Rapid peptide mapping of monoclonal antibodies with direct infusion mass spectrometry
Peptide mapping is a critical tool for characterizing biotherapeutic proteins and is essential for the development of monoclonal antibody drugs. Here we describe a new direct infusion technology that streamlines peptide mapping data collection and analysis, accelerating the method by up to 100-fold. This method, which we term RaPiD-mAb-MS, combines high-throughput plate-based sample preparation with direct infusion mass spectrometry analysis. RaPiD-mAb-MS allows analysis of 96 samples within ∼ 1.5 to 2 hours, routinely achieves >95% sequence coverage, and has been successfully applied to 28 unique antibodies and over 2,000 samples. Here we demonstrate that RaPiD-mAb-MS detects and quantifies oxidation, deamidation, isomerization, glycosylation, and sequence variants with results comparable to conventional LC-MS based methods in a fraction of the time. Further, by eliminating chromatography, data analysis is greatly streamlined and simplified. By allowing for the collection of ∼ 1,000 peptide maps per day, RaPiD-mAb-MS is positioned to accelerate all phases of antibody-based drug discovery & development and sets the stage for collection of massive datasets that would allow artificial intelligent prediction of optimal antibody variants and formulations.
Authors
- John S. Chlystek (ORCID: https://orcid.org/0000-0002-4647-889X)
- Gihoon Lee (ORCID: https://orcid.org/0000-0003-0783-9899)
- Benton J. Anderson (ORCID: https://orcid.org/0000-0001-6156-342X)
- Joomi Ahn
- Pavel G. Sinitcyn (ORCID: https://orcid.org/0000-0002-2653-1702)
- Alayna M. George Thompson
- Harsha P. Gunawardena (ORCID: https://orcid.org/0000-0003-3245-3293)
- Lloyd M. Smith (ORCID: https://orcid.org/0000-0002-6652-8639)
- Marcel Morgenstern (ORCID: https://orcid.org/0000-0001-6880-4839)
- Lia R. Serrano (ORCID: https://orcid.org/0000-0001-5662-5884)
- Alexander S. Hebert (ORCID: https://orcid.org/0000-0003-4882-2241)
- Bhavin R. Patel
- Scott T. Quarmby (ORCID: https://orcid.org/0000-0003-2991-5637)
- Austin Z. Salome (ORCID: https://orcid.org/0000-0001-7360-3759)
- Keaton L. Mertz (ORCID: https://orcid.org/0000-0001-9858-5331)
- Ian J. Miller (ORCID: https://orcid.org/0000-0001-5084-9035)
- Malika P. Godamudunage
- Craig D. Wenger (ORCID: https://orcid.org/0000-0002-7361-8456)
- Joshua J. Coon (ORCID: https://orcid.org/0000-0002-0004-8253)
- Erik Miller-Galow (ORCID: https://orcid.org/0009-0004-4637-163X)
- Michael Batt
Institutions
- Johnson & Johnson (United States) (US)
- University of Wisconsin–Madison (US)
- Eli Lilly (United States) (US)
- AbbVie (United States) (US)
- Morgridge Institute for Research (US)
Publication Details
- Journal
- Communications Chemistry
- Published
- 2026-11-06
- DOI
- https://doi.org/10.1038/s42004-026-02260-8
- Citations
- 1
- Primary Topic
- Mass Spectrometry Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 1.36
Funders
- University of Wisconsin-Madison
- National Institutes of Health
- National Institute of Standards and Technology
- Genentech
- National Institute of General Medical Sciences