About Unimod
| Important News |
November 2006
You will have noticed that Unimod has a new user interface, which is faster and
supports more flexible searches. More significantly, a new short name field has been introduced
for each modification: PSI-MS Name.
This is a standardised name that has been agreed
by members of the protein modification
workgroup of the Proteomics Standards Initiative. The goal is for all proteomics software
applications to use these standardised name, eliminating the confusion which exists at the moment.
PSI-MS Names are chosen according to these Naming guidelines.
Of course, in the short term, changing most of the modification names creates a certain amount of pain. As far as
possible, the original Unimod short names have been retained in the Interim Name field.
This makes it relatively easy to cross-reference the old and new names.
Other changes:
- A single specificity can now have multiple neutral losses.
- Cross references can be formatted as hyperlinks.
- Simple search includes text fields from all database tables.
- Advanced search includes numeric ranges and boolean operators.
- When an Administrator has checked a record
and a PSI-MS Name has been agreed, the record is marked as verified.
- All amino acid substitutions caused by single base substitutions have been added.
- Can now combine any terminus and protein terminus specificities
in a single record
- Additional XML export format that reflects the logical structure of Unimod.
- Revised help pages
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Unimod is a public domain database, distributed under a copyleft
licence: "a copyright notice that permits unrestricted redistribution and modification, provided that
all copies and derivatives retain the same permissions."
The aim is to create a community supported, comprehensive database of protein modifications for mass
spectrometry applications. That is,
accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of
natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs
during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on
the position of the modification within the protein or peptide).
The goal is not to place this information in a biological context. There are already many high quality
sources of biological information about post-translational modifications:
- RESID for post-translational modifications
- Swiss-Prot protein sequence database
- Prosite database of protein families and domains
- Glycan Database from the Consortium for Functional Glycomics
Other compilations of modifications with a mass spectrometry bias:
Acknowledgements
Thanks to Achim Treumann and Saskia Severin of The Royal College Of Surgeons in Ireland for curation work.
On the Unimod public web site, the database engine is MySQL and the
user interface was developed using PHPRunner 3.1
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