New Modification

Type

The type of modification has to be specified according to OMSSA standards:


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Name

The name of the modification 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).

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.

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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.

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.

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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.

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