residue, potential modification mass

# residue, potential modification mass ## Syntax The value of this parameter is an ASCII string, of the format M1@X1,M2@X2,..., Mn@Xn where Mi is a floating point number (potential modification mass in Daltons) and Xi is a single letter abbreviation for a type of amino acid residue. ## Notes No error is produced if a non-standard amino acid abbreviation is used. If a residue type is listed more than once, the last instance of the residue is used to set the modification. Both positive and negative potential modification masses may be used. ## Description In the course of isolating a protein and generating peptides for use in protein identification experiments,some fraction of the residues of a particular type may be modified (e.g., methionine residues are often oxidized). Additionally, other residues may be have been modified in the original protein through a process commonly referred to as post-translational modification. These modifications may be quite rare in a protein sample, but knowing which residues are modified in this way may be very important biologically. These post-translational modifications are normally the result of enzyme reactions and are therefore very specific to the type of residue modified. The modifications encoded in this value are applied sequentially to every possible combination of modified and unmodified residues in a particular peptide. The number of possibilities for a particular peptide (N) depends on the number of residues with potential modifications in a peptide (n): N = 2n The exponential nature of this expression makes calculating all possible potentially modified pepides increasingly difficult as the number of modifications increases. If long lists of relatively rare potential modifications are to be applied, it is better to use the refine, potential modification mass parameter when looking at large numbers of mass spectra. 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. Add the value L1@C to the residue, modification mass parameter 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. NOTE: When a peptide starts with E or Q, TANDEM automatically checks for the formation of pyroglutamic acid, i.e., the loss of water or ammonia, respectively. This modification happens spontaneously in solution and failure to test for it can result in missing significant peptide hits. The analogous reaction for iodoacetimide blocked cysteine (loss of ammonia) is also considered. This modification is considered to be an N-terminal modification only, so it does not affect any potential modifications specified for Q, E or C. see also: residue, modification mass | refine, potential modification mass X! TANDEM API description project