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Discovery of protein modifications using high resolution differential mass spectrometry proteomics

Paolo Cifani, Zhi Li, Danmeng Luo, Mark Grivainis, Andrew M. Intlekofer, David Fenyö, Alex Kentsis
doi: https://doi.org/10.1101/2020.06.19.162321
Paolo Cifani
1Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
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Zhi Li
2Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
3Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
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Danmeng Luo
1Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
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Mark Grivainis
2Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
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Andrew M. Intlekofer
4Human Oncology & Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
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David Fenyö
2Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
3Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
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  • For correspondence: kentsisresearchgroup@gmail.com David@FenyoLab.org
Alex Kentsis
1Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021, USA
5Department of Pediatrics, Memorial Sloan Kettering Cancer Center, and Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, 10021, USA
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  • For correspondence: kentsisresearchgroup@gmail.com David@FenyoLab.org
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Summary

Recent studies have revealed diverse amino acid, post-translational and non-canonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for Spectral Alignment-based Modified PEptide Identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate its high specificity and sensitivity for the discovery of sub-stoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI’s robust parameterization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules. SAMPEI is implemented as a Python package, and is available open-source from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://doi.org/10.5281/zenodo.3899480

  • https://github.com/FenyoLab/SAMPEI

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 20, 2020.
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Discovery of protein modifications using high resolution differential mass spectrometry proteomics
Paolo Cifani, Zhi Li, Danmeng Luo, Mark Grivainis, Andrew M. Intlekofer, David Fenyö, Alex Kentsis
bioRxiv 2020.06.19.162321; doi: https://doi.org/10.1101/2020.06.19.162321
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Discovery of protein modifications using high resolution differential mass spectrometry proteomics
Paolo Cifani, Zhi Li, Danmeng Luo, Mark Grivainis, Andrew M. Intlekofer, David Fenyö, Alex Kentsis
bioRxiv 2020.06.19.162321; doi: https://doi.org/10.1101/2020.06.19.162321

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