Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2022 Mar 15

PMID 35290070

Authors

Richard D LeDuc

Eric W Deutsch

Pierre-Alain Binz

Ryan T Fellers

Anthony J Cesnik

Joshua A Klein

Tim Van Den Bossche

Ralf Gabriels

Arshika Yalavarthi

Yasset Perez-Riverol

Jeremy Carver

Wout Bittremieux

Shin Kawano

Benjamin Pullman

Nuno Bandeira

Neil L Kelleher

Paul M Thomas

Juan Antonio Vizcaino

Affiliations

Soon will be listed here.

Abstract

It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemically induced, and artifactual modifications. The Human Proteome Organization Proteomics Standards Initiative in collaboration with several members of the Consortium for Top-Down Proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://psidev.info/proforma.

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