Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

Daniel P Donnelly; Catherine M Rawlins; Caroline J DeHart; Luca Fornelli; Luis F Schachner; Ziqing Lin; Jennifer L Lippens; Krishna C Aluri; Richa Sarin; Bifan Chen; Carter Lantz; Wonhyeuk Jung; Kendall R Johnson; Antonius Koller; Jeremy J Wolff; Iain D G Campuzano; Jared R Auclair; Alexander R Ivanov; Julian P Whitelegge; Ljiljana Paša-Tolić; Julia Chamot-Rooke; Paul O Danis; Lloyd M Smith; Yury O Tsybin; Joseph A Loo; Ying Ge; Neil L Kelleher; Jeffrey N Agar

doi:10.1038/s41592-019-0457-0

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

Nat Methods. 2019 Jul;16(7):587-594. doi: 10.1038/s41592-019-0457-0. Epub 2019 Jun 27.

Authors

Daniel P Donnelly¹, Catherine M Rawlins¹, Caroline J DeHart², Luca Fornelli², Luis F Schachner², Ziqing Lin³, Jennifer L Lippens⁴, Krishna C Aluri^{1

5}, Richa Sarin^{1

6}, Bifan Chen³, Carter Lantz⁷, Wonhyeuk Jung⁷, Kendall R Johnson¹, Antonius Koller¹, Jeremy J Wolff⁸, Iain D G Campuzano⁴, Jared R Auclair⁹, Alexander R Ivanov¹, Julian P Whitelegge¹⁰, Ljiljana Paša-Tolić¹¹, Julia Chamot-Rooke¹², Paul O Danis¹³, Lloyd M Smith¹⁴, Yury O Tsybin¹⁵, Joseph A Loo⁷, Ying Ge³, Neil L Kelleher², Jeffrey N Agar¹⁶

Affiliations

¹ Barnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.
² Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
³ Department of Cell and Regenerative Biology, Department of Chemistry, Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, USA.
⁴ Amgen Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, CA, USA.
⁵ Alnylam Pharmaceuticals, Cambridge, MA, USA.
⁶ Biogen, Cambridge, MA, USA.
⁷ Department of Chemistry and Biochemistry, Department of Biological Chemistry, and UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.
⁸ Bruker Daltonics, Billerica, MA, USA.
⁹ Biopharmaceutical Analysis Training Laboratory, Northeastern University, Burlington, MA, USA.
¹⁰ The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
¹¹ Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
¹² Mass Spectrometry for Biology Unit, Institut Pasteur, USR 2000, CNRS, Paris, France.
¹³ Eastwoods Consulting, Boylston, MA, USA.
¹⁴ Department of Chemistry, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
¹⁵ Spectroswiss, Lausanne, Switzerland.
¹⁶ Barnett Institute of Chemical and Biological Analysis and Departments of Chemistry & Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA. j.agar@northeastern.edu.

Abstract

One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass. Top-down mass spectrometry enables the analysis of intact proteins and proteoforms. Here members of the Consortium for Top-Down Proteomics provide a decision tree that guides researchers to robust protocols for mass analysis of intact proteins (antibodies, membrane proteins and others) from mixtures of varying complexity. We also present cross-platform analytical benchmarks using a protein standard sample, to allow users to gauge their proficiency.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Benchmarking*
Mass Spectrometry / methods*
Protein Denaturation
Protein Processing, Post-Translational
Proteins / chemistry*
Proteomics

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding