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O-Pair Search with MetaMorpheus for O-glycopeptide characterization

Nature Methods volume 17, pages 1133–1138 (2020)Cite this article

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Abstract

We report O-Pair Search, an approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides via an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus.

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Fig. 1: O-Pair Search through MetaMorpheus for fast and confident identification of O-glycopeptides.
Fig. 2: Performance of O-Pair Search for O-glycopeptide characterization.

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Data availability

The data used in this manuscript are available through the Proteome-Xchange Consortium via the PRIDE partner repository48 with the dataset identifier PXD017646 (ref. 15) and via MassIVE with identifier MSV000083070 (ref. 9). Processed data using Byonic and Protein Prospector for the urinary O-glycopeptide dataset were downloaded from ref. 8.

Code availability

O-Pair Search is available in MetaMorpheus (v.0.0.307 for HCD–EThcD data and v.0.0.308 for HCD–HCD and HCD–sceHCD data), and is open source and freely available at https://github.com/smith-chem-wisc/MetaMorpheus under a permissive license. All source code was written in Microsoft C# with.NET CORE 3.1 using Visual Studio.

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Acknowledgements

We appreciate discussions with Z. Rolfs, R.J. Millikin and other Smith group members to enhance software analysis speed and address challenges in implementing ideas. This work was supported by National Institute of Health (NIH) grant no. R35 GM126914 awarded to L.M.S. and grant no. R01 CA200423 awarded to C.R.B., as well as with support from the Howard Hughes Medical Institute. N.M.R. was funded through an NIH Predoctoral to Postdoctoral Transition Award (grant no. K00 CA212454-03).

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Author notes

  1. These authors contributed equally: Lei Lu, Nicholas M. Riley.

Authors and Affiliations

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

    Lei Lu, Michael R. Shortreed & Lloyd M. Smith

  2. Department of Chemistry, University of Stanford, Stanford, CA, USA

    Nicholas M. Riley & Carolyn R. Bertozzi

  3. Howard Hughes Medical Institute, Stanford, CA, USA

    Carolyn R. Bertozzi

Authors
  1. Lei Lu
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Contributions

L.L. and N.M.R. contributed equally to this work. L.L. conceived the project and software design, wrote software, analyzed data and wrote the paper. N.M.R. conceived the project and software design, advised on software development, analyzed most of the data and wrote the paper. M.R.S. designed software and supervised the project. C.R.B. and L.M.S. supervised the project. All authors discussed results and edited the paper.

Corresponding author

Correspondence to Lloyd M. Smith.

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Competing interests

C.R.B. is a cofounder and Scientific Advisory Board member of Lycia Therapeutics, Palleon Pharmaceuticals, Enable Bioscience, Redwood Biosciences (a subsidiary of Catalent) and InterVenn Biosciences, and a member of the Board of Directors of Eli Lilly & Company.

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Editor recognition statement Arunima Singh was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–17, Notes 1–4 and Note Fig. 1, and Tables 1–3.

Reporting Summary

Supplementary Data 1

O-Pair Search analysis of mucin standards.

Supplementary Data 2

O-Pair Search analysis of urinary O-glycopeptides.

Supplementary Data 3

Protein database and glycan database.

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Lu, L., Riley, N.M., Shortreed, M.R. et al. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 17, 1133–1138 (2020). https://doi.org/10.1038/s41592-020-00985-5

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