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Mass Spectrometry-Based Protein Footprinting Products

End-to-end solution for your MS-based Protein Footprinting higher order structural analysis

Our entire workflow has been meticulously optimized to provide you with the highest level of insight, eliminating any uncertainty when it comes to selecting the most suitable configuration for your experiments. We offer a comprehensive solution that encompasses all necessary components, along with a wide range of resources to support you throughout the entire workflow.

Separations optimized for MS-based Protein Footprinting

Vanquish Neo UHPLC System

For experiments that require high reproducibility and sensitivity with low carryover. The Thermo Scientific Vanquish Neo UHPLC System enables high-sensitivity LC-MS applications. It flawlessly integrates with the industry-leading Thermo Scientific mass spectrometry portfolio and ESI sources.

EASY-Spray PepMap Neo UHPLC Columns

Thermo Scientific EASY-Spray PepMap Neo UHPLC Columns feature easy connectivity, high reproducibility, and excellent separations. Neo columns provide 1500 bar pressure capability, improved column-to-column consistency, and increased efficiency. The click-and-spray format enables perfect connections to our mass spectrometers every time.

FAIMS Pro Duo interface - For experiments that require extended dynamic range

The Thermo Scientific FAIMS Pro Duo interface offers improved selectivity and sensitivity, even at very low picogram loading levels. This enables the generation of deeper sequence coverage, allowing for the detection of subtle differences in low abundance relevant modification sites. The advanced high field asymmetric ion mobility technology employed by this interface enables precise targeting of peptides within the ion cloud, while effectively maintaining the cleanliness of the mass spectrometer and ensuring the purity of the spectra.

Mass spectrometers for Protein Footprinting

The Thermo Scientific Orbitrap family of mass spectrometers offers reliable, proven technology to support MS-based Footprinting analysis with accuracy and precision.

 

Differentiating features of all Orbitrap instruments

  • Automatic gain control to enable consistent spectral quality and quantitative accuracy from picogram to microgram loading levels without user intervention
  • Normalized collision energy to enable reproducible fragmentation efficiency of all precursors without optimization within and across sample cohorts
  • Complete mass range (m/z) of MS/MS scans to enable unambiguous sequence annotation
  • Exceptional spectral quality and intra-spectrum dynamic range enabled by the Orbitrap mass analyzer

Orbitrap Astral Mass Spectrometer - For experiments that require unprecedented depth

The Thermo Scientific Orbitrap Astral Mass Spectrometer offers a new level of depth in characterization of the proteins, with industry leading sensitivity of analysis, while maintaining the ability to analyze samples of high dynamic range. The platform supports samples of low amount (<pg) and high amount (>ug) without compromise or saturation of analysis.

Orbitrap Ascend Structural Biology Mass Spectrometer for experiments that require ultimate characterization and versatility

The Thermo Scientific Orbitrap Ascend Tribrid Mass Spectrometer leverages exceptional versatility of analysis to enable ultimate characterization of labeled samples.

 

Flexible fragmentation modes with CID, HCD, ETD, EtHCD and UVPD enable complementary spectra to provide unambiguous identification of modified amino acids by bottom-up or top-down approaches.

Orbitrap Exploris 480 Mass Spectrometer for experiments that require Orbitrap accuracy and enhanced selectivity for accurate quantitation

The Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer offers proven reliability and spectral quality to support accurate identification of modification sites. The platform offers versatile operation to support data-dependent or data-independent acquisitions for discovery and quantitation with high-resolution accurate mass.

Orbitrap Exploris 240 Mass Spectrometer for experiments that require application flexibility and quantitative precision and accuracy

The Thermo Scientific Orbitrap Exploris 240 Mass Spectrometer offers proven reliability and spectral quality to support accurate identification and quantification of modification sites.

 

High-quality Orbitrap DDA spectra in conjunction with Thermo Scientific BioPharma Finder Software or Proteome Discoverer Software ensures confident and rapid identification of all peptides.

Data analysis for Protein Footprinting

Proteome Discoverer Software - For experiments that require flexible data analysis

Thermo Scientific Proteome Discoverer Software offers predefined workflows to support both LFQ and TMT quantification, PTMs.

BioPharma Finder Software

Thermo Scientific BioPharma Finder Software supports all MS-based Protein Footprinting data analysis, including peptide identification, PTM analysis and quantification.

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.