Unimod Help
Database fields
Adding or modifying
Naming guidelines
Symbols & mass values
Cross-link entries


The entire contents of Unimod are available for download in various formats


An XML file that reflects the table structure of the Unimod relational database, suitable for importing into another relational database or machine translation into other formats. (schema)

An XML file that reflects the logical structure of Unimod. (schema)


The error tolerant search in Mascot 2.2.06 and earlier has a limit of 1024 modifications. The number of specificities in Unimod has recently exceeded this limit.
Mascot 2.3: No action necessary

Mascot 2.2: Ensure you update to 2.2.07 before downloading the latest unimod.xml.

Mascot 2.1 and earlier: The total number of the entries in mod_file and substitutions must not exceed 1024. After downloading mod_file, open it in a text editor and delete entries that are not of interest. Alternatively, delete entries from subsitutions, or some from each file. You cannot have an empty substitutions file, but it can be reduced to a single entry.

Download one of these files to update the list of modifications on your local Mascot server

unimod.xml for Mascot 2.2 and later.

mod_file for Mascot 2.1 and earlier.

Archived mod_file for Mascot 2.1 and earlier. This is the last mod_file generated from the original Unimod database, before the switch to PSI-MS approved names, (11 Nov 2006).

Note: In unimod.xml, there is a flag called hidden at the specificity level. Modifications with hidden="1" are only displayed by Mascot when the checkbox for Display all modifications is checked. Otherwise, you see a shorter list of common modifications (hidden="0"). Some 3rd party software is not aware of this switch, and only ever displays the short list of common modifications. The work-around is to change the hidden flag so that all modifications are treated as common. To do this, use the search and replace function of any text editor to replace all instances of hidden="1" with hidden="0". If you use a word processor, make sure the file is saved as a plain text file.

Other files

Archived XML file generated from the original Unimod database, before the switch to PSI-MS approved names, (11 Nov 2006). This file conforms to the earlier unimod_1.xsd schema.

unimod.obo is Unimod transformed into OBO format by an XSLT style sheet written by Martin Eisenacher, Ruhr-Universitat Bochum.

Table relationship diagram (PDF) for the Unimod relational database

The text of the Design Science copyleft licence.