Peptide Sequencing by Mass Spectrometry | Thermo Fisher Scientific

Identification of proteins

The majority of proteomics applications involve peptide sequencing by liquid chromatography mass spectrometry (LC-MS). Proteins are enzymatically digested to their peptide components, and analyzed by LC-MS. The resulting sequence data is used to determine the original protein components of the sample. Information on posttranslational modifications (PTMs) and stoichiometry can also be obtained with this approach. For single proteins, the sequence can confirm identity and characterize PTMs. For protein complexes this approach determines the identity of the individual proteins that make up the complex, stoichiometry of the subunits and PTMs.

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Featured products for peptide sequencing by mass spectrometry

Orbitrap Exploris 480 Mass Spectrometer

Orbitrap Eclipse Tribrid Mass Spectrometer

Proteome Discoverer Software

Resources

Webinar: Benchmarking the Q Exactive HF-X MS for Shotgun Proteomics
Peer Reviewed article: The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer
Richard Alexander Scheltema, Jan-Peter Hauschild, Oliver Lange, Daniel Hornburg, Eduard Denisov, Eugen Damoc, Andreas Kuehn, Alexander Makarov and Matthias Mann
Molecular & Cellular Proteomics, 13, 3698-3708, 2014
Peer Reviewed article: Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer
Christian D. Kelstrup, Rosa R. Jersie-Christensen, Tanveer S. Batth, Tabiwang N. Arrey, Andreas Kuehn, Markus Kellmann and Jesper V. Olsen
J. Proteome Res., 2014, 13 (12), pp 6187-6195
Peer Reviewed article: >Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates
Michael W. Senko, Philip M. Remes, Jesse D. Canterbury, Raman Mathur, Qingyu Song, Shannon M. Eliuk, Chris Mullen, Lee Earley, Mark Hardman, Justin D. Blethrow, Huy Bui, August Specht, Oliver Lange, Eduard Denisov, Alexander Makarov, Stevan Horning, and Vlad Zabrouskov
Anal. Chem., 2013, 85 (24), 11710–11714

The LC-MS 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 Products have not been tested or validated for such applications and their use for in vitro diagnostic purposes may result in inaccurate results and, more seriously, health and safety risks. They are designated for Research Use Only Applications.

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.