11. Can tandem provide dual modifications like an ICAT experiment?
Tandem will allow two modifications on the same residue like in an ICAT experiment. The following is
taken from the API description of the residue, modification mass parameter:
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.
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12. What do the asterisks in the sequences in fasta files signify?
Two types of fasta files are created with asterisks (*) embedded in the sequence data.
In files containing sequence data derived from nucleotide sequences (e.g EST's) the asterisks indicate the placement of
stop codons in the originating nucleotide sequence. In files of
proteotypic peptides
the asterisks indicate the placement of missing (i.e. non-proteotypic) peptides within the protein sequence.
In both cases it is suitable thus to treat the residue immediately before the asterisk as the end of
one peptide and the residue immediately following the asterisk as the beginning of a new peptide.
This is what X! Tandem does.
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13. How do I specify a modification to only the N or C terminus of each peptide?
In the specify your owninput boxes in
4. residue modifications,
use a left square bracket, "[" for the residue to indicate the N-terminus of each peptide, or right square bracket,
"]" to indicate the C-terminus.
E.g. a peptide N-terminal modification of 146 would be specified: 146@[ .
Note: This is distinguished from input boxes 4.4 and 4.5 on the GPM advanced search page, which provide modifications
of the N and C termini of the entire protein.
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