ProForma version 2.0 is published in the Journal of Proteome Research.
ProForma is now being actively maintained by HUPO-PSI. Please see https://github.com/HUPO-PSI/ProForma.
ProForma version 1.0 is also published in the Journal of Proteome Research.
A numbered version of the standard notation PDF is found here.
The work-in-progress version of the standard is here.
Our subcommittee was tasked to propose a notation that can be used to write the sequence of a given proteoform. A proteoform is a specific set of amino acids arranged in a particular order, which may be further modified (cotranslationally, posttranslationally, or chemically) at designated locations. We met via phone, working on electronically shared documents, for an hour a week between November and December 2016. Our task is described below:
Task: provide an unambiguous notation for writing an individual proteoform. The notation must:
We welcome comments, suggestions and extensions to the notation to ensure its widespread usage. They can be submitted as issues and will then be discussed to find a common solution.
Software such as stand-alone tools, plugins, libraries can be added via pull requests and will be carefully evaluated by the committee.
Validator software checks a file with proteoform sequences for inconsistencies such as wrong usage of the nomenclature rules.
Convertors allow conversion to and from files containing files annotated according to the notation.