Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A five-level classification system for proteoform identifications

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    Smith, L. M. & Kelleher, N. L. Nat. Methods 10, 186–187 (2013).

    CAS  Article  Google Scholar 

  2. 2.

    Anderson, L. C. et al. J. Prot. Res. 16, 1087–1096 (2017).

    CAS  Article  Google Scholar 

  3. 3.

    Lubeckyj, R. A. et al. Anal. Chem. 89, 12059–12067 (2017).

    CAS  Article  Google Scholar 

  4. 4.

    Schaffer, L. V. et al. J. Prot. Res. 17, 3526–3536 (2018).

    CAS  Article  Google Scholar 

  5. 5.

    Bush, D. R., Zang, L., Belov, A. M., Ivanov, A. R. & Karger, B. L. Anal. Chem. 88, 1138–1146 (2016).

    CAS  Article  Google Scholar 

  6. 6.

    Lermyte, F., Tsybin, Y. O., O’Connor, P. B. & Loo, J. A. J Am. Soc. Mass. Spectrom. 30, 1149–1157 (2019).

    CAS  Article  Google Scholar 

  7. 7.

    LeDuc, R. D. et al. J. Prot. Res. 13, 3231–3240 (2014).

    CAS  Article  Google Scholar 

  8. 8.

    Kou, Q. et al. J. Prot. Res. 15, 2422–2432 (2016).

    CAS  Article  Google Scholar 

  9. 9.

    LeDuc, R. D. et al. J. Prot. Res. 17, 1321–1325 (2018).

    CAS  Article  Google Scholar 

  10. 10.

    Natale, D. A. et al. Nucleic Acids Res. 45, D339–D346 (2017).

    CAS  Article  Google Scholar 

Download references

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

Authors

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

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing