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Related Experiment Video

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Direct Injection Mass Spectrometry and iFishMass for the High-Throughput Analysis of Antibody Modifications.

Jennifer Aguilan1, Carlos Madrid-Aliste2,3, Fereshteh Zandkarimi4

  • 1Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, New York 10461, United States.

ACS Pharmacology & Translational Science
|January 15, 2026
PubMed
Summary

A new mass spectrometry (MS) protocol enables rapid, quantitative analysis of modified peptides in ~30 seconds. This high-throughput platform accelerates drug development by efficiently screening conjugation sites on proteins like antibody drug conjugates (ADCs).

Keywords:
NanoMateantibody−drug conjugatesautomationdirect injectionhigh-throughput screeningiFishMassmass spectrometry

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Area of Science:

  • Analytical Chemistry
  • Chemical Biology
  • Biochemistry

Background:

  • High-throughput screening is crucial for drug development, demanding efficient analysis of large compound libraries.
  • Mass spectrometry (MS)-based proteomics is vital for identifying and quantifying protein modifications, including post-translational modifications (PTMs).
  • The rise of antibody drug conjugates (ADCs) necessitates faster methods for analyzing protein modifications.

Purpose of the Study:

  • To present a novel, rapid protocol for quantitative analysis of modified peptides.
  • To develop a high-throughput platform for screening conjugation sites on proteins, particularly for ADCs.
  • To introduce new software (iFishMass) for efficient data extraction and analysis.

Main Methods:

  • Direct injection MS approach combined with a novel software, iFishMass.
  • Quantitative data acquisition for modified peptides in approximately 30 seconds of MS time.
  • Parallelized sample preparation for up to 384 samples using multichannel pipettes and 96-well plates.

Main Results:

  • Achieved quantitative data for modified peptides with a rapid MS acquisition time of ~30 seconds.
  • Developed iFishMass software for automated extraction of targeted signals and generation of plots/statistics from numerous runs.
  • Demonstrated potential for parallelized sample processing, enabling cost-effective high-throughput screening.

Conclusions:

  • The presented platform enables significantly faster analysis of synthetic modifications on monoclonal antibodies for ADC development.
  • The protocol is potentially scalable for analyzing biological post-translational modifications (PTMs).
  • This inexpensive and effective platform facilitates high-throughput screening of protein conjugation sites.