Selenocysteine
David Fenyö and Ron Beavis have a short paper in J. Proteome Research that draws attention to a potential problem with peptides containing selenocysteine (1-letter code U, 3-letter code Sec). Samples are frequently alkylated, yet modified U is unlikely to be considered in the search.
This need not be an issue for Mascot searches, but you may have no modifications with specificity U available because it was only recently added to Unimod as a target residue. Check which version of Mascot you are running by looking at the top of the database status page. If you are using Mascot 2.2 or later, from your local Mascot home page, choose Configuration Editor; Amino acids. If U is listed (composition H(5) C(3) N O Se) then it will be available as a target residue.
If U is not listed, you simply need to update your local Unimod database:
- Mascot 2.5 and later
- From your local Mascot home page, choose Configuration Editor; Modifications; Check Unimod (button at the bottom right). Any modifications that you have added or edited using the configuration editor will be kept.
- Mascot 2.3 and 2.4
- Download unimod.xml from http://www.unimod.org/downloads.html to your Mascot config directory. Any modifications that you have added or edited will be over-written and lost.
- Mascot 2.2
- Ensure you are patched to 2.2.07 before downloading unimod.xml from http://www.unimod.org/downloads.html to your Mascot config directory. Any modifications that you have added or edited will be over-written and lost.
(In Mascot 2.1 and earlier, modifications are defined in a text file called mod_file, in the Mascot config directory. You can edit mod_file in any text editor to add new modifications, but note that it is limited to 1024 entries. The syntax is described in Chapter 6 of the Mascot Installation & Setup Manual.)
After updating Unimod, you should find that the search form lists these modifications for selenocysteine, plus any that you have defined locally:
- Carbamidomethyl (U)
- Carboxymethyl (U)
- Dioxidation (U)
- MolybdopterinGD (U)
- Oxidation (U)
Whether you see many additional matches when you select one of these modifications for a search is another matter; selenocysteine is a very rare residue. In the current SwissProt, there are 329 U compared with 2,700,893 C. In NCBInr, 4,980 U compared with 362,787,456 C. Fenyö and Beavis report that there are 46 Sec residues in the human proteome, and that the human protein richest in Sec is selenoprotein P (SEPP1) with 10 residues.
If you need to search for other non-standard residues, or create modifications for them, see the earlier blog article about Non-standard amino acid residues.
Keywords: modification, selenocysteine, Unimod
This post matches exactly what I commented here http://www.matrixscience.com/blog/non-standard-amino-acid-residues.html#comments in 2013