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Protein Therapeutics Analysis Applications

Applications for protein therapeutics analysis

Thermo Fisher Scientific provides tailored solutions for precise and reliable analysis of protein therapeutic analysis. Our comprehensive range of applications ensures accurate identification, purity determination, quality assessment, and strength analysis. For detailed information on these specific applications, please refer to the sections below.

Comprehensive characterization

Complete protein characterization is a vital process that involves analyzing the composition, structure, and behavior of proteins. Through advanced techniques like mass spectrometry and bioinformatics, scientists can uncover valuable insights about proteins, including their amino acid composition, molecular weight, and post-translational modifications.

 

This knowledge has significant applications in fields such as drug discovery, biotechnology, personalized medicine, and improving food quality and nutrition. Overall, complete protein characterization is essential for understanding proteins and harnessing their full potential.

Complete characterization of monoclonal antibodies under native and denaturing conditions

This application note details a study by Thermo Fisher Scientific, using the Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer to analyze and characterize the complexity and heterogeneity of monoclonal antibodies.

Bottom-up characterization

Bottom-up protein characterization poses several challenges and requires effective solutions to achieve accurate and comprehensive analysis. This approach involves digesting proteins into smaller peptides for analysis, which can lead to issues such as peptide complexity, dynamic range limitations, and the need for robust data analysis tools.

 

However, advancements in mass spectrometry, sample preparation techniques, and bioinformatics have provided solutions to overcome these challenges and enable in-depth bottom-up protein characterization. We propose a more efficient method that leverages Thermo Scientific Orbitrap-based LC-HRAM MS platforms for the comprehensive characterization and monitoring of protein therapeutics.​

Peptide mapping of challenging monoclonal antibodies

This application note explores solutions for peptide mapping of complex monoclonal antibodies. Discover the use of alternative enzymes and automated preparation methods to address challenges with traditional trypsin digestion, aiming to enhance the quality and safety of biotherapeutic drugs.

Host cell protein (HCP) profiling and quantitation in gene therapy products with the Orbitrap Astral mass spectrometer

This webinar provides an overview of HCP profiling and quantitation in gene therapy products using a high-resolution accurate mass (HRAM) platform. It aims to address the challenges in AAV HCP analysis and demonstrate approaches to accurately identify and quantify low abundant HCPs for safe and effective production of advanced biotherapeutics.

The MAM 2.0 workflow enables seamless transition from research and development to quality control

This application note discusses the challenges in transferring the Multi-Attribute Method (MAM) from research to quality control in biopharmaceuticals. It presents the Thermo Scientific MAM 2.0 Workflow as a solution for seamless method transition.​

Top/middle-down characterization

Top/middle-down protein characterization methods face unique challenges that require effective solutions for accurate and comprehensive analysis. These approaches involve analyzing intact or partially fragmented proteins, which can be challenging due to their size, complexity, and heterogeneity.

 

The challenges include limited fragmentation efficiency, low sensitivity, and difficulties in data interpretation. However, advancements in mass spectrometry instrumentation, fragmentation techniques, and bioinformatics have paved the way for innovative solutions in top-down and middle-down protein characterization.

IdeS-cleaved mAb subunit analysis with LC-HRAM-MS: a quick and accurate comparison of biosimilar and originator biotherapeutics

This application note presents a study that uses high-resolution, accurate-mass spectrometry to quickly and reliably characterize monoclonal antibody (mAb) therapeutics and their biosimilars.

Increased sensitivity and throughput for native intact mass analysis using a NativePac OBE-1 SEC column and an Orbitrap Ascend Tribrid mass spectrometer

This application note presents how the Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer is used for comprehensive characterization of complex monoclonal antibodies, ensuring their safety and efficacy.​

Proton transfer charge reduction (PTCR) improves spectral matching and sequence coverage in middle-down analysis of monoclonal antibodies

This application note explores the use of proton transfer charge reduction (PTCR) to improve the sequence coverage of monoclonal antibodies by addressing the current limitations in sequencing methods that often result in incomplete sequence coverage.

Hydrogen deuterium exchange mass spectrometry for the masses

This white paper introduces hydrogen deuterium exchange mass spectrometry (HDX-MS), a tool for studying protein structures. It discusses its advantages, the information it provides, and how it complements traditional techniques. It also highlights the latest tools and workflows that simplify HDX-MS.

Lifetime stability of size exclusion chromatography columns for protein aggregate analysis

This study demonstrates the durability of the Thermo Scientific MAbPac SEC-1 Column in analyzing monoclonal antibody aggregates, a key quality control step in the biopharmaceutical industry.​

Evaluation and application of salt- and pH-based ion-exchange chromatography gradients for analysis of therapeutic monoclonal antibodies

This document introduces a streamlined method for analyzing charge variants in monoclonal antibodies using a pH gradient in ion-exchange chromatography, aimed at improving efficiency in biopharmaceutical processes.

Our general purpose product lines, including LC-MS products, are not intended for in vitro diagnostic purposes in accordance with our product documentation, manuals, and labels. They are designated for General Laboratory Use Only.

 

Our general purpose product lines have not been tested or validated for such applications and their use for in vitro diagnostic purposes may result in health and safety risks. They are designated for Research Use Only Applications.

 

For Research Use Only - Not For Use In Diagnostic Procedures.

General Laboratory Equipment – Not For Diagnostic Procedures. © 2026 Thermo Fisher Scientific Inc. All rights reserved. Thermo Scientific™ products are designated as General Laboratory Equipment and are not intended for use in diagnostic procedures or for in vitro diagnostic purposes. These products are intended for general laboratory use only and have not been tested or validated for diagnostic applications; use for such purposes may result in inaccurate results and may pose health and safety risks. They are designed for research, academic, and industrial applications and for general-purpose analytical use, including high-resolution and accurate-mass measurements, without reference to specific clinical conditions, analytes, or diagnostic decisions.

The Thermo Scientific Orbitrap Exploris and Excedion series mass spectrometers are Orbitrap instruments with an atmospheric pressure ionization (API) source for liquid chromatography (LC) mass spectrometry (MS) high-throughput applications. The instruments are designed to be placed on a bench in the laboratory and maintain mass accuracy across chromatographic peaks, supporting confident identification and quantitation using high-resolution accurate-mass detection.