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

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

Author information

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.

PMID:
31249407
PMCID:
PMC6719561
[Available on 2020-07-01]
DOI:
10.1038/s41592-019-0457-0
[Indexed for MEDLINE]

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