mspire 0.6.1 → 0.6.2

data/Rakefile

@@ -13,10 +13,11 @@ Jeweler::Tasks.new do |gem|
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince", "Simon Chiang"]
   gem.add_dependency "nokogiri", "~> 1.5"
+  gem.add_dependency "bsearch", ">= 1.5.0"
+  gem.add_dependency "obo", ">= 0.1.0"
   gem.add_development_dependency "rspec", "~> 2.6"
   gem.add_development_dependency "jeweler", "~> 1.5.2"
   gem.add_development_dependency "rcov", ">= 0"
-  gem.add_development_dependency "obo", ">= 0.1.0"
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.6.1
+0.6.2

data/lib/ms/mass.rb

@@ -16,6 +16,7 @@ module MS
       end.reduce(:+)
     end
 
+    ELECTRON = 0.0005486 # www.mikeblaber.org/oldwine/chm1045/notes/Atoms/.../Atoms03.htm
     H_PLUS = 1.00727646677
     #  + http://www.unimod.org/masses.html
     MONO_STR = {
@@ -37,6 +38,7 @@ module MS
       'h' => 1.007825035,  # +
       'h2o' => 18.0105647,
       'oh' => 17.002739665,
+      'e' => 0.0005486,
     }
     AVG_STR = {
       'h+' => 1.007276, # using Mascot_H_plus mass (is this right for AVG??)

data/lib/ms/mzml.rb

@@ -113,6 +113,9 @@ module MS
         base64 = binary_data_array_n.xpath('./binary').text
         MS::Mzml.unpack_binary(base64, accessions)
       end
+      # if there is no spectrum, we will still return a spectrum object, it
+      # just has no mzs or intensities
+      data_arrays = [[], []] if data_arrays.size == 0
       MS::Spectrum.new(data_arrays)
     end
 

data/lib/ms/spectrum.rb

@@ -1,171 +1,134 @@
-module MS
-  class Spectrum
-    include Enumerable
-
-    # The underlying data store.
-    attr_reader :data
-    
-    # data takes an array: [mzs, intensities]
-    # @return [MS::Spectrum]
-    # @param [Array] data two element array of mzs and intensities
-    def initialize(data)
-      @data = data
-    end
-
-    def self.from_peaks(ar_of_doublets)
-      _mzs = []
-      _ints = []
-      ar_of_doublets.each do |mz, int|
-        _mzs << mz
-        _ints << int
-      end
-      self.new([_mzs, _ints])
-    end
-
-    # found by querying the size of the data store.  This should almost always
-    # be 2 (m/z and intensities)
-    def size
-      @data.size
-    end
-
-    def ==(other)
-      mzs == other.mzs && intensities == other.intensities
-    end
-      
-    # An array of the mz data.
-    def mzs
-      @data[0]
-    end
-      
-    # An array of the intensities data, corresponding to mzs.
-    def intensities
-      @data[1]
-    end
-
-    def mzs_and_intensities
-      [@data[0], @data[1]]
-    end
-
-    # retrieve an m/z and intensity doublet at that index
-    def [](array_index)
-      [mzs[array_index], intensities[array_index]]
-    end
-
-    # yields(mz, inten) across the spectrum, or array of doublets if no block
-    def peaks(&block)
-      (m, i) = mzs_and_intensities
-      m.zip(i, &block)
-    end
-
-    alias_method :each, :peaks
-    alias_method :each_peak, :peaks
-
-    # if the mzs and intensities are the same then the spectra are considered
-    # equal
-    def ==(other)
-      mzs == other.mzs && intensities == other.intensities
-    end
-
-    # returns a new spectrum whose intensities have been normalized by the tic
-    def normalize
-      tic = self.intensities.inject(0.0) {|sum,int| sum += int }
-      MS::Spectrum.new([self.mzs, self.intensities.map {|v| v / tic }])
-    end
-
-    ## uses index function and returns the intensity at that value
-    #def intensity_at_mz(mz)
-      #if x = index(mz)
-        #intensities[x]
-      #else
-        #nil
-      #end
-    #end
-
-    ## index mz, tolerance = :nearest(1), Float, :nearest_within_integer
-
-    ## returns the index of the first value matching that m/z.  the argument m/z
-    ## may be less precise than the actual m/z (rounding to the same precision
-    ## given) but must be at least integer precision (after rounding)
-    ## implemented as binary search (bsearch from the web)
-    #def index(mz)
-      #mz_ar = mzs
-      #return_val = nil
-      #ind = mz_ar.bsearch_lower_boundary{|x| x <=> mz }
-      #if mz_ar[ind] == mz
-        #return_val = ind
-      #else 
-        ## do a rounding game to see which one is it, or nil
-        ## find all the values rounding to the same integer in the locale
-        ## test each one fully in turn
-        #mz = mz.to_f
-        #mz_size = mz_ar.size
-        #if ((ind < mz_size) and equal_after_rounding?(mz_ar[ind], mz))
-          #return_val = ind
-        #else # run the loop
-          #up = ind
-          #loop do
-            #up += 1
-            #if up >= mz_size
-              #break
-            #end
-            #mz_up = mz_ar[up]
-            #if (mz_up.ceil  - mz.ceil >= 2)
-              #break
-            #else
-              #if equal_after_rounding?(mz_up, mz)
-                #return_val = up
-                #return return_val
-              #end
-            #end
-          #end
-          #dn= ind
-          #loop do
-            #dn -= 1
-            #if dn < 0
-              #break
-            #end
-            #mz_dn = mz_ar[dn]
-            #if (mz.floor - mz_dn.floor >= 2)
-              #break
-            #else
-              #if equal_after_rounding?(mz_dn, mz)
-                #return_val = dn
-                #return return_val
-              #end
-            #end
-          #end
-        #end
-      #end
-      #return_val
-    #end
-
-    ## less_precise should be a float
-    ## precise should be a float
-    #def equal_after_rounding?(precise, less_precise) # :nodoc:
-      ## determine the precision of less_precise
-      #exp10 = precision_as_neg_int(less_precise)
-      ##puts "EXP10: #{exp10}"
-      #answ = ((precise*exp10).round == (less_precise*exp10).round)
-      ##puts "TESTING FOR EQUAL: #{precise} #{less_precise}"
-      ##puts answ
-      #(precise*exp10).round == (less_precise*exp10).round
-    #end
-
-    ## returns 1 for ones place, 10 for tenths, 100 for hundredths
-    ## to a precision exceeding 1e-6
-    #def precision_as_neg_int(float) # :nodoc:
-      #neg_exp10 = 1
-      #loop do
-        #over = float * neg_exp10
-        #rounded = over.round
-        #if (over - rounded).abs <= 1e-6
-          #break
-        #end
-        #neg_exp10 *= 10
-      #end
-      #neg_exp10
-    #end
-
-
-  end
-end
+require 'bsearch'
+
+module MS
+  class Spectrum
+    include Enumerable
+
+    # The underlying data store. methods are implemented so that data[0] is
+    # the m/z's and data[1] is intensities
+    attr_reader :data
+    
+    # data takes an array: [mzs, intensities]
+    # @return [MS::Spectrum]
+    # @param [Array] data two element array of mzs and intensities
+    def initialize(data)
+      @data = data
+    end
+
+    def self.from_peaks(ar_of_doublets)
+      _mzs = []
+      _ints = []
+      ar_of_doublets.each do |mz, int|
+        _mzs << mz
+        _ints << int
+      end
+      self.new([_mzs, _ints])
+    end
+
+    # found by querying the size of the data store.  This should almost always
+    # be 2 (m/z and intensities)
+    def size
+      @data.size
+    end
+
+    def ==(other)
+      mzs == other.mzs && intensities == other.intensities
+    end
+      
+    # An array of the mz data.
+    def mzs
+      @data[0]
+    end
+      
+    # An array of the intensities data, corresponding to mzs.
+    def intensities
+      @data[1]
+    end
+
+    def mzs_and_intensities
+      [@data[0], @data[1]]
+    end
+
+    # retrieve an m/z and intensity doublet at that index
+    def [](array_index)
+      [@data[0][array_index], @data[1][array_index]]
+    end
+
+    # yields(mz, inten) across the spectrum, or array of doublets if no block
+    def peaks(&block)
+      @data[0].zip(@data[1], &block)
+    end
+
+    alias_method :each, :peaks
+    alias_method :each_peak, :peaks
+
+    # if the mzs and intensities are the same then the spectra are considered
+    # equal
+    def ==(other)
+      mzs == other.mzs && intensities == other.intensities
+    end
+
+    # returns a new spectrum whose intensities have been normalized by the tic
+    # of another given value
+    def normalize(norm_by=:tic)
+      norm_by = tic if norm_by == :tic
+      MS::Spectrum.new([self.mzs, self.intensities.map {|v| v / norm_by }])
+    end
+
+    def tic
+      self.intensities.reduce(:+)
+    end
+
+    # ensures that the m/z values are monotonically ascending (some
+    # instruments are bad about this)
+    # returns self
+    def sort!
+      _peaks = peaks.to_a
+      _peaks.sort!
+      _peaks.each_with_index {|(mz,int), i| @data[0][i] = mz ; @data[1][i] = int }
+      self
+    end
+
+    # returns the m/z that is closest to the value, favoring the lower m/z in
+    # the case of a tie. Uses a binary search.
+    def find_nearest(val)
+      mzs[find_nearest_index(val)]
+    end
+
+    # same as find_nearest but returns the index of the peak
+    def find_nearest_index(val)
+      find_all_nearest_index(val).first
+    end
+
+    def find_all_nearest_index(val)
+      _mzs = mzs
+      index = _mzs.bsearch_lower_boundary {|v| v <=> val }
+      if index == _mzs.size
+        [_mzs.size-1]
+      else
+        # if the previous m/z diff is smaller, use it
+        if index == 0
+          [index]
+        else
+          case (val - _mzs[index-1]).abs <=> (_mzs[index] - val).abs
+          when -1
+            [index-1]
+          when 0
+            [index-1, index]
+          when 1
+            [index]
+          end
+        end
+      end
+    end
+
+    def find_all_nearest(val)
+      find_all_nearest_index(val).map {|i| mzs[i] }
+    end
+
+  end
+end
+
+
+  
+

data/spec/ms/ident/pepxml_spec.rb

@@ -10,12 +10,11 @@ require 'ms/ident/pepxml/search_hit'
 require 'ms/ident/pepxml/search_hit/modification_info'
 
 describe "creating an MS::Ident::Pepxml" do
-  include MS::Ident
 
   it "can be creating in a nested fashion reflecting internal structure" do
     tags_that_should_be_present = %w(msms_pipeline_analysis msms_run_summary sample_enzyme search_summary spectrum_query search_result search_hit modification_info mod_aminoacid_mass search_score)
 
-    pepxml = Pepxml.new do |msms_pipeline_analysis|
+    pepxml = MS::Ident::Pepxml.new do |msms_pipeline_analysis|
       msms_pipeline_analysis.merge!(:summary_xml => "020.xml") do |msms_run_summary|
         # prep the sample enzyme and search_summary
         msms_run_summary.merge!(
@@ -39,16 +38,16 @@ describe "creating an MS::Ident::Pepxml" do
               :max_num_internal_cleavages => 2,
               :min_number_termini => 2
             )
-            modifications << Pepxml::AminoacidModification.new(
+            modifications << MS::Ident::Pepxml::AminoacidModification.new(
               :aminoacid => 'M', :massdiff => 15.9994, :mass => MS::Mass::AA::MONO['M']+15.9994,
               :variable => 'Y', :symbol => '*')
               # invented, for example, a protein terminating mod
-            modifications << Pepxml::TerminalModification.new( 
+            modifications << MS::Ident::Pepxml::TerminalModification.new( 
               :terminus => 'c', :massdiff => 23.3333, :mass => MS::Mass::MONO['oh'] + 23.3333, 
               :variable => 'Y', :symbol => '[', :protein_terminus => 'c', 
               :description => 'leave protein_terminus off if not protein mod'
             )
-            modifications << Pepxml::TerminalModification.new( 
+            modifications << MS::Ident::Pepxml::TerminalModification.new( 
               :terminus => 'c', :massdiff => 25.42322, :mass => MS::Mass::MONO['h+'] + 25.42322, 
               :variable => 'N', :symbol => ']', :description => 'example: c term mod'
             )
@@ -58,18 +57,18 @@ describe "creating an MS::Ident::Pepxml" do
                               :enzyme_info => 'Trypsin(KR/P) 1 1 KR P', # etc.... 
                              )
           end
-          spectrum_query1 = Pepxml::SpectrumQuery.new(
+          spectrum_query1 = MS::Ident::Pepxml::SpectrumQuery.new(
             :spectrum  => '020.3.3.1', :start_scan => 3, :end_scan => 3, 
             :precursor_neutral_mass => 1120.93743421875, :assumed_charge => 1
           ) do |search_results|
-            search_result1 = Pepxml::SearchResult.new do |search_hits|
+            search_result1 = MS::Ident::Pepxml::SearchResult.new do |search_hits|
               modpositions = [[1, 243.1559], [6, 167.0581], [7,181.085]].map do |pair|  
-                Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(*pair)
+                MS::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(*pair)
               end
               # order(modified_peptide, mod_aminoacid_masses, :mod_nterm_mass, :mod_cterm_mass)
               # or can be set by hash
-              mod_info = Pepxml::SearchHit::ModificationInfo.new('Y#RLGGS#T#K', modpositions)
-              search_hit1 = Pepxml::SearchHit.new( 
+              mod_info = MS::Ident::Pepxml::SearchHit::ModificationInfo.new('Y#RLGGS#T#K', modpositions)
+              search_hit1 = MS::Ident::Pepxml::SearchHit.new( 
                 :hit_rank=>1, :peptide=>'YRLGGSTK', :peptide_prev_aa => "R", :peptide_next_aa => "K",
                 :protein => "gi|16130113|ref|NP_416680.1|", :num_tot_proteins => 1, :num_matched_ions => 5,
                 :tot_num_ions => 35, :calc_neutral_pep_mass => 1120.93163442, :massdiff => 0.00579979875010395,

data/spec/ms/mzml/plms1_spec.rb

@@ -22,12 +22,12 @@ describe 'converting mzml to plms1' do
       plms1.times.should == times
       plms1.scan_numbers.should == scan_nums
       plms1.spectra.each do |spec|
-        p spec.size
-        p spec.class
-        p spec.mzs
-        p spec.intensities
+        spec.size.should == 2
+        spec.class.should == MS::Spectrum
+        spec.mzs.should == []
+        spec.intensities.should == []
       end
-      plms1.write("tmp.tmp.bin")
+      #plms1.write("tmp.tmp.bin")
     end
 
   end
@@ -47,13 +47,14 @@ describe 'converting mzml to plms1' do
       #times =[6604.58, 6605.5, 6605.91, 6606.48, 6606.98, 6607.53, 6607.93, 6608.49, 6608.92, 6609.49, 6609.94, 6610.53]
       plms1 = @mzml.to_plms1
       plms1.spectra.respond_to?(:each).should be_true
-      p plms1.times
-      p plms1.scan_numbers
-      plms1.spectra.each do |spec|
-        p spec.size
-        p spec.class
-        p spec.mzs.size
-        p spec.intensities.size
+      plms1.times.should == [1981.5726, 1982.1077, 1982.4020999999998]
+      plms1.scan_numbers.should == [1, 2, 3] 
+      sizes = [20168, 315, 634]
+      plms1.spectra.zip(sizes).each do |spec,exp_size|
+        spec.class.should == MS::Spectrum
+        spec.size.should == 2
+        spec.mzs.size.should == exp_size
+        spec.intensities.size.should == exp_size
       end
       #plms1.write("tmp.tmp.bin")
     end

data/spec/ms/quant/qspec_spec.rb

@@ -5,17 +5,17 @@ require 'csv'
 
 describe 'running qspec' do 
   before do
-    @file = TESTFILES + '/ms/quant/max_quant_output.txt'
-    rows = IO.readlines(@file).map {|line| line.chomp.split("\t") }
-    p rows.map(&:size)
-    abort 'here'
-    #columns = IO.readlines(@file).map {|line| line.split("\t") }.transpose
-    headers = columns.map(&:first)
-    p headers
+    #@file = TESTFILES + '/ms/quant/max_quant_output.txt'
+    #rows = IO.readlines(@file).map {|line| line.chomp.split("\t") }
+    #p rows.map(&:size)
+    #abort 'here'
+    ##columns = IO.readlines(@file).map {|line| line.split("\t") }.transpose
+    #headers = columns.map(&:first)
+    #p headers
   end
 
   describe 'on spectral count data' do
-    it 'works' do
+    xit 'works' do
       1.should == 1
     end
   end

data/spec/ms/spectrum_spec.rb

@@ -0,0 +1,48 @@
+require 'spec_helper'
+
+require 'ms/spectrum'
+
+describe MS::Spectrum do
+
+  describe 'useful utilities' do
+    subject { MS::Spectrum.new [ [10.1, 10.5, 10.7, 11.5], [1, 2, 3, 4] ] }
+    it 'finds the nearest m/z or index' do
+
+      queries = {
+        10.4 => 1,
+        10.5 => 1,
+        10.6 => 1,
+        10.61 => 2,
+        -100.0 => 0,
+        200.0 => 3,
+      }
+      queries.each {|mz, exp_i| subject.find_nearest_index(mz).should == exp_i }
+
+      all = Hash[ queries.map {|k,v| [k,[v]] } ]
+      all[10.6] = [1,2]
+      all.each {|mz, exp_mz| subject.find_all_nearest_index(mz).should == exp_mz }
+
+      queries = { 
+        10.4 => 10.5,
+        10.5 => 10.5,
+        10.6 => 10.5,
+        10.61 => 10.7,
+        -100.0 => 10.1,
+        200.0 => 11.5,
+      }
+      queries.each {|mz, exp_mz| subject.find_nearest(mz).should == exp_mz }
+
+      all = Hash[ queries.map {|k,v| [k,[v]] } ]
+      all[10.6] = [10.5, 10.7]
+      all.each {|mz, exp_mz| subject.find_all_nearest(mz).should == exp_mz }
+    end
+
+    it 'can sort itself by m/z' do
+      spec = MS::Spectrum.new [[10.5, 10.1, 11.5, 10.7], [2, 1, 4, 3]]
+      spec.sort!
+      spec.mzs.should == subject.mzs
+      spec.intensities.should == subject.intensities
+    end
+  end
+
+end

data/spec/spec_helper.rb

@@ -13,8 +13,8 @@ Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
 RSpec.configure do |config|
   config.color_enabled = true
   config.tty = true
-  #config.formatter = :documentation  # :progress, :html, :textmate
-  config.formatter = :progress # :progress, :html, :textmate
+  config.formatter = :documentation  # :progress, :html, :textmate
+  #config.formatter = :progress # :progress, :html, :textmate
 end
 
 

metadata

@@ -1,83 +1,92 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: mspire
-version: !ruby/object:Gem::Version 
+version: !ruby/object:Gem::Version
+  version: 0.6.2
   prerelease: 
-  version: 0.6.1
 platform: ruby
-authors: 
+authors:
 - John T. Prince
 - Simon Chiang
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-01-25 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-02-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: nokogiri
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &8784820 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        version: "1.5"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :runtime
+  prerelease: false
+  version_requirements: *8784820
+- !ruby/object:Gem::Dependency
+  name: bsearch
+  requirement: &8782400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.0
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: rspec
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *8782400
+- !ruby/object:Gem::Dependency
+  name: obo
+  requirement: &8781260 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *8781260
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &8780220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        version: "2.6"
+      - !ruby/object:Gem::Version
+        version: '2.6'
   type: :development
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: jeweler
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *8780220
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &8795440 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
+      - !ruby/object:Gem::Version
         version: 1.5.2
   type: :development
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: rcov
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: *8795440
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &8792600 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: obo
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 0.1.0
-  type: :development
-  version_requirements: *id005
-description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems
+  version_requirements: *8792600
+description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
+  merging of ms-* gems
 email: jtprince@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
 - README.rdoc
-files: 
+files:
 - LICENSE
 - README.rdoc
 - Rakefile
@@ -147,6 +156,7 @@ files:
 - spec/ms/mzml_spec.rb
 - spec/ms/plms1_spec.rb
 - spec/ms/quant/qspec_spec.rb
+- spec/ms/spectrum_spec.rb
 - spec/msplat_spec.rb
 - spec/obo_spec.rb
 - spec/spec_helper.rb
@@ -175,31 +185,28 @@ files:
 - spec/testfiles/ms/quant/unlog_transform.rb
 - spec/testfiles/plms1/output.key
 homepage: http://github.com/princelab/mspire
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.15
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools
 test_files: []
-