Class: Sequest::PepXML::SpectrumQuery

Inherits:

Object

• Object
• Sequest::PepXML::SpectrumQuery

Includes:

SpecIDXML

Defined in:

lib/ms/sequest/pepxml.rb

Class Method Summary

• .calc_precursor_neutral_mass(by, *args) ⇒ Object

  Returns the precursor_neutral based on the scans and an array indexed by scan numbers.

• .from_pepxml_node(node) ⇒ Object

Instance Method Summary

• #from_pepxml_node(node) ⇒ Object
• #to_pepxml ⇒ Object

  FOR PEPXML:.

Class Method Details

.calc_precursor_neutral_mass(by, *args) ⇒ Object

Returns the precursor_neutral based on the scans and an array indexed by scan numbers. first and last scan and charge should be integers. This is the precursor_mz - h_plus! by=:prec_mz_arr|:deltamass if prec_mz_arr then the following arguments must be supplied: :first_scan = int, :last_scan = int, :prec_mz_arr = array with the precursor m/z for each product scan, :charge = int if deltamass then the following arguments must be supplied: m_plus_h = float, deltamass = float For both flavors, a final additional argument ‘average_weights’ can be used. If true (default), average weights will be used, if false, monoisotopic weights (currently this is simply the mass of the proton)

# File 'lib/ms/sequest/pepxml.rb', line 1252

def self.calc_precursor_neutral_mass(by, *args)
  average_weights = true
  case by
  when :prec_mz_arr
    (first_scan, last_scan, prec_mz_arr, charge, average_weights) = args
  when :deltamass
    (m_plus_h, deltamass, average_weights) = args
  end

  if average_weights 
    mass_h_plus = SpecID::AVG[:h_plus] 
  else
    mass_h_plus = SpecID::MONO[:h_plus] 
  end

  case by
  when :prec_mz_arr
    mz = nil
    if first_scan != last_scan
      sum = 0.0
      tot_num = 0
      (first_scan..last_scan).each do |scan|
        val = prec_mz_arr[scan]
        if val  # if the scan is not an mslevel 2
          sum += val
          tot_num += 1
        end
      end
      mz = sum/tot_num
    else
      mz = prec_mz_arr[first_scan]
    end
    charge * (mz - mass_h_plus)
  when :deltamass
    m_plus_h - mass_h_plus + deltamass
  else
    abort "don't recognize 'by' in calc_precursor_neutral_mass: #{by}"
  end
end

.from_pepxml_node(node) ⇒ Object

# File 'lib/ms/sequest/pepxml.rb', line 1226

def self.from_pepxml_node(node)
  self.new.from_pepxml_node(node)
end

Instance Method Details

#from_pepxml_node(node) ⇒ Object

# File 'lib/ms/sequest/pepxml.rb', line 1230

def from_pepxml_node(node)
  self[0] = node['spectrum']
  self[1] = node['start_scan'].to_i
  self[2] = node['end_scan'].to_i
  self[3] = node['precursor_neutral_mass'].to_f
  self[4] = node['index'].to_i
  self[5] = node['assumed_charge'].to_i
  self
end

#to_pepxml ⇒ Object

FOR PEPXML:

# File 'lib/ms/sequest/pepxml.rb', line 1217

def to_pepxml
  case Sequest::PepXML.pepxml_version
  when 18
    element_xml("spectrum_query", [:spectrum, :start_scan, :end_scan, :precursor_neutral_mass, :assumed_charge, :index]) do
      search_results.collect { |sr| sr.to_pepxml }.join
    end
  end
end