How should I define the XML files to customize mass of Amino Acids in the computation of Molecular Weight?

There are two XML files which you would need to define in order to customize mass of Amino Acids.

1) ElementMass - This file should define the name and mass of elements and isotopes.

2) AminoAcidComposition - This file should define all the elements and isotopes that are contained for each Amino Acid.

Required Attributes in XML files

  • AminoAcidComposition
    • “symbol” - Single character and case-sensitive but must not be repeated.
      • Note: This symbol will be used in identifying characters in protein sequence to the amino acid it defines.
    • “name” - Case-sensitive and must be defined in the ElementMass XML file.
    • “count” - Must be greater than 0.
  • ElementMass
    • “name” - Case-senstitive.
    • “mass” - Mass of the element/isotope. Must be greater than 0.


For ease of use, the standard mass of elements and isotopes are already saved in ElementMass.xml. Likewise, the standard composition of amino acids are also stored in AminoAcidComposition.xml.


Also, for ease of understanding and manipulation, we have also defined another two files which are contains the minimum requirements needed.
MinElementMass.xml and MinAminoAcidComposition.xml.


For advance users who would like to use modified amino acids such as radioactive labelled or phosphorylated, another two XML files demonstrating this have also been defined. AdvancedElementMass.xml and AdvancedAminoAcidComposition.xml. Note: The symbols used to identify the amino acids are case-sensitive. Also, any characters including number and special characters such as ‘!@#$%^&*)(‘ etc are allowed to enable users to define a large numbers of modified amino acids.