residue, modification mass

Syntax

The value of this parameter is an ASCII string, of the format M₁@X₁,M₂@X₂,..., M_n@X_n

where M_i is a floating point number (modification mass in Daltons) and X_i is a single letter abbreviation for a type of amino acid residue.

Notes

1. No error is produced if a non-standard amino acid abbreviation is used.
2. If a residue type is listed more than once, the last instance of the residue is used to set the modification.
3. Both positive and negative modification masses may be used.

Description

In the course of isolating a protein and generating peptides for use in protein identification experiments, it is often necessary to treat the protein sample with reagents that will modify all of the residues of a particular type. Commonly, cysteine residues are modified to disrupt and prevent the reformation of disulphide bonds. Additionally, other residues may be modified as a predictable side product of the protein-to-peptide cleavage process. The modifications encoded in this value are applied to every residue of a particular type of amino acid, without exception.

If there is some possibility that a residue modification process has not been 100% efficient, it may be more practical to include the modification in the residue, potential modification mass parameter list.

If a residue labelling strategy is being used where there are two types of reagents for modifying a residue (e.g., C), one with mass L₁ and the other with mass L₂, the following method can be used to find both types of labelled peptide in the same analysis.

1. Add the value L₁@C to the residue, modification mass parameter
2. Add the value (L₂-L₁)@C to the residue, potential modification mass parameter

Because potential and complete modifications are treated separately internally by TANDEM, this will result in finding peptides modified with both types of parameters.