New Modification
Type
The type of ptm has to be specified according to OMSSA standards:
- modaa -- modification at particular amino acids
- modn -- at the N terminus of a protein
- modnaa -- at the N terminus of a protein at particular amino acids
- modc -- at the C terminus of a protein
- modcaa -- at the C terminus of a protein at particular amino acids
- modnp -- at the N terminus of a peptide
- modnpaa -- at the N terminus of a peptide at particular amino acids
- modcp -- at the C terminus of a peptide
- modcpaa -- at the C terminus of a peptide at particular amino acids
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Name
The name of the ptm should be unique and not contain '_'.
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Mass
Please type here the monoisotopic mass of the modification. Average mass is currently not
supported. If needed, please contact the developers.
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Residues
For some types of modification, it is necessary to specify the amino acids concerned by the
modification. Please type the single letter coded amino-acids separated by a comma (for example: "S, T, Y").
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Neutral Losses
Some modifications can result in so-called neutral losses. This can result in fragment ions
with a mass lower than the normal mass of the fragment ion. The most common neutral losses
are water and ammonia. There are also neutral losses related to phosphorylation, e.g., H3PO4 (97.97689499).
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Reporter Ions
Reporter ions are ions that can be used as indicators that the peptide is modified by a
given modification. The most common reporter ions are iTRAQ and TMT marker ions. But reporter
ions can also be found for other modifications, e.g., 126 (and 143) for lysine acetylation,
and 216.043 for phosphorylation of tyrosine.
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PSI-MOD Mapping
If the search results are to be later opened in PeptideShaker and then submitted to
PRIDE it is recommended to map the user defined modifications to the standard PSI-MOD
modifications. This ensures that the given modification is understood in the same way by all users.
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