protein, modified residue mass file

Syntax

This parameter is a text string corresponding to the path to a file containing specifications for the residues to be modified.

Notes

The file path name may be full or relative.

Description

X! Tandem uses default values for the mass of each peptide residue. These masses correspond to the monoisotopic mass of the corresponding amino acid, less the mass of water (m_aa - 18.01056470). In some cases, samples may be created inwhich one or more of the amino acids has been deliberately substituted with an amino acid with an isotopic label. If only a small number of residues have been substituted, the residue, modification mass command may be used to inform X! Tandem. However, if most (or all) of the residues have been modified, it is simpler to create a file containing this information and use the protein, modified residue mass file command.

The format of the file pointed to be this command is illustrated below, which is the file needed to deal with the case of an all-¹⁵N labelled organism:

<?xml version="1.0"?>
<bioml title="peptide residue molecular mass values for an all 15N organism">
<aa type="A" mass="72.0341485" />
<aa type="B" mass="116.036998" />
<aa type="C" mass="104.0062203" />
<aa type="D" mass="116.0239777" />
<aa type="E" mass="130.0396277" />
<aa type="F" mass="148.0654485" />
<aa type="G" mass="58.0184985" />
<aa type="H" mass="140.0500163" />
<aa type="I" mass="114.0810985" />
<aa type="J" mass="0.0" />
<aa type="K" mass="130.0890324" />
<aa type="L" mass="114.0810985" />
<aa type="M" mass="132.0375203" />
<aa type="N" mass="116.0369970" />
<aa type="O" mass="0.0" />
<aa type="P" mass="98.0497985" />
<aa type="Q" mass="130.0526470" />
<aa type="R" mass="160.0892502" />
<aa type="S" mass="88.0290631" />
<aa type="T" mass="102.0447131" />
<aa type="U" mass="151.9506693" />
<aa type="V" mass="100.0654485" />
<aa type="W" mass="188.0733824" />
<aa type="X" mass="112.057034" />
<aa type="Y" mass="164.0603631" />
<aa type="Z" mass="130.052648" />
<molecule type="NH3" mass="18.02358311" />
<molecule type="H2O" mass="18.01056470" />
</bioml>

NOTE: the ambiquity code symbols (BJXZ*) have special interpretations in X! Tandem and they cannot be redefined with this mechanism. Lower case letters a-z cannot be assigned residue masses: they are reserved for internal use by X! Tandem.