mspire 0.8.2 → 0.8.3

data/README.md

@@ -37,19 +37,120 @@ Mspire is the *only* converter from mzml into imzml.
 
 ## Examples
 
-### mzml
-
-    require 'ms/mzml'
+```ruby
+mzml_file = "yourfile.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
+### mzml
 
-    require 'ms/mass/aa'
+See Mspire::Mzml, Mspire::CV::Paramable, Mspire::Mzml::Spectrum and other
+objects associated with Mzml files.
+
+#### reading
 
-    MS::Mass::AA::MONO['A'] # or access by symbol
+```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
 

data/VERSION

@@ -1 +1 @@
-0.8.2
+0.8.3

data/lib/core_ext/enumerable.rb

@@ -5,4 +5,9 @@ module Enumerable
     return to_enum :index_by unless block_given?
     Hash[map { |elem| [yield(elem), elem] }]
   end
+
+  def uniq_by
+    h = {}
+    inject([]) {|a,x| h[yield(x)] ||= a << x}
+  end
 end

data/lib/mspire/molecular_formula.rb

@@ -134,9 +134,14 @@ module Mspire
 
     def to_s(alphabetize=true)
       h = alphabetize ? self.sort : self
-      h.flat_map {|k,v| 
-        [k.capitalize, v > 1 ? v : '']
-      }.join
+      st = ''
+      h.each do |k,v|
+        if v > 0
+          st << k.to_s.capitalize
+          st << v.to_s if v > 1
+        end
+      end 
+      st
     end
 
     def to_hash

data/lib/mspire/mzml.rb

@@ -1,5 +1,4 @@
 
-# TODO: trim down these require statements to only include upper level
 require 'mspire'
 require 'builder'
 require 'core_ext/enumerable'
@@ -19,6 +18,23 @@ module Mspire
   #         spectrum.peaks do |mz,intensity|
   #           puts "mz: #{mz} intensity: #{intensity}" 
   #         end
+  #
+  #         spectrum.params  # list all the params associated with an object
+  #
+  #         # 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.to_i
+  #           puts "begin scan at #{low_mz} m/z"
+  #         end
+  #       end
+  #
+  #       mzml.each_chromatogram do |chrm|
+  #         chrm.times
+  #         chrm.intensities
   #       end
   #     end
   #
@@ -29,38 +45,68 @@ module Mspire
   #
   # Writing an mzml file from scratch:
   #
-  #     spec1 = Mspire::Mzml::Spectrum.new('scan=1') do |spec|
-  #       spec.describe_many! ['MS:1000127', ['MS:1000511', 1]]
-  #       spec.data_arrays = [[1,2,3], [4,5,6]]
-  #       spec.scan_list = Mspire::Mzml::ScanList.new do |sl|
-  #         scan = Mspire::Mzml::Scan.new do |scan|
-  #           # retention time of 40 seconds
-  #           scan.describe! ['MS:1000016', 40.0, 'UO:0000010']
-  #         end
-  #         sl << scan
-  #       end
-  #     end
-  #
-  #     mzml = Mspire::Mzml.new do |mzml|
-  #       mzml.id = 'the_little_example'
-  #       mzml.cvs = Mspire::Mzml::CV::DEFAULT_CVS
-  #       mzml.file_description = Mspire::Mzml::FileDescription.new  do |fd|
-  #         fd.file_content = Mspire::Mzml::FileContent.new
-  #         fd.source_files << Mspire::Mzml::SourceFile.new
-  #       end
-  #       default_instrument_config = Mspire::Mzml::InstrumentConfiguration.new("IC",[])
-  #       default_instrument_config.describe! 'MS:1000031'
-  #       mzml.instrument_configurations << default_instrument_config
-  #       software = Mspire::Mzml::Software.new
-  #       mzml.software_list << software
-  #       default_data_processing = Mspire::Mzml::DataProcessing.new("did_nothing")
-  #       mzml.data_processing_list << default_data_processing
-  #       mzml.run = Mspire::Mzml::Run.new("little_run", default_instrument_config) do |run|
-  #         spectrum_list = Mspire::Mzml::SpectrumList.new(default_data_processing)
-  #         spectrum_list.push(spec1)
-  #         run.spectrum_list = spectrum_list
-  #       end
-  #     end
+  #    spec1 = Mspire::Mzml::Spectrum.new('scan=1') do |spec|
+  #      # profile and ms_level 1
+  #      spec.describe_many!(['MS:1000128', ['MS:1000511', 1]])
+  #      spec.data_arrays = [
+  #        Mspire::Mzml::DataArray[1,2,3].describe!('MS:1000514'),  
+  #        Mspire::Mzml::DataArray[4,5,6].describe!('MS:1000515')   
+  #      ]
+  #      spec.scan_list = Mspire::Mzml::ScanList.new do |sl|
+  #        scan = Mspire::Mzml::Scan.new do |scan|
+  #          # retention time of 42 seconds
+  #          scan.describe! 'MS:1000016', 40.0, 'UO:0000010'
+  #        end
+  #        sl << scan
+  #      end
+  #    end
+  #  
+  #    spec2 = Mspire::Mzml::Spectrum.new('scan=2') do |spec| 
+  #      # centroid,  ms_level 2, MSn spectrum, 
+  #      spec.describe_many!(['MS:1000127', ['MS:1000511', 2], "MS:1000580"])
+  #      spec.data_arrays = [
+  #        Mspire::Mzml::DataArray[1,2,3.5].describe!('MS:1000514'),  
+  #        Mspire::Mzml::DataArray[5,6,5].describe!('MS:1000515')   
+  #      ]
+  #      spec.scan_list = Mspire::Mzml::ScanList.new do |sl|
+  #        scan = Mspire::Mzml::Scan.new do |scan|
+  #          # retention time of 42 seconds
+  #          scan.describe! 'MS:1000016', 45.0, 'UO:0000010'
+  #        end
+  #        sl << scan
+  #      end
+  #      precursor = Mspire::Mzml::Precursor.new( spec1.id )
+  #      si = Mspire::Mzml::SelectedIon.new
+  #      # the selected ion m/z:
+  #      si.describe! "MS:1000744", 2.0
+  #      # the selected ion charge state
+  #      si.describe! "MS:1000041", 2
+  #      # the selected ion intensity
+  #      si.describe! "MS:1000042", 5
+  #      precursor.selected_ions = [si]
+  #      spec.precursors = [precursor]
+  #    end
+  #  
+  #    mzml = Mspire::Mzml.new do |mzml|
+  #      mzml.id = 'ms1_and_ms2'
+  #      mzml.cvs = Mspire::Mzml::CV::DEFAULT_CVS
+  #      mzml.file_description = Mspire::Mzml::FileDescription.new  do |fd|
+  #        fd.file_content = Mspire::Mzml::FileContent.new
+  #        fd.source_files << Mspire::Mzml::SourceFile.new
+  #      end
+  #      default_instrument_config = Mspire::Mzml::InstrumentConfiguration.new("IC").describe!('MS:1000031')
+  #      mzml.instrument_configurations << default_instrument_config
+  #      software = Mspire::Mzml::Software.new
+  #      mzml.software_list << software
+  #      default_data_processing = Mspire::Mzml::DataProcessing.new("did_nothing")
+  #      mzml.data_processing_list << default_data_processing
+  #      mzml.run = Mspire::Mzml::Run.new("little_run", default_instrument_config) do |run|
+  #        spectrum_list = Mspire::Mzml::SpectrumList.new(default_data_processing, [spec1, spec2])
+  #        run.spectrum_list = spectrum_list
+  #      end
+  #    end
+  #    
+  #    mzml.write("writtenxml.mzML")
   class Mzml
     include Enumerable  # each_spectrum
 

data/lib/mspire/mzml/io_indexable_list.rb

@@ -20,7 +20,7 @@ module Mspire
       # similar to an array but is really pulling objects by reading an io
       # object.  Sets the spectrum_list attribute of array_like if it can be
       # set.
-      def initialize(default_data_processing, array_like, id_to_index=nil)
+      def initialize(default_data_processing, array_like=[], id_to_index=nil)
         if array_like.respond_to?(:spectrum_list=)
           array_like.spectrum_list = self
         end

data/lib/mspire/mzml/software.rb

@@ -10,7 +10,7 @@ module Mspire
 
       attr_accessor :id, :version
 
-      def initialize(id='mspire', version=Mspire::VERSION)
+      def initialize(id="mspire_#{Mspire::VERSION}", version=Mspire::VERSION)
         @id, @version = id, version
         params_init
         yield(self) if block_given?

data/lib/mspire/mzml/source_file.rb

@@ -8,8 +8,6 @@ module Mspire
       include Mspire::CV::Paramable
       extend Mspire::Mzml::List
 
-      DEFAULT_SOURCEFILE_ID = 'sourcefile1'
-
       # (required) An identifier for this file.
       attr_accessor :id
       # (required) Name of the source file, without reference to location
@@ -18,9 +16,11 @@ module Mspire
       # (required) URI-formatted location where the file was retrieved.
       attr_accessor :location
 
-      # expands the path and sets the name and location
+      # expands the path and sets the name and location.  Sets the id to the
+      # basename.
       def self.[](path, opts={})
-        self.new DEFAULT_SOURCEFILE_ID, *uri_basename_and_path(path)
+        (name, path) = uri_basename_and_path(path)
+        self.new(name, name, path)
       end
 
       # takes a filename (with a relative or expanded path) and returns the

data/spec/mspire/molecular_formula_spec.rb

@@ -33,6 +33,15 @@ describe Mspire::MolecularFormula do
       Mspire::MolecularFormula['Ni7SE3'].to_hash.should == {:ni=>7, :s=>1, :e=>3}
     end
 
+    describe 'correct to_s' do
+      subject {
+        Mspire::MolecularFormula.new({:c=>669, :h=>1129, :o=>185, :n=>215, :s=>4, :p=>0, :se=>0})
+      }
+      it 'to_s gives output' do
+        subject.to_s.should == "C669H1129N215O185S4"
+      end
+    end
+
     describe 'conversion' do
 
       subject {

data/spec/mspire/mzml_spec.rb

@@ -62,22 +62,28 @@ describe Mspire::Mzml do
       @file = TESTFILES + "/mspire/mzml/j24z.idx_comp.3.mzML"
     end
 
-    specify 'adding to source file, software, and data processing'
-      #Mspire::Mzml.open(@file) do |mzml|
-      #  mzml.source
-      #end
-
     specify 'normalize highest peak of each spectrum to 100' do
-      # this is very bad form to not change data_processing etc, but it
-      # demonstrates the minimal amount to normalize the spectra.
       outfile = TESTFILES + "/mspire/mzml/j24z.idx_comp.3.NORMALIZED.mzML" 
+
       Mspire::Mzml.open(@file) do |mzml|
+
+        # MS:1000584 -> an mzML file
+        mzml.file_description.source_files << Mspire::Mzml::SourceFile[@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(mzml.run.spectrum_list.default_data_processing, spectra)
+        mzml.run.spectrum_list = Mspire::Mzml::SpectrumList.new(normalize_processing, spectra)
         mzml.write(outfile)
       end
       # this output was checked to be accurate with TOPPView

data/spec/mspire/readme_spec.rb

@@ -0,0 +1,117 @@
+require 'spec_helper'
+
+# we aren't testing for preciseness in these examples (that is done
+# elsewhere), but we are verifying that it runs with no errors (i.e., the
+# syntax and api is all current)
+
+describe 'performing what is on the readme' do
+  describe 'mzml' do
+    let(:mzml_file) { TESTFILES + "/mspire/mzml/j24z.idx_comp.3.mzML" }
+    let(:outfile) { TESTFILES + "/mspire/mzml/j24z.idx_comp.3.NORMALIZED.mzML" }
+
+    specify "reading an mzml file" do
+
+      reply = capture_stdout do
+
+        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
+
+      end
+      reply.each_line.map.to_a.size.should == 6
+      reply.include?('begin scan at 120').should be_true
+    end
+
+    specify "normalizing and writing an mzml file" do
+      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
+      file_check(outfile)
+    end
+
+  end
+
+  specify 'masses' do
+    require 'mspire/mass/aa'
+
+    # 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)
+  end
+
+  specify 'isotopes and molecular formulas' do
+    reply = capture_stdout do
+
+      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
+    end
+  end
+
+  specify 'digestion' do
+    reply = capture_stdout do
+      require 'mspire/digester'
+      trypsin = Mspire::Digester[:trypsin]
+      p trypsin.digest("AACCKDDEERFFKPGG") # => ["AACCK", "DDEER", "FFKPGG"]
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -44,5 +44,21 @@ def file_check(filename, delete=true, &block)
 end
 
 def sanitize_mspire_version_xml(string)
-  string.gsub(/"mspire" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
+  string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
 end
+
+require 'stringio'
+ 
+module Kernel
+ 
+  def capture_stdout
+    out = StringIO.new
+    $stdout = out
+    yield
+    out.string
+  ensure
+    $stdout = STDOUT
+  end
+
+end
+

data/spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML

@@ -9,12 +9,15 @@
       <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
       <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum"/>
     </fileContent>
-    <sourceFileList count="1">
+    <sourceFileList count="2">
       <sourceFile id="RAW1" name="j24.raw" location="file://.">
         <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
         <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file"/>
         <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="6023d121fb6ca7f19fada3b6c5e4d5da09c95f12"/>
       </sourceFile>
+      <sourceFile id="j24z.idx_comp.3.mzML" name="j24z.idx_comp.3.mzML" location="file:///home/jtprince/dev/mspire/spec/testfiles/mspire/mzml">
+        <cvParam cvRef="MS" accession="MS:1000584" name="mzML file"/>
+      </sourceFile>
     </sourceFileList>
   </fileDescription>
   <referenceableParamGroupList count="1">
@@ -23,13 +26,15 @@
       <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN1025B"/>
     </referenceableParamGroup>
   </referenceableParamGroupList>
-  <softwareList count="2">
+  <softwareList count="3">
     <software id="Xcalibur" version="2.4 SP1">
       <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/>
     </software>
     <software id="pwiz" version="2.1.2086">
       <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard"/>
     </software>
+    <software id="mspire_0.8.2" version="0.8.2">
+    </software>
   </softwareList>
   <instrumentConfigurationList count="2">
     <instrumentConfiguration id="IC1">
@@ -65,16 +70,21 @@
       <softwareRef ref="Xcalibur"/>
     </instrumentConfiguration>
   </instrumentConfigurationList>
-  <dataProcessingList count="1">
+  <dataProcessingList count="2">
     <dataProcessing id="pwiz_Reader_Thermo_conversion">
       <processingMethod order="0" softwareRef="pwiz">
         <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
       </processingMethod>
     </dataProcessing>
+    <dataProcessing id="ms1_normalization">
+      <processingMethod order="0" softwareRef="mspire_0.8.2">
+        <cvParam cvRef="MS" accession="MS:1001484" name="intensity normalization"/>
+      </processingMethod>
+    </dataProcessing>
   </dataProcessingList>
   <run id="j24" defaultInstrumentConfigurationRef="IC1" defaultSourceFileRef="RAW1" startTimeStamp="2010-07-08T11:34:52Z">
-    <spectrumList count="3" defaultDataProcessingRef="pwiz_Reader_Thermo_conversion">
-      <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="20168">
+    <spectrumList count="3" defaultDataProcessingRef="ms1_normalization">
+      <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="20168" dataProcessingRef="pwiz_Reader_Thermo_conversion">
         <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
         <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
         <cvParam cvRef="MS" accession="MS:1000130" name="positive scan"/>
@@ -113,7 +123,7 @@
           </binaryDataArray>
         </binaryDataArrayList>
       </spectrum>
-      <spectrum index="1" id="controllerType=0 controllerNumber=1 scan=2" defaultArrayLength="315">
+      <spectrum index="1" id="controllerType=0 controllerNumber=1 scan=2" defaultArrayLength="315" dataProcessingRef="pwiz_Reader_Thermo_conversion">
         <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
         <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum"/>
         <cvParam cvRef="MS" accession="MS:1000130" name="positive scan"/>
@@ -173,7 +183,7 @@
           </binaryDataArray>
         </binaryDataArrayList>
       </spectrum>
-      <spectrum index="2" id="controllerType=0 controllerNumber=1 scan=3" defaultArrayLength="634">
+      <spectrum index="2" id="controllerType=0 controllerNumber=1 scan=3" defaultArrayLength="634" dataProcessingRef="pwiz_Reader_Thermo_conversion">
         <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
         <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum"/>
         <cvParam cvRef="MS" accession="MS:1000130" name="positive scan"/>

data/spec/testfiles/mspire/mzml/mspire_simulated.MSn.CHECK.mzML

@@ -14,7 +14,7 @@
     </sourceFileList>
   </fileDescription>
   <softwareList count="1">
-    <software id="mspire" version="0.6.22">
+    <software id="mspire_0.6.22" version="0.6.22">
     </software>
   </softwareList>
   <instrumentConfigurationList count="1">

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.8.2
+  version: 0.8.3
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-27 00:00:00.000000000 Z
+date: 2012-09-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -342,6 +342,7 @@ files:
 - spec/mspire/peaklist_spec.rb
 - spec/mspire/plms1_spec.rb
 - spec/mspire/quant/qspec_spec.rb
+- spec/mspire/readme_spec.rb
 - spec/mspire/spectrum_spec.rb
 - spec/mspire/user_param_spec.rb
 - spec/mspire_spec.rb
@@ -402,7 +403,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.18
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools