Literature DB >> 34183830

Universal Spectrum Identifier for mass spectra.

Eric W Deutsch1, Yasset Perez-Riverol2, Jeremy Carver3, Shin Kawano4, Luis Mendoza5, Tim Van Den Bossche6,7, Ralf Gabriels6,7, Pierre-Alain Binz8, Benjamin Pullman3, Zhi Sun5, Jim Shofstahl9, Wout Bittremieux10,11, Tytus D Mak12, Joshua Klein13, Yunping Zhu14, Henry Lam15, Juan Antonio Vizcaíno2, Nuno Bandeira16,17.   

Abstract

Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USI enables greater transparency of spectral evidence, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

Entities:  

Year:  2021        PMID: 34183830     DOI: 10.1038/s41592-021-01184-6

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  1 in total

1.  The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

Authors:  Eric W Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Perez-Riverol; Jeremy J Carver; Deepti J Kundu; David García-Seisdedos; Andrew F Jarnuczak; Suresh Hewapathirana; Benjamin S Pullman; Julie Wertz; Zhi Sun; Shin Kawano; Shujiro Okuda; Yu Watanabe; Henning Hermjakob; Brendan MacLean; Michael J MacCoss; Yunping Zhu; Yasushi Ishihama; Juan A Vizcaíno
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

  1 in total
  8 in total

1.  A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.

Authors:  Xiyang Luo; Wout Bittremieux; Johannes Griss; Eric W Deutsch; Timo Sachsenberg; Lev I Levitsky; Mark V Ivanov; Julia A Bubis; Ralf Gabriels; Henry Webel; Aniel Sanchez; Mingze Bai; Lukas Käll; Yasset Perez-Riverol
Journal:  J Proteome Res       Date:  2022-05-13       Impact factor: 5.370

Review 2.  Advances and Utility of the Human Plasma Proteome.

Authors:  Eric W Deutsch; Gilbert S Omenn; Zhi Sun; Michal Maes; Maria Pernemalm; Krishnan K Palaniappan; Natasha Letunica; Yves Vandenbrouck; Virginie Brun; Sheng-Ce Tao; Xiaobo Yu; Philipp E Geyer; Vera Ignjatovic; Robert L Moritz; Jochen M Schwenk
Journal:  J Proteome Res       Date:  2021-10-21       Impact factor: 5.370

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

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 Vizcaíno
Journal:  J Proteome Res       Date:  2022-03-15       Impact factor: 4.466

4.  MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates.

Authors:  Arthur Declercq; Robbin Bouwmeester; Aurélie Hirschler; Christine Carapito; Sven Degroeve; Lennart Martens; Ralf Gabriels
Journal:  Mol Cell Proteomics       Date:  2022-07-06       Impact factor: 7.381

5.  NPvis: An Interactive Visualizer of Peptidic Natural Product-MS/MS Matches.

Authors:  Olga Kunyavskaya; Alla Mikheenko; Alexey Gurevich
Journal:  Metabolites       Date:  2022-07-29

6.  The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.

Authors:  Yasset Perez-Riverol; Jingwen Bai; Chakradhar Bandla; David García-Seisdedos; Suresh Hewapathirana; Selvakumar Kamatchinathan; Deepti J Kundu; Ananth Prakash; Anika Frericks-Zipper; Martin Eisenacher; Mathias Walzer; Shengbo Wang; Alvis Brazma; Juan Antonio Vizcaíno
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

7.  iProX in 2021: connecting proteomics data sharing with big data.

Authors:  Tao Chen; Jie Ma; Yi Liu; Zhiguang Chen; Nong Xiao; Yutong Lu; Yinjin Fu; Chunyuan Yang; Mansheng Li; Songfeng Wu; Xue Wang; Dongsheng Li; Fuchu He; Henning Hermjakob; Yunping Zhu
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

8.  Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics.

Authors:  Magnus Palmblad; Sebastian Böcker; Sven Degroeve; Oliver Kohlbacher; Lukas Käll; William Stafford Noble; Mathias Wilhelm
Journal:  J Proteome Res       Date:  2022-02-04       Impact factor: 5.370

  8 in total

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