Copyright
MIT license. See LICENSE for details.
