mspire

mzml_file = "yourfile.mzML"

require 'mspire/mzml'

# get the intensity of the highest peak from each spectrum
intensities = Mspire::Mzml.foreach(mzml_file).map do |spectrum|
  spectrum.intensities.max
end

# open the file for other operations
Mspire::Mzml.open(mzml_file) do |mzml|
  # read each spectra
  mzml.each do |spectrum|
    # do something with each spectrum ...
  end

  # or random access by index or id (even if file wasn't indexed)
  spectrum = mzml[0]
  spectrum = mzml["controllerType=0 controllerNumber=1 scan=2"]

  # some things to do with a spectrum
  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

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

# 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::Element::MONO[:C] # carbon
Mspire::Mass::Subatomic::MONO[:electron]

require 'mspire/isotope'
isotopes = Mspire::Isotope::ISOTOPES  # 288 isotopes
# same as Mspire::Isotope::Neese::ISOTOPES ; compare to Mspire::Isotope::NIST::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

require 'mspire/digester'
trypsin = Mspire::Digester[:trypsin].
trypsin.digest("AACCKDDEERFFKPGG") # => ["AACCK", "DDEER", "FFKPGG"]