Proteomics Mass Spectrometry Workflows

Elucidating protein identity and function

Protein digestion and labeling technologies, when coupled to liquid chromatography-mass spectrometry (LC-MS), offer powerful methods for identifying and quantifying peptides, proteins, and posttranslational modifications (PTMs), such as phosphorylation and glycosylation. We offer a wide variety of product solutions, methods and protocols for your proteomics mass spectrometry workflows from protein discovery and quantitation to the study and analysis of protein structure and function.

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A qualitative, or bottom-up proteomics workflow, is designed to identify as many protein components in a biological sample as possible through a series of methods and protocols that include protein digestion, LC separation, mass spectrometry and data interpretation.

One of the most studied and important posttranslational modification in proteins, phosphorylation, commonly known as phosphoproteomics, plays a central role in regulating many cellular processes, and workflows involving sample enrichment, separation, mass spectrometry and data mining and measurement of phosphopeptide data.

Glycosylation plays a vital role in a variety of biochemical processes as many glycans undergo disease-related expression level changes, and the detection and quantification of the changes offer critical diagnostic information. Standard workflows involve sample enrichment, mass spectrometry analysis with multiple fragmentation methods to determine glycan composition.

Our translational proteomics workflows deliver the standardization and reproducibility needed for large-scale studies while they help lead the way and accelerate the journey from discovery to clinical applications, including the discovery of protein biomarkers which can lead to tests, treatments and practices to improve human health.

Quantitative proteomics workflows

High-throughput multiplexed protein quantification with a highly sensitive and advanced workflow using TMT label reagents, LC-MS instrumentation and proteomics data software which enables relative quantitation of more samples simultaneously.

Proteins are labeled in vivo substituting an isotopically heavy form of an amino acid for the naturally occurring light form, followed by HRAM Thermo Scientific Orbitrap MS analysis and peptide calculation software for accelerated, accurate identification and relative quantification.

Relative quantitation of protein samples from any origin, tested and analyzed individually with high performing LC-MS instruments and then evaluated and interpreted with scale using the advanced label-free quantitation node within our Thermo Scientific Proteome Discoverer software.

Our newest absolute quantitation of target proteins building on the PRM approach, using Thermo Scientific SureQuant Targeted Assay Kits and Orbitrap MS, enabling reliable detection and quantification of hundreds to thousands of targets in a wide range of samples while maintaining speed, sensitivity, and overall performance.

Protein structure analysis workflows

In top-down proteomics there is no prior digestion of proteins into their corresponding peptide species before MS analysis which brings advantages such as localizing PTMs, detecting degradation products and determining sequence variants.

A powerful technique for examining protein-protein interactions which can be used with cryo-EM or X-ray crystallography to obtain structural information and enable the visualization of interacting regions by letting researchers create distant maps within protein complexes or individual proteins.

HDX-MS exchanges protons from the protein with deuterium in deuterated solutions, and the rate of exchange provides information used to infer protein structure and conformation information, and in protein complexes protein-protein or protein-ligand interaction sites.

Study intact protein, non-covalent protein-protein and protein-ligand complexes in their biological state with native mass spectrometry and for single proteins, examine expected pattern and degree of posttranslational modifications at a particular site.

For a dynamic view of protein-protein interactions, affinity purification can be coupled to mass spectrometry to examine a subset of proteins in complex samples or look at a protein at the interactome level using the proximity biotinylation approach; it also examines the role PTMs play.

Full characterization of intact proteins is often performed on proteins that have been enriched or purified, and then they can be introduced into the mass spectrometer by direct infusion or liquid chromatography and electrospray ionization.

Determine original protein components of a sample, or for protein complexes identify individual proteins, stoichiometry of subunits and PTMs by using sequence data resulting from proteins being enzymatically digested to their peptide components and then analyzed by LC-MS/MS.

Perform sequencing and probe the quaternary structure of protein complexes by introducing enzymes in a limited amount and then mass spectrometry acquisition is done similar to a bottom-up proteomics workflow.

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.

Greater proteome coverage and sensitivity

The Thermo Scientific FAIMS Pro Duo 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.

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