A five-level classification system for proteoform identifications

Lloyd M Smith¹, Paul M Thomas^{2

3}, Michael R Shortreed⁴, Leah V Schaffer⁴, Ryan T Fellers^{2

3}, Richard D LeDuc^{2

3}, Trisha Tucholski⁴, Ying Ge⁵, Jeffrey N Agar⁶, Lissa C Anderson⁷, Julia Chamot-Rooke⁸, Joseph Gault⁹, Joseph A Loo¹⁰, Ljiljana Paša-Tolić¹¹, Carol V Robinson⁹, Hartmut Schlüter¹², Yury O Tsybin¹³, Marta Vilaseca¹⁴, Juan Antonio Vizcaíno¹⁵, Paul O Danis¹⁶, Neil L Kelleher^{17

18}

Affiliations

¹ Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. smith@chem.wisc.edu.
² Department of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA.
³ National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA.
⁴ Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
⁵ Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA.
⁶ Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
⁷ Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, USA.
⁸ Mass Spectrometry for Biology Unit, Institut Pasteur, Paris, France.
⁹ Department of Chemistry, University of Oxford, Oxford, UK.
¹⁰ Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
¹¹ Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
¹² University Medical Center, Hamburg-Eppendorf, Hamburg, Germany.
¹³ Spectroswiss CH, Lausanne, Switzerland.
¹⁴ Institute for Research in Biomedicine, Barcelona, Spain.
¹⁵ European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
¹⁶ Consortium for Top Down Proteomics, Cambridge, MA, USA.
¹⁷ Department of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
¹⁸ National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.

PMID: 31451767
PMCID: PMC6857706
DOI: 10.1038/s41592-019-0573-x

A five-level classification system for proteoform identifications

Lloyd M Smith et al. Nat Methods. 2019 Oct.

. 2019 Oct;16(10):939-940.

doi: 10.1038/s41592-019-0573-x.

Authors

Affiliations

¹ Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. smith@chem.wisc.edu.
² Department of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA.
³ National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA.
⁴ Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
⁵ Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA.
⁶ Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
⁷ Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, USA.
⁸ Mass Spectrometry for Biology Unit, Institut Pasteur, Paris, France.
⁹ Department of Chemistry, University of Oxford, Oxford, UK.
¹⁰ Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
¹¹ Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
¹² University Medical Center, Hamburg-Eppendorf, Hamburg, Germany.
¹³ Spectroswiss CH, Lausanne, Switzerland.
¹⁴ Institute for Research in Biomedicine, Barcelona, Spain.
¹⁵ European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
¹⁶ Consortium for Top Down Proteomics, Cambridge, MA, USA.
¹⁷ Department of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.
¹⁸ National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA. n-kelleher@northwestern.edu.

PMID: 31451767
PMCID: PMC6857706
DOI: 10.1038/s41592-019-0573-x

No abstract available

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Conflict of interest statement

Competing Financial Interests

The authors declare no competing financial interests.

References

1. Smith LM & Kelleher NL Proteoform: a single term describing protein complexity. Nature methods 10, 186–187 (2013). - PMC - PubMed
1. Anderson LC et al. Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. Journal of proteome research 16, 1087–1096 (2017). - PMC - PubMed
1. Lubeckyj RA et al. Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms. Analytical chemistry 89, 12059–12067 (2017). - PMC - PubMed
1. Schaffer LV et al. Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. Journal of proteome research 17, 3526–3536 (2018). - PMC - PubMed
1. Bush DR, Zang L, Belov AM, Ivanov AR & Karger BL High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-beta1. Analytical chemistry 88, 1138–1146 (2016). - PubMed

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A five-level classification system for proteoform identifications

Affiliations

A five-level classification system for proteoform identifications

Authors

Affiliations

Conflict of interest statement

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources