New Modification
Type
The type of modification 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
top of page
Name
The name of the modification should be unique and not contain '_'.
top of page
Mass
Please type here the monoisotopic mass of the modification. Average mass is currently not
supported. If needed, please contact the developers.
top of page
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").
top of page
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).
Neutral losses can be either fixed or variable. A fixed neutral loss means that the loss
always occurs. Fixed neutral losses should be used with care as they affect how the search engines
treat the modification itself.
top of page
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.
Please provide the mass of the reporter ion as m/z, i.e., the exact m/z value of the peak you want to annotate.
top of page
Unimod 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 Unimod
modifications (http://www.unimod.org). This ensures that the given modification is understood in
the same way by all users. For example, Oxidation is Unimod accession 35.
Find the wanted modification and insert the Unimod accession number and Unimod name. The Unimod modification name is listed as PSI-MS Name
(or as Interim Name if no PSI-MS Name is given). For example, for oxidation: accession:35 and PSI-MS Name:Oxidation.
top of page