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A five-level classification system for proteoform identifications

Nature Methods volume 16, pages939–940(2019)Cite this article

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Acknowledgements

This work was supported by grants R35 GM126914 (to L.M.S.) and P41 GM108569 (to N.L.K.) from the NIH National Institute of General Medical Sciences, R21 LM013097 (to P.M.T.) from the National Library of Medicine, and the Sherman Fairchild Foundation (to N.L.K.).

Author information

Affiliations

  1. Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA

    Lloyd M. Smith, Michael R. Shortreed, Leah V. Schaffer & Trisha Tucholski

  2. Department of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA

    Paul M. Thomas, Ryan T. Fellers, Richard D. LeDuc & Neil L. Kelleher

  3. National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA

    Paul M. Thomas, Ryan T. Fellers, Richard D. LeDuc & Neil L. Kelleher

  4. Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA

    Ying Ge

  5. Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA

    Jeffrey N. Agar

  6. Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, USA

    Lissa C. Anderson

  7. Mass Spectrometry for Biology Unit, Institut Pasteur, Paris, France

    Julia Chamot-Rooke

  8. Department of Chemistry, University of Oxford, Oxford, UK

    Joseph Gault & Carol V. Robinson

  9. Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA

    Joseph A. Loo

  10. Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

    Ljiljana Paša-Tolić

  11. University Medical Center, Hamburg-Eppendorf, Hamburg, Germany

    Hartmut Schlüter

  12. Spectroswiss CH, Lausanne, Switzerland

    Yury O. Tsybin

  13. Institute for Research in Biomedicine, Barcelona, Spain

    Marta Vilaseca

  14. European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK

    Juan Antonio Vizcaíno

  15. Consortium for Top Down Proteomics, Cambridge, MA, USA

    Paul O. Danis

Authors
  1. Lloyd M. Smith
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  2. Paul M. Thomas
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  3. Michael R. Shortreed
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  4. Leah V. Schaffer
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  6. Richard D. LeDuc
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  7. Trisha Tucholski
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  8. Ying Ge
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  9. Jeffrey N. Agar
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  10. Lissa C. Anderson
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  12. Joseph Gault
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  13. Joseph A. Loo
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  14. Ljiljana Paša-Tolić
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  15. Carol V. Robinson
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  16. Hartmut Schlüter
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  17. Yury O. Tsybin
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  18. Marta Vilaseca
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  19. Juan Antonio Vizcaíno
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  20. Paul O. Danis
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  21. Neil L. Kelleher
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Corresponding authors

Correspondence to Lloyd M. Smith or Neil L. Kelleher.

Ethics declarations

Competing interests

Y.O.T. is an employee of Spectroswiss. R.T.F., N.L.K. and R.D.L. declare a competing interest in the development and commercialization of proteoform search and management software. All other authors declare no competing interests.

Integrated supplementary information

Supplementary Figure 1 Examples of proteoform level assignments.

Different examples of proteoform identifications and the corresponding assigned level number in red.

Supplementary information

Supplementary Information

Supplementary Fig. 1 and Supplementary Table 1

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Smith, L.M., Thomas, P.M., Shortreed, M.R. et al. A five-level classification system for proteoform identifications. Nat Methods 16, 939–940 (2019). https://doi.org/10.1038/s41592-019-0573-x

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