mzml 0.2.2 → 0.3.0

data/lib/mzml.rb

@@ -1,245 +1,5 @@
 require 'nokogiri'
-require 'base64'
-require 'zlib'
-
-#--
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Library or "Lesser" General Public
-# License (LGPL) as published by the Free Software Foundation;
-# either version 2 of the License, or (at your option) any later
-# version.
-# Author: Angel Pizarro
-# Date: 12/05/2009
-# Copyright: Angel Pizarro, Copyright (c) University of Pennsylvania.  All rights reserved.
-#
-
-# == MzML
-#
-# A non-validating mzML v 1.1.0 parser. Most annotation is left as XML DOM
-# objects. See the Nokogiri::XML::Node and Nokogiri::XML::NodeSet
-# documentation on how to work with these.
-#
-# ===USAGE:
-#
-#     require 'mzml'
-#     mzml =  MzML::Doc.new("test.mzXML")
-
-module MzML
-
-  # An internal module containing useful regular expressions
-  module RGX
-    # The file byte offset of the start of the file index
-    INDEX_OFFSET = /<indexListOffset>(\d+)<\/indexListOffset>/
-    # The start of a either a spectrumList or chromatographList
-    DATA_LIST_START =  /<(spectrum|chromatogram)List\s.*count\=["'](\d+)/m
-    # The start spectrum or chromatogram element
-    DATA_START = /<(spectrum|chromatogram)\s.*id=["']([^'"]+)["']/m
-    # The end spectrum or chromatogram element
-    DATA_END = /(<\/(spectrum|chromatogram)>)/
-  end
-
-  def parse(xml)
-    Nokogiri::XML.parse(xml).root
-  end
-
-  class UnsupportedFileFormat < Exception
-  end
-  class BadIdentifier < Exception
-  end
-
-  class Doc < File
-    attr_reader :index, :fname, :spectrum_count, :chromatogram_count, :node
-
-    def initialize(mz_fname)
-      unless mz_fname =~ /\.mzML$/
-        raise MzML::UnsupportedFileFormat.new  "File extension must be .\"mzML\""
-      end
-      super(mz_fname, "r")
-      @index = parse_index_list
-    end
-
-    def chromatogram(chromatogram_id)
-      if @index[:chromatogram].has_key? chromatogram_id
-        self.seek @index[:chromatogram][chromatogram_id]
-        parse_next
-      else
-        raise MzML::BadIdentifier.new("Invalid ID '#{chromatogram_id}'")
-      end
-    end
-
-    def spectrum(spectrum_id)
-      if @index[:spectrum].has_key? spectrum_id
-        self.seek @index[:spectrum][spectrum_id]
-        return Spectrum.new(parse_next())
-
-      else
-        raise MzML::BadIdentifier.new("Invalid ID '#{spectrum_id}'")
-      end
-    end
-
-    # private
-    # Parses the IndexList
-    def parse_index_list
-      self.seek(self.stat.size - 200)
-      # parse the index offset
-      tmp = self.read
-      tmp  =~  MzML::RGX::INDEX_OFFSET
-      offset = $1
-      # if I didn't match anything, compute the index and return
-      unless (offset)
-        return compute_index_list
-      end
-      @index = {}
-      self.seek(offset.to_i)
-      tmp = Nokogiri::XML.parse(self.read).root
-      tmp.css("index").each do |idx|
-        index_type = idx[:name].to_sym
-        @index[index_type] = {}
-        idx.css("offset").each do |o|
-          @index[index_type][o[:idRef]] = o.text().to_i
-        end
-      end
-      return @index
-    end
-
-    def compute_index_list
-      @index = {}
-      # start at the beginning.
-      self.rewind
-      # fast forward to the first spectrum or chromatograph
-      buffer = ''
-      while !self.eof
-        buffer += self.read(1024)
-        if start_pos = buffer =~ MzML::RGX::DATA_START
-          self.seek start_pos
-          break
-        end
-      end
-      # for each particular entity start to fill in the index
-      buffer = ''
-      rgx_start = /<(spectrum|chromatogram)\s.*id=["']([^"']+)["']/
-      while !self.eof
-        buffer += self.read(1024)
-        if start_pos = buffer =~ rgx_start
-          start_pos = self.pos - buffer.length + start_pos
-          @index[$1.to_sym][$2] = start_pos
-          buffer = ''
-        end
-      end
-      return @index
-    end
-
-    def parse_next
-      buffer = self.read(1024)
-      end_pos = nil
-      while(!self.eof)
-        if end_pos = buffer =~ MzML::RGX::DATA_END
-          buffer = buffer.slice(0..(end_pos + $1.length))
-          break
-        end
-        buffer += self.read(1024)
-      end
-      return Nokogiri::XML.parse(buffer)
-    end
-  end
-
-  class Spectrum
-    attr_accessor :id, :default_array_length, :spot_id, :type,\
-    :charge, :precursor, :base_peak_mz, :base_peak_intensity, :ms_level, \
-    :high_mz, :low_mz, :title, :tic, :polarity, :representation, :mz_node, :intensity_node, \
-    :mz, :intensity, :precursor_list, :scan_list, :retention_time, :precursor_mass, :precursor_intensity
-    
-    attr_reader :node, :params
-
-    # mz & intensity arrays will be don by proper methods maybe.
-    def initialize(spectrum_node)
-      @node = spectrum_node
-      @params = {}
-      @precursor_list = []
-      parse_element()
-    end
-
-    protected
-    # This method pulls out all of the annotation from the XML node
-    def parse_element
-      # id
-      @id = @node.xpath("spectrum")[0][:id]
-      @default_array_length = @node.xpath("spectrum")[0][:defaultArrayLength]
-      @spot_id = @node.xpath("spectrum")[0][:spotID]
-      # now reaching into params
-      @params = @node.xpath("spectrum/cvParam").inject({}) do  |memo,prm|
-        memo[prm[:name]] = prm[:value]
-        memo
-      end
-      @ms_level = @params["ms level"].to_i
-      @low_mz = @params["lowest observed m/z"].to_f if @params.has_key?("lowest observed m/z")
-      @high_mz = @params["highest observed m/z"].to_f if @params.has_key?("highest observed m/z")
-      @tic = @params["total ion current"].to_i if @params.has_key?("total ion current")
-      @base_peak_mz = @params["base peak m/z"].to_i if @params.has_key?("base peak m/z")
-      @base_peak_intensity = @params["base peak intensity"].to_i if @params.has_key?("base peak intensity")
-      # polarity
-      # representation
-      # precursor list
-      if (! @node.xpath("spectrum/precursorList")[0].nil?)
-        parse_precursor_list()
-        get_parent_info()
-      else
-        @precursor_list = []
-      end
-      # scan list
-      if (@node.xpath("spectrum/scanList")[0])
-        @scan_list = parse_scan_list()
-      else
-        @scan_list = nil
-      end
-      # binary data
-      parse_binary_data()
-    end
-
-    def parse_precursor_list
-      @node.css("precursorList > precursor").each do |p|
-        [p[:spectrumRef], p]
-        @precursor_list << p
-      end
-    end
-
-    def get_parent_info
-      
-      unless @precursor_list.empty?
-        
-        @precursor_mass = @precursor_list[0].xpath("selectedIonList/selectedIon/cvParam[@accession='MS:1000744']")[0][:value] unless @precursor_list[0].xpath("selectedIonList/selectedIon/cvParam[@accession='MS:1000744']")[0].nil?
-        @precursor_intensity = @precursor_list[0].xpath("selectedIonList/selectedIon/cvParam[@accession='MS:1000042']")[0][:value] unless @precursor_list[0].xpath("selectedIonList/selectedIon/cvParam[@accession='MS:1000042']")[0].nil?
-        
-      end
-        
-      
-    end
-
-    def parse_scan_list
-      @scan_list = @node.xpath("spectrum/scanList/scan")
-      @retention_time = @node.xpath("spectrum/scanList/scan/cvParam[@accession='MS:1000016']")[0][:value] unless @node.xpath("spectrum/scanList/scan/cvParam[@accession='MS:1000016']")[0].nil?
-    end
-
-    def parse_binary_data
-      @mz_node = @node.xpath("spectrum/binaryDataArrayList/binaryDataArray/cvParam[@accession='MS:1000514']").first.parent
-      data = Base64.decode64(@mz_node.xpath("binary").text)
-      if @mz_node.xpath("cvParam[@accession='MS:1000574']")[0]
-        # need to uncompress the data
-        data = Zlib::Inflate.inflate(data)
-      end
-      # 64-bit floats? default is 32-bit
-      dtype = @mz_node.xpath("cvParam[@accession='MS:1000523']")[0] ? "E*" : "e*"
-      @mz = data.unpack(dtype)
-      
-      @intensity_node = @node.xpath("spectrum/binaryDataArrayList/binaryDataArray/cvParam[@accession='MS:1000515']").first.parent
-      data = Base64.decode64(@intensity_node.xpath("binary").text)
-      if @intensity_node.xpath("cvParam[@accession='MS:1000574']")[0]
-        # need to uncompress the data
-        data = Zlib::Inflate.inflate(data)
-      end
-      # 64-bit floats? default is 32-bit
-      dtype = @intensity_node.xpath("cvParam[@accession='MS:1000523']")[0] ? "E*" : "e*"
-      @intensity = data.unpack(dtype)
-    end
-  end
-end
+require 'mzml/doc'
+require 'mzml/chromatogram'
+require 'mzml/spectrum'
+require 'mzml/version'

data/mzml.gemspec

@@ -1,65 +1,21 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
 # -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "mzml/version"
 
 Gem::Specification.new do |s|
-  s.name = %q{mzml}
-  s.version = "0.2.2"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Angel Pizarro"]
-  s.date = %q{2010-10-01}
-  s.default_executable = %q{mzML2mgf.rb}
-  s.description = %q{A non-validating mzML parser. MzML is a standard data format for representing mass spectrometry data.}
-  s.email = %q{angel@delagoya.com}
-  s.executables = ["mzML2mgf.rb"]
-  s.extra_rdoc_files = [
-    "LICENSE",
-     "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-     ".gitignore",
-     ".yardoc",
-     "LICENSE",
-     "README.rdoc",
-     "Rakefile",
-     "VERSION",
-     "bin/mzML2mgf.rb",
-     "lib/mzml.rb",
-     "mzml.gemspec",
-     "spec/mzml_spec.rb",
-     "spec/sample.compressed.mzML",
-     "spec/sample.mgf",
-     "spec/sample.mzML",
-     "spec/spec.opts",
-     "spec/spec_helper.rb"
-  ]
-  s.homepage = %q{http://github.com/delagoya/mzml}
-  s.rdoc_options = ["--charset=UTF-8"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.7}
+  s.name        = "mzml"
+  s.version     = MzML::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Angel Pizarro"]
+  s.email       = ["angel@upenn.edu"]
   s.summary = %q{A non-validating mzML parser}
-  s.test_files = [
-    "spec/mzml_spec.rb",
-     "spec/spec_helper.rb"
-  ]
-
-  if s.respond_to? :specification_version then
-    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
-    s.specification_version = 3
+  s.description = %q{A non-validating mzML parser. MzML is a standard data format for representing mass spectrometry data.}
+  s.homepage    = "http://github.com/delagoya/mzml"
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<rspec>, ["= 1.3.0"])
-      s.add_runtime_dependency(%q<nokogiri>, ["= 1.4.1"])
-    else
-      s.add_dependency(%q<rspec>, ["= 1.3.0"])
-      s.add_dependency(%q<nokogiri>, ["= 1.4.1"])
-    end
-  else
-    s.add_dependency(%q<rspec>, ["= 1.3.0"])
-    s.add_dependency(%q<nokogiri>, ["= 1.4.1"])
-  end
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.require_paths = ["lib"]
+  s.add_dependency("nokogiri", ["~> 1.5"])
+  s.add_development_dependency "rake"
+  s.add_development_dependency "yard"
 end
-

data/spec/mzml_spec.rb

@@ -5,6 +5,7 @@ describe MzML do
     # set the input file name
     @file = File.join(File.dirname(__FILE__),  "sample.mzML")
     @compressed = File.join(File.dirname(__FILE__),  "sample.compressed.mzML")
+    @unindexed = File.join(File.dirname(__FILE__),  "sample.unindexed.mzML")
     @mgf = File.join(File.dirname(__FILE__),  "sample.mgf")
   end
 
@@ -95,4 +96,19 @@ describe MzML do
       s.intensity.should_not be_nil
     end
   end
+
+  # TOPPView outputs mzML with no indexedmzML wrapper
+  context 'Given a valid mzML file without an index wrapper' do
+    it 'should be able to retrieve by index' do
+      mz = MzML::Doc.new(@unindexed)
+      s = mz.spectrum(mz.index[:spectrum].keys.first)
+      s.intensity.should_not be_nil
+    end
+    it 'does not fail when parsing a spectrum without binary data' do
+      mz = MzML::Doc.new(@unindexed)
+      s = mz.spectrum(mz.index[:spectrum].keys.last)
+      s.should_not be_nil
+      s.intensity.should be_nil
+    end
+  end
 end

data/spec/sample.unindexed.mzML

@@ -0,0 +1,221 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+    <cvList count="2">
+        <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+        <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+    </cvList>
+    <fileDescription>
+        <fileContent>
+            <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+        </fileContent>
+        <sourceFileList count="1">
+            <sourceFile id="sf_ru_0" name="file://MSALLY2/S/RAW/HEK_cells/Hek_cells_100904050914.RAW" location="">
+                <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2b6ebe1d5f900a445f82adb40b24cd77ed476ecb" />
+                <cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData file" />
+                <cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
+            </sourceFile>
+        </sourceFileList>
+    </fileDescription>
+    <sampleList count="1">
+        <sample id="sa_0" name="">
+            <cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0"  unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+            <cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
+            <cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
+        </sample>
+    </sampleList>
+    <softwareList count="4">
+        <software id="so_in_0" version="2.5.5" >
+            <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
+        </software>
+        <software id="so_default" version="" >
+            <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+        </software>
+        <software id="so_dp_sp_0_pm_0" version="4.3.1(build Sep  9 2009 12:30:29)" >
+            <cvParam cvRef="MS" accession="MS:1000541" name="ReAdW" />
+        </software>
+        <software id="so_dp_sp_0_pm_1" version="1.7.0" >
+            <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />
+        </software>
+    </softwareList>
+    <instrumentConfigurationList count="1">
+        <instrumentConfiguration id="ic_0">
+            <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+            <componentList count="3">
+                <source order="0">
+                    <cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />
+                </source>
+                <analyzer order="0">
+                    <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
+                    <cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
+                    <cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
+                    <cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
+                    <cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />
+                </analyzer>
+                <detector order="0">
+                    <cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
+                    <cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
+                    <cvParam cvRef="MS" accession="MS:1000026" name="detector type" />
+                </detector>
+            </componentList>
+            <softwareRef ref="so_in_0" />
+        </instrumentConfiguration>
+    </instrumentConfigurationList>
+    <dataProcessingList count="1">
+        <dataProcessing id="dp_sp_0">
+            <processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
+                <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
+                <userParam name="#type" type="xsd:string" value="conversion"/>
+            </processingMethod>
+            <processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
+                <cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
+                <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-02-07+21:50" />
+            </processingMethod>
+        </dataProcessing>
+    </dataProcessingList>
+    <run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
+        <spectrumList count="5" defaultDataProcessingRef="dp_sp_0">
+            <spectrum id="scan=9033" index="562" defaultArrayLength="75">
+                <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+                <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+                <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+                <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+                <scanList count="1">
+                    <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+                    <scan>
+                        <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5207.31" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+                    </scan>
+                </scanList>
+                <binaryDataArrayList count="2">
+                    <binaryDataArray encodedLength="800">
+                        <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                        <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+                        <binary>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</binary>
+                    </binaryDataArray>
+                    <binaryDataArray encodedLength="400">
+                        <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
+                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+                        <binary>CZMLRfdvCEWM1ydFdZ/pRDWvDUapXF5FlQ4eRRgd20W1P3BFe9EqRecTCEWk6gdF1TyQRf3eDEblhfxEGkkWRua92UXCoaVFknjfRD2F80RS3hxFwbDrRHJiRkUUbSBFv2McRTEaQ0VvUwlFi68fRUv5hkVEwIZFBrRRRdTF6UVEzxJF+UYTRd/nH0Ui83tFox8MRUrwG0X3gWpFmtUURQjH20UWMTRFwc8pRTNRCEWsaQlFcrUXRSkJwUWZkBxGrgIxRuMio0WU/etEmWwtReGvbEUa4JZFyoffRPtHlEUI/lBFsW2ARV4xUEWtvS5FBi06RdwJEkWojBJGPIxHRvKcE0UAqGNGzdmkRQ+aFkXsqlpFvtcwRRLkYUV/WFRFSJQLRQy4BkV29CNF</binary>
+                    </binaryDataArray>
+                </binaryDataArrayList>
+            </spectrum>
+            <spectrum id="scan=9034" index="563" defaultArrayLength="79">
+                <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+                <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+                <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+                <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+                <scanList count="1">
+                    <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+                    <scan>
+                        <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5208.68" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+                    </scan>
+                </scanList>
+                <binaryDataArrayList count="2">
+                    <binaryDataArray encodedLength="844">
+                        <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                        <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+                        <binary>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</binary>
+                    </binaryDataArray>
+                    <binaryDataArray encodedLength="424">
+                        <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
+                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+                        <binary>pb8PRZMGWEVVn1lFubaqRfkR9kQDlm9FT/ACRWNkKEWd/O9Ep2c3RawNg0XKUEtFGxvcRdjRFUZWyWdFw0hhRVb/BkUlNVtFoqkRRZLe+USzSApFXQv6RLsYMkWBsjFFk6OBRXLSNUVydedEVt7jRE/ECkUVMA5FHQ4YRbGREUWA9fZE+j5lRY5hx0UBRAxFY6cBRc2+OkU4JBBFsFsiRcmD+0Q9B4dF327GRZ1oDkVZ1w5FF5sLRfppFEW51lJFmBM4RXZCpEUdjvREDS6TRftxVUY/pL1FGRb1RCPjUEU0HGVFckCBRfDWH0V+wx9FkXcrRlr3bEVTNjdFvosIRVkXc0U5klxGCiYnRt0xHEa/RsVF1IQNRUNWNEXMaftEvNkPRRWB+ETuG19FMOLURL+sQUUdew5FuDkARQ==</binary>
+                    </binaryDataArray>
+                </binaryDataArrayList>
+            </spectrum>
+            <spectrum id="scan=9035" index="564" defaultArrayLength="0">
+                <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+                <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
+                <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+                <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+                <scanList count="1">
+                    <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+                    <scan>
+                        <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5209.18" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+                    </scan>
+                </scanList>
+                <precursorList count="1">
+                    <precursor>
+                        <isolationWindow>
+                            <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="868.46765137" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                            <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                            <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                        </isolationWindow>
+                        <selectedIonList count="1">
+                            <selectedIon>
+                                <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="868.46765137" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                                <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
+                                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="12840.7001953125" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
+                            </selectedIon>
+                        </selectedIonList>
+                        <activation>
+                            <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
+                            <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
+                        </activation>
+                    </precursor>
+                </precursorList>
+            </spectrum>
+            <spectrum id="scan=9036" index="565" defaultArrayLength="83">
+                <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+                <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+                <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+                <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+                <scanList count="1">
+                    <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+                    <scan>
+                        <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5209.63" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+                    </scan>
+                </scanList>
+                <binaryDataArrayList count="2">
+                    <binaryDataArray encodedLength="888">
+                        <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                        <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+                        <binary>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</binary>
+                    </binaryDataArray>
+                    <binaryDataArray encodedLength="444">
+                        <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
+                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+                        <binary>Q4ImReexMkXWN0VF1fbbRA9nB0Xe/Q1Fa/urRX8rTEWmbiRFiZoORfixFUUuPEZFPmYCRftqzURuxC9FfZg1RbgrYEYmLB5FsK+FRoIRlEUDV4NF+TAaRecZNUW5phhFoIsjRa5JBUU+ezVFC3PqRNAl80TsNepE+vMgRfW5hEVv6VxFHYMFRV2NEUXvJCpFvHYNRQXMUUVMBFBFvGrvRLUEBEXs2OpEd8n6RBYJJkWzmyhFEaklRXVEp0UrKVtGKosjRUYeJEUJ8FVGN5knRjHQ7kX6AUNFxeEpRdmiD0V8QjpFpaUaRSSwn0UBmPZFtF8TRYJfB0VugzZF+AwJRf/G8EWjC4hGhv0sRYyvq0XuxoxFuKYdRaJqBEWvwCFFaZYgRdncL0W/dR1FrHL4REkECkUJ8lJFRDYXRatv+0Tha01Fr8E2RWCNDkU=</binary>
+                    </binaryDataArray>
+                </binaryDataArrayList>
+            </spectrum>
+            <spectrum id="scan=9037" index="566" defaultArrayLength="0">
+                <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
+                <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
+                <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+                <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+                <scanList count="1">
+                    <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+                    <scan>
+                        <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5210.17" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+                    </scan>
+                </scanList>
+                <precursorList count="1">
+                    <precursor>
+                        <isolationWindow>
+                            <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1045.84021" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                            <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                            <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                        </isolationWindow>
+                        <selectedIonList count="1">
+                            <selectedIon>
+                                <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1045.84021" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+                                <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
+                                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="17405.5" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
+                            </selectedIon>
+                        </selectedIonList>
+                        <activation>
+                            <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
+                            <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
+                        </activation>
+                    </precursor>
+                </precursorList>
+            </spectrum>
+        </spectrumList>
+    </run>
+</mzML>