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Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

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Abstract

We introduce a method for sequencing peptides by mass spectrometry using a metalloendopeptidase that cleaves proteins at the amino side of lysine (Lys-N). When analyzed by electron transfer dissociation (ETD)–based mass spectrometric sequencing, Lys-N–digested peptides that contain a single lysine residue produce spectra dominated by c-type fragment ions, providing simple ladders for sequence determination. This method should be a valuable strategy for de novo sequencing and the analysis of post-translational modifications.

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Figure 1: ETcaD peptide fragmentation spectra of doubly charged ions originating from Lys-C– and Lys-N–digested peptides.
Figure 2: Propensity of c-ion formation by ETcaD fragmentation for peptides originating from Lys-N and Lys-C digests.

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Acknowledgements

We thank A.F.M. Altelaar and B. van Breukelen for fruitful discussions and support. This work was supported by the Netherlands Proteomics Centre.

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Authors and Affiliations

  1. Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, Utrecht, 3584 CA, The Netherlands

    Nadia Taouatas, Madalina M Drugan, Albert J R Heck & Shabaz Mohammed

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  1. Nadia Taouatas
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  2. Madalina M Drugan
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  3. Albert J R Heck
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  4. Shabaz Mohammed
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Contributions

N.T. and S.M. performed experiments; S.M. and A.J.R.H. designed experiments; N.T., A.J.R.H. and S.M. wrote the paper; M.M.D. analyzed peptide and fragment ion occurences.

Corresponding authors

Correspondence to Albert J R Heck or Shabaz Mohammed.

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Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1–3, Supplementary Methods (PDF 451 kb)

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Taouatas, N., Drugan, M., Heck, A. et al. Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase. Nat Methods 5, 405–407 (2008). https://doi.org/10.1038/nmeth.1204

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