Proteomics Mass Spectrometry

Comprehensive and confident proteomic analysis

To better understand the functions of individual proteins and their place in complex biological systems, it’s necessary to measure changes in protein abundance relative to those of the system, and proteomics mass spectrometry makes that possible. Modern proteomics has shifted from its initial qualitative outlook to a continuum of qualitative and quantitative technologies and approaches which include state-of-the-art sample preparation, liquid chromatography separation, high-resolution, accurate-mass Thermo Scientific Orbitrap mass spectrometry, and proteomic software solutions for mass spectrometry data analysis.

We’re supporting successful laboratories in their discovery and study of proteomes as they combine these components into integrated workflows which maximize productivity and enable broader, deeper proteomic analysis. Our proven scientific network, publications, and pioneering solutions, driven by advances in Orbitrap mass spectrometry systems and consumables, are producing novel, stringent and reproducible results that are pushing proteomics research and discovery forward.

Speak to a specialist   Why Orbitrap Exploris 240 MS?

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Triple quadrupole vs Orbitrap mass spec for proteomic analysis

Triple quadrupole vs Orbitrap mass spec for proteomic analysis

Targeted quantitation is frequently performed on triple quadrupole mass spectrometers such as the Thermo Scientific TSQ family, but it can also be accomplished using the HRAM and MS/MS capabilities of Orbitrap-based mass spectrometers. Using the same type of mass spectrometers for discovery and targeted quantitation experiments can simplify the transition to targeted quantitation methods. Orbitrap-based mass spectrometers can simultaneously quantify and confirm identification of multiple targeted proteins and peptides even in complex biological matrices.


Go Beyond with leading performance and versatility

Expand your capabilities from small- to large-scale studies across a variety of applications from protein identification, quantitation, to multiplexing proteomics studies. With optimized methods, the Thermo Scientific Orbitrap Exploris 240 mass spectrometer delivers a fast turnaround of sample to results with operational simplicity. Best-in-class performance, all within a compact footprint, so you can go beyond with everyday versatility.

Go beyond with more actionable outcomes

Obtain maximum quantitative insights from untargeted proteome profiles to targeted proteomics experiments with industry leading single-cell sensitivity and extraordinary accuracy, precision and simplicity. With curated workflows that deliver greater usability, the Thermo Scientific Orbitrap Exploris 480 mass spectrometer accelerates your path to large-scale studies, delivering proven high data quality and time savings, so you can go beyond faster to actionable outcomes.

Go beyond today's discovery

Obtain maximum insights on your most complex molecules and biological systems, from whole proteome profiling and quantitation, structural characterization to multiplexed single-cell proteomics. With new innovations that deliver the ultimate flexibility in experimental scope, the Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer accelerates your path to new, impactful results, so you can drive your science beyond today’s discovery.

Reduce sample interference, not system efficiency

Targeted MS, and in particular selected reaction monitoring (SRM), is the quantitative analysis method of choice on the Thermo Scientific TSQ Altis Triple Quadrupole Mass Spectrometer, enabling monitoring of up to 250 peptide-specific precursor pairs (precursors and product ions) per second while using 0.2 Dalton resolution for precursor ion selection. This dramatically reduces chemical interferences while maintaining high transmission efficiency.

Greater proteome coverage and sensitivity

Thermo Scientific FAIMS Pro interface enhances precursor selectivity, improving qualitative and quantitative results for most peptide and protein applications while reducing time consuming sample preparation steps. The FAIMS Pro interface increases analytical performance through gas phase fractionation and selective enhancement of peptidic compounds, reducing the complexity of MS spectra, and improving the analyte signal-to-noise ratio. The end result is greater proteome coverage, enhanced sensitivity and more accurate quantitation.


Proteomics liquid chromatography (LC) separations

Large-scale proteomics experiments are typically analyzed at the peptide level. For successful characterization, peptides and proteins must be separated prior to introduction into the mass spectrometer. Minimizing complexity ensures that peptides and proteins can be detected and sequenced even if they are present at low abundance. The gold standard for peptide separation in bottom-up proteomics is reversed phase (RP)-LC because it offers the broadest peptide coverage. Separation using our low-flow systems easily integrate into proteomics mass spectrometry workflows and seamlessly combine with our Orbitrap mass spectrometers for broader and deeper analyses into the proteome.

Acclaim PepMap 100 C18 LC Columns

Obtain high resolution separations of low abundant peptides in complex proteomic samples using columns with high loading capacity.

Trap Column Cartridges Holders with nanoViper Fittings

Thermo Scientific Trap Column Cartridges Holders with nanoViper fittings do not "grab" the tubing at a single point but seal at the tip without using a ferrule. This gives nanoViper fittings their UHPLC, ensuing virtually dead-volume-free capabilities.

Ensure robust nano and capillary flow LC-MS with Thermo Scientific EASY-Spray LC Columns. The integrated column/emitter design eliminates dead volume and is temperature-controlled for maximum reliability and performance. Rigourously tested to ensure maximum quality, these columns are designed for maximum simplicity and ease-of-use.


Our workflows combine different biological sample processing kits with highly sensitive yet powerful instrumentation and integrated software platforms. This results in accurate and reproducible mass spectrometry data from targeted as well as untargeted analysis experiments.

Scientists are using our mass spectrometers and their robust, complementary products to go beyond identification to understanding how proteins act, interact and function under various conditions over time, creating impressive insights about complex biological systems.

Explore multiple products and workflows for protein structure analysis plus learn more about integrative structural biology solutions that bring together mass spectrometry and cryo-electron microscopy to solve large dynamic complexes.

Analysis of proteomics experimental data ranges from mass spectra identification to quantitation to extraction of meaningful biological information. Thermo Fisher Scientific offers a suite of proteomics software products that enable you to quickly transform complex data into meaningful results.

Mass spectrometry calibration solutions are ready-to-use liquid formulations that can quickly calibrate LC-MS instrumentation. Validated standards are available for sensitivity assessment, determination of digestion efficiency, or as a control for complex sample analysis.

Learn more about our reagents, assays, kits and columns that enable robust and reproducible protein extraction from different samples, as well as peptide digestion, enrichment, and clean-up for mass spectrometry analysis.


Proteomics mass spectrometry workflow

Proteomics and protein mass spectrometry workflow


Proteomics mass spectrometry videos


White Paper: An Urgent Need for Expanded Virus Research

An Urgent Need for Expanded Virus Research

Mass spectrometry (MS) offers many approaches to gain insights into viral behavior by studying intact viral particles, their surfaces and binding characteristics, their protein compositions, and their impacts on the biochemical pathways of host cells upon infection.

Download the white paper to read about all the MS-based approaches that enable researchers to develop strategies to better tackle virus studies.


Single-cell proteomics

Single-cell proteomics is now a reality

Single-cell proteomics is now a reality

By collaborating with the scientific community, Thermo Fisher Scientific has developed innovations that allow you to move away from bulk sample to single-cell proteomics analysis.

The latest generation Thermo Scientific Orbitrap mass spectrometers deliver more proteins per cell, from tens to hundreds of cells per day from cell populations, cell types and states, on a cell-to-cell basis, generating maximum insights.

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On-demand webinar

Quantitative approaches in discovery proteomics: How do they measure up?

Quantitative approaches in discovery proteomics: How do they measure up?

Get an overview of the current state-of-the art techniques utilized in the field of quantitative discovery proteomics plus a review of the most common workflows and approaches, featuring a comparative study which objectively evaluates the performance of different quantitative approaches using the latest mass spectrometry instrumentation and analysis tools. This webinar will help participants set reasonable expectations and will help in the selection of appropriate workflows according to experimental objectives

Watch webinar