Module: Ms::Mass::AA

Defined in:

lib/ms/mass/aa.rb

Overview

A module for working with commonly used residue masses in proteomics.

require 'ms/mass/aa'
include Ms::Mass::AA

MONO['A'] # => 71.0371137878
AVG['A']  # => 71.0779

# or use symbols
MONO[:A]  # => 71.0371137878

molecules is built on constants and constants on ruby-units and it seems impossible to get ruby-units 1.9 compatible. Until that point, values will remain hard coded and these values are free of dependencies.

The values are built using the excellent ‘molecules’ library. See that library for more serious work with masses.

Constant Summary

AVG_STRING =

amino_acids keys as strings, average masses

{
  "*"=>118.88603,
  "A"=>71.0779,
  "B"=>172.1405,
  "C"=>103.1429,
  "D"=>115.0874,
  "E"=>129.11398,
  "F"=>147.17386,
  "G"=>57.05132,
  "H"=>137.13928,
  "I"=>113.15764,
  "K"=>128.17228,
  "L"=>113.15764,
  "M"=>131.19606,
  "N"=>114.10264,
  "O"=>211.28076,
  "P"=>97.11518,
  "Q"=>128.12922,
  "R"=>156.18568,
  "S"=>87.0773,
  "T"=>101.10388,
  "U"=>150.0379,
  "V"=>99.13106,
  "W"=>186.2099,
  "X"=>118.88603,
  "Y"=>163.17326,
  "Z"=>128.6231
}

MONO_STRING =

amino_acids keys as strings, monoisotopic masses

{
  "*"=>118.805716,
  "A"=>71.0371137878,
  "B"=>172.048405,
  "C"=>103.0091844778,
  "D"=>115.026943032,
  "E"=>129.0425930962,
  "F"=>147.0684139162,
  "G"=>57.0214637236,
  "H"=>137.0589118624,
  "I"=>113.0840639804,
  "K"=>128.0949630177,
  "L"=>113.0840639804,
  "M"=>131.0404846062,
  "N"=>114.0429274472,
  "O"=>211.1446528645,
  "P"=>97.052763852,
  "Q"=>128.0585775114,
  "R"=>156.1011110281,
  "S"=>87.0320284099,
  "T"=>101.0476784741,
  "U"=>150.9536355878,
  "V"=>99.0684139162,
  "W"=>186.0793129535,
  "X"=>118.805716,
  "Y"=>163.0633285383,
  "Z"=>128.550585
}

MONO_SYM =

amino_acids keys as symbols, monoisotopic masses

Hash[MONO_STRING.map {|aa,mass| [aa.to_sym, mass]

AVG_SYM =

amino_acids keys as symbols, average masses

MONO =

Monoisotopic amino acid masses keyed as symbols and also strings (all upper case). Also includes Ms::Mass::MONO for things like protons (‘h+’)

MONO_SYM.merge(MONO_STRING).merge(Ms::Mass::MONO)

AVG =

Average amino acid masses keyed as symbols and also strings (all uppder case). Also includes Ms::Mass::AVG for things like protons (‘h+’)

AVG_SYM.merge(AVG_STRING).merge(Ms::Mass::AVG)