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ProForma: A Standard Proteoform Notation.

Richard D LeDuc1, Veit Schwämmle2, Michael R Shortreed3

  • 1National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.

Journal of Proteome Research
|February 6, 2018
PubMed
Summary
This summary is machine-generated.

The Consortium for Top-Down Proteomics developed ProForma, a standard way to write proteoform sequences. This ensures clear communication and easier analysis of proteomic data.

Keywords:
human readablemachine readableproteoformstandard

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Biochemistry

Background:

  • Accurate communication of proteoform sequences is crucial for reproducibility in proteomics.
  • Current methods for annotating proteoforms can be ambiguous and lack standardization.
  • The Consortium for Top-Down Proteomics (CTDP) identified the need for a unified notation system.

Purpose of the Study:

  • To introduce ProForma, a standardized notation for writing fully characterized proteoform sequences.
  • To establish a human-readable and machine-parsable system for proteoform annotation.
  • To facilitate compatibility and reproducibility across proteomic studies.

Main Methods:

  • Developed ProForma based on seven core rules.
  • Utilized standard one-letter amino acid notation.
  • Incorporated a bracket system for specifying modifications and mass shifts following amino acids.

Main Results:

  • ProForma enables unambiguous representation of any proteoform.
  • The notation is human-readable and easily processed by bioinformatic tools.
  • The system supports diverse use cases, enhancing compatibility and reproducibility.

Conclusions:

  • Standardizing proteoform sequences with ProForma simplifies data storage, comparison, and reanalysis.
  • ProForma promotes consistency and reduces errors in proteomic research.
  • The CTDP encourages community input for ongoing development and maintenance of the ProForma standard.