Class: MS::Sequest::Pepxml::Modifications

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/sequest/pepxml/modifications.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(params = nil, modification_symbols_string = '') ⇒ Modifications

The modification symbols string looks like this: (M* 15.90000) (M# 29.00000) (S@ 80.00000) (C^ 12.00000) (ct[ 12.33000) (nt] 14.20000) ct is cterminal peptide (differential) nt is nterminal peptide (differential) the C is just cysteine will set_modifications and aa_mod_to_tot_mass hash



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 36

def initialize(params=nil, modification_symbols_string='')
  @params = params
  if @params
    set_modifications(params, modification_symbols_string)
  end
end

Instance Attribute Details

#aa_mod_to_tot_mass ⇒ Object

a hash of all differential modifications present by aa_one_letter_symbol and special_symbol. This is NOT the mass difference but the total mass { ‘M*’ => 155.5, ‘S@’ => 190.3 }. NOTE: Since the termini are dependent on the amino acid sequence, they are give the differential mass. The termini are given the special symbol as in sequest e.g. ‘[’ => 12.22, # cterminus ‘]’ => 14.55 # nterminus



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 20

def aa_mod_to_tot_mass
  @aa_mod_to_tot_mass
end

#aa_mods ⇒ Object

array holding AAModifications



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 11

def aa_mods
  @aa_mods
end

#mod_symbols_hash ⇒ Object

a hash, key is [AA_one_letter_symbol.to_sym, difference.to_f] values are the special_symbols



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 23

def mod_symbols_hash
  @mod_symbols_hash
end

#params ⇒ Object

sequest params object



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 9

def params
  @params
end

#term_mods ⇒ Object

array holding TerminalModifications



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 13

def term_mods
  @term_mods
end

Instance Method Details

#create_static_mods(params) ⇒ Object

returns an array of static mod objects and static terminal mod objects



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 73

def create_static_mods(params)

  ####################################
  ## static mods
  ####################################

  static_mods = [] # [[one_letter_amino_acid.to_sym, add_amount.to_f], ...]
  static_terminal_mods = [] # e.g. [add_Cterm_peptide, amount.to_f]

  params.mods.each do |k,v|
    v_to_f = v.to_f
    if v_to_f != 0.0
      if k =~ /add_(\w)_/
        static_mods << [$1.to_sym, v_to_f]
      else
        static_terminal_mods << [k, v_to_f]
      end
    end
  end
  aa_hash = params.mass_index(:precursor)

  ## Create the static_mods objects
  static_mods.map! do |mod|
    hash = {
      :aminoacid => mod[0].to_s,
      :massdiff => mod[1],
      :mass => aa_hash[mod[0]] + mod[1],
      :variable => 'N',
      :binary => 'Y',
    } 
    MS::Ident::Pepxml::AminoacidModification.new(hash)
  end

  ## Create the static_terminal_mods objects
  static_terminal_mods.map! do |mod|
    terminus = if mod[0] =~ /Cterm/ ; 'c'
               else                 ; 'n' # only two possible termini
               end
    protein_terminus = case mod[0] 
                       when /Nterm_protein/ ; 'n'
                       when /Cterm_protein/ ; 'c'
                       else nil
                       end

    # create the hash                            
    hash = {
      :terminus => terminus,
      :massdiff => mod[1],
      :variable => 'N',
      :description => mod[0],
    }
    hash[:protein_terminus] = protein_terminus if protein_terminus
    MS::Ident::Pepxml::TerminalModification.new(hash)
  end
  [static_mods, static_terminal_mods]
end

#modification_info(mod_peptide) ⇒ Object

takes a peptide sequence with modifications but no preceding or trailing amino acids. (e.g. expects “]PEPT*IDE” but not ‘K.PEPTIDE.R’) returns a ModificationInfo object 

if there are no modifications, returns nil



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 203

def modification_info(mod_peptide)
  return nil if @aa_mod_to_tot_mass.size == 0 
  mod_info = MS::Ident::Pepxml::SearchHit::ModificationInfo.new( mod_peptide.dup )
  mass_table = @params.mass_index(:precursor)

  # TERMINI:
  ## only the termini can match a single char
  if @aa_mod_to_tot_mass.key? mod_peptide[0,1]
    # AA + H + differential_mod
    mod_info.mod_nterm_mass = mass_table[mod_peptide[1,1].to_sym] + mass_table['h+'] + @aa_mod_to_tot_mass[mod_peptide[0,1]]
    mod_peptide = mod_peptide[1...(mod_peptide.size)]
  end
  if @aa_mod_to_tot_mass.key? mod_peptide[(mod_peptide.size-1),1]
    # AA + OH + differential_mod
    mod_info.mod_cterm_mass = mass_table[mod_peptide[(mod_peptide.size-2),1].to_sym] + mass_table['oh'] + @aa_mod_to_tot_mass[mod_peptide[-1,1]]
    mod_peptide = mod_peptide[0...(mod_peptide.size-1)]
  end

  # OTHER DIFFERENTIAL MODS:
  mod_array = []
  mod_cnt = 1
  bare_cnt = 1
  last_normal_aa = mod_peptide[0,1]
  (1...mod_peptide.size).each do |i|
    if @aa_mod_to_tot_mass.key?( last_normal_aa + mod_peptide[i,1] )
      # we don't save the result because most amino acids will not be
      # modified
      mod_array << MS::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(bare_cnt, @aa_mod_to_tot_mass[last_normal_aa + mod_peptide[i,1]])
    else
      last_normal_aa = mod_peptide[i,1]
      bare_cnt += 1
    end
    mod_cnt += 1
  end
  if mod_cnt == bare_cnt
    nil
  else
    mod_info.mod_aminoacid_masses = mod_array if mod_array.size > 0
    mod_info
  end
end

#modifications ⇒ Object

returns an array of all modifications (aa_mods, then term_mods)



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 26

def modifications
  aa_mods + term_mods
end

#set_hashes(modification_symbols_string) ⇒ Object

set the aa_mod_to_tot_mass and mod_symbols_hash from



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 44

def set_hashes(modification_symbols_string)

  @mod_symbols_hash = {}
  @aa_mod_to_tot_mass = {}
  if (modification_symbols_string == nil || modification_symbols_string == '')
    return nil
  end
  table = @params.mass_index(:precursor)
  modification_symbols_string.split(/\)\s+\(/).each do |mod|
    if mod =~ /\(?(\w+)(.) (.[\d\.]+)\)?/
      if $1 == 'ct' || $1 == 'nt' 
        mass_diff = $3.to_f
        @aa_mod_to_tot_mass[$2] = mass_diff
        @mod_symbols_hash[[$1.to_sym, mass_diff]] = $2.dup
        # changed from below to match tests, is this right?
        # @mod_symbols_hash[[$1, mass_diff]] = $2.dup
      else
        symbol_string = $2.dup 
        mass_diff = $3.to_f
        $1.split('').each do |aa|
          aa_as_sym = aa.to_sym
          @aa_mod_to_tot_mass[aa+symbol_string] = mass_diff + table[aa_as_sym]
          @mod_symbols_hash[[aa_as_sym, mass_diff]] = symbol_string
        end
      end
    end
  end
end

#set_modifications(params, modification_symbols_string) ⇒ Object

  1. sets aa_mods and term_mods from a sequest params object

  2. sets @params

  3. sets @aa_mod_to_tot_mass



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# File 'lib/ms/sequest/pepxml/modifications.rb', line 133

def set_modifications(params, modification_symbols_string)
  @params = params

  set_hashes(modification_symbols_string)
  (static_mods, static_terminal_mods) = create_static_mods(params)

  aa_hash = params.mass_index(:precursor)
  #################################
  # Variable Mods:
  #################################
  arr = params.diff_search_options.rstrip.split(/\s+/)
  # [aa.to_sym, diff.to_f]
  variable_mods = []
  (0...arr.size).step(2) do |i|
    if arr[i].to_f != 0.0
      variable_mods << [arr[i+1], arr[i].to_f]
    end
  end
  mod_objects = []
  variable_mods.each do |mod|
    mod[0].split('').each do |aa|
      hash = {

        :aminoacid => aa,
        :massdiff => mod[1],
        :mass => aa_hash[aa.to_sym] + mod[1],
        :variable => 'Y',
        :binary => 'N',
        :symbol => @mod_symbols_hash[[aa.to_sym, mod[1]]],
      }
      mod_objects << MS::Ident::Pepxml::AminoacidModification.new(hash)
    end
  end

  variable_mods = mod_objects
  #################################
  # TERMINAL Variable Mods:
  #################################
  # These are always peptide, not protein termini (for sequest)
  (nterm_diff, cterm_diff) = params.term_diff_search_options.rstrip.split(/\s+/).map{|v| v.to_f }

  to_add = []
  if nterm_diff != 0.0
    to_add << ['n',nterm_diff.to_plus_minus_string, @mod_symbols_hash[:nt, nterm_diff]]
  end
  if cterm_diff != 0.0
    to_add << ['c', cterm_diff.to_plus_minus_string, @mod_symbols_hash[:ct, cterm_diff]]
  end

  variable_terminal_mods = to_add.map do |term, mssdiff, symb|
    hash = {
      :terminus => term,
      :massdiff => mssdiff,
      :variable => 'Y',
      :symbol => symb,
    }
    MS::Ident::Pepxml::TerminalModification.new(hash)
  end

  #########################
  # COLLECT THEM
  #########################
  @aa_mods = static_mods + variable_mods
  @term_mods = static_terminal_mods + variable_terminal_mods
end