Literature DB >> 29397739

ProForma: A Standard Proteoform Notation.

Richard D LeDuc1, Veit Schwämmle2, Michael R Shortreed3, Anthony J Cesnik3, Stefan K Solntsev3, Jared B Shaw4, Maria J Martin5, Juan A Vizcaino5, Emanuele Alpi5, Paul Danis6, Neil L Kelleher1, Lloyd M Smith3,7, Ying Ge3, Jeffrey N Agar8, Julia Chamot-Rooke9, Joseph A Loo10, Ljiljana Pasa-Tolic4, Yury O Tsybin11.   

Abstract

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.

Entities:  

Keywords:  human readable; machine readable; proteoform; standard

Mesh：

Substances：

Year:  2018        PMID： 29397739      PMCID： PMC5837035          DOI： 10.1021/acs.jproteome.7b00851

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  16 in total

1.  Unimod: Protein modifications for mass spectrometry.

Authors:  David M Creasy; John S Cottrell
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2.  The RESID Database of Protein Modifications as a resource and annotation tool.

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3.  Sickle cell anemia a molecular disease.

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Journal:  Biochem Mol Biol Int       Date:  1997-12

5.  Proteoform: a single term describing protein complexity.

Authors:  Lloyd M Smith; Neil L Kelleher
Journal:  Nat Methods       Date:  2013-03       Impact factor: 28.547

6.  Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

Authors:  Xinping Yang; Jasmin Coulombe-Huntington; Shuli Kang; Gloria M Sheynkman; Tong Hao; Aaron Richardson; Song Sun; Fan Yang; Yun A Shen; Ryan R Murray; Kerstin Spirohn; Bridget E Begg; Miquel Duran-Frigola; Andrew MacWilliams; Samuel J Pevzner; Quan Zhong; Shelly A Trigg; Stanley Tam; Lila Ghamsari; Nidhi Sahni; Song Yi; Maria D Rodriguez; Dawit Balcha; Guihong Tan; Michael Costanzo; Brenda Andrews; Charles Boone; Xianghong J Zhou; Kourosh Salehi-Ashtiani; Benoit Charloteaux; Alyce A Chen; Michael A Calderwood; Patrick Aloy; Frederick P Roth; David E Hill; Lilia M Iakoucheva; Yu Xia; Marc Vidal
Journal:  Cell       Date:  2016-02-11       Impact factor: 41.582

7.  A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.

Authors:  Joel M Chick; Deepak Kolippakkam; David P Nusinow; Bo Zhai; Ramin Rad; Edward L Huttlin; Steven P Gygi
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8.  Global Post-Translational Modification Discovery.

Authors:  Qiyao Li; Michael R Shortreed; Craig D Wenger; Brian L Frey; Leah V Schaffer; Mark Scalf; Lloyd M Smith
Journal:  J Proteome Res       Date:  2017-03-01       Impact factor: 4.466

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Authors: 
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

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Journal:  J Proteome Res       Date:  2016-03-16       Impact factor: 4.466
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Authors:  Timothy K Toby; Luca Fornelli; Kristina Srzentić; Caroline J DeHart; Josh Levitsky; John Friedewald; Neil L Kelleher
Journal:  Nat Protoc       Date:  2019-01       Impact factor: 13.491

2.  BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.

Authors:  Paul F Lang; Yassmine Chebaro; Xiaoyue Zheng; John A P Sekar; Bilal Shaikh; Darren A Natale; Jonathan R Karr
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Journal:  J Proteome Res       Date:  2019-05-23       Impact factor: 4.466

4.  Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics.

Authors:  Zach Rolfs; Lloyd M Smith
Journal:  J Proteome Res       Date:  2021-11-05       Impact factor: 4.466

Review 5.  Identification and Quantification of Proteoforms by Mass Spectrometry.

Authors:  Leah V Schaffer; Robert J Millikin; Rachel M Miller; Lissa C Anderson; Ryan T Fellers; Ying Ge; Neil L Kelleher; Richard D LeDuc; Xiaowen Liu; Samuel H Payne; Liangliang Sun; Paul M Thomas; Trisha Tucholski; Zhe Wang; Si Wu; Zhijie Wu; Dahang Yu; Michael R Shortreed; Lloyd M Smith
Journal:  Proteomics       Date:  2019-05       Impact factor: 3.984

6.  Ion Activation Methods for Peptides and Proteins.

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Review 7.  Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms.

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Review 8.  Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.

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Journal:  Nat Methods       Date:  2019-06-27       Impact factor: 28.547

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10.  Top-Down Proteomics of Medicinal Cannabis.

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