unimod-package: Managing amino acid modifications for mass spectrometry in R.

In ComputationalProteomicsUnit/unimod: Managing amino acid modifications for mass spectrometry

Managing amino acid modifications for mass spectrometry in R.

Description

An interface to the community supported database for amino acid/protein modifications using mass spectrometry.

Details

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:

• Delta Mass

• FindMod

Author(s)

Sebastian Gibb [e-mail]

References

Source and more details: http://www.unimod.org/unimod_help.html

https://github.com/ComputationalProteomicsUnit/unimod/

ComputationalProteomicsUnit/unimod documentation built on Feb. 12, 2023, 2:57 a.m.