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ProForma: A Standard Proteoform Notation

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† National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
‡ Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
§ Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
∥ Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
⊥ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
# Consortium for Top-Down Proteomics, Cambridge, Massachusetts 02142, United States
▽ Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
○ Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
◆ Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris Cedex 15, France
Department of Chemistry and Biochemistry and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
+ Spectroswiss, 1015 Lausanne, Switzerland
*E-mail: [email protected]. Tel: +1.847.467.4362.
Cite this: J. Proteome Res. 2018, 17, 3, 1321–1325
Publication Date (Web):February 5, 2018
https://doi.org/10.1021/acs.jproteome.7b00851
Copyright © 2018 American Chemical Society
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    Abstract

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    The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, for writing the sequence of fully characterized proteoforms. ProForma provides a means to communicate any proteoform by writing the amino acid sequence using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain amino acids. The notation is unambiguous, human-readable, and can easily be parsed and written by bioinformatic tools. This system uses seven rules and supports a wide range of possible use cases, ensuring compatibility and reproducibility of proteoform annotations. Standardizing proteoform sequences will simplify storage, comparison, and reanalysis of proteomic studies, and the Consortium welcomes input and contributions from the research community on the continued design and maintenance of this standard.

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