Quantitative proteomics workflows, methods, and resources for advanced insights
Proteomics has evolved from a qualitative technique to a continuum of qualitative and quantitative using highly sensitive and accurate mass spectrometry to gain significant biological insights that span a wide range of applications including biology, biochemistry, biomarker discovery and precision medicine to name a few.
Quantitative proteomics using mass spectrometry (LC-MS) allows system-wide identification and quantification of proteins for both discovery-based (untargeted) proteomics applications and targeted proteomics applications. With less sample than western blotting and no antibodies needed, modern quantitative mass spectrometry analyses can detect and quantify thousands of proteins in a single experiment across multiple conditions, and the dynamics can be studied at a level that provides much greater understanding of how biological processes respond to different stimuli, or how they change within a cell, tissue, or organism over time, or while in a disease state.
Harness the power of quantitative proteomics to gain insights on the dynamic processes that drive the biology of cells, tissues and organisms.
By collaborating with key opinion leaders and the scientific community, Thermo Fisher Scientific is redefining the new benchmark in proteomics—quantifying all identified proteins and delivering high precision and accuracy.
Quantitative proteomics review: Magic of multiplexing in LC-MS
How MS based proteomics overcome issues and limitations of older quantitative proteomics methods
Western blotting is a traditional method used for quantitative protein measurement, but it requires knowledge of the system and expected changes in order to obtain an appropriate target antibody. Antibodies are not always available, not specific, or they’re expensive, and for posttranslational modifications they can be even more difficult to obtain. In addition, western blotting is sample intensive, it has limited linear dynamic range, and typically only a single target is quantified in each western blot.
Modern quantitative proteomics methods such as liquid chromatography coupled to mass spectrometry (LC-MS) can measure changes in the abundance of protein-specific posttranslational modifications (PTMs), facilitating location of the modified residue. Compared to the western blotting method, quantitative proteomics mass spectrometry analyses require less sample, no antibodies, and can detect and quantify multiple proteins in a single experiment across multiple conditions.
|Traditional quantitative proteomics methods||Issues and limitations of older proteomics methods||Benefits and capabilities of MS based proteomics|
Triple Quadrupole LC-MS and Orbitrap LC-MS technology is advancing quantitative proteomics
Our mass spectrometers created and defined the benchmark in proteomics during the 90s, identifying and cataloging proteins in a proteome or biological system. This remains the foundation of proteomics, but to understand biology, we knew we had to go beyond identification. With continued advancements in sensitivity, dynamic range and throughput, our instruments are helping researchers capture more complete profiles to achieve a new benchmark which includes quantitation. We understand the scientific community needs to understand the functions of individual proteins, protein complexes, and their place in complex biological systems, and easily translate protein abundance changes into valuable discoveries. In addition to our leading instrumentation, we’re committed to and invested in developing fit-for-purpose reagents, software and workflows to meet the high demands of modern proteomics.
Recommended mass spectrometers for quantitative proteomics
Choosing the most appropriate quantitative proteomics technique depends on experimental demands and instrumental capabilities. We offer multiple mass spectrometers for quantitative proteomics experiments plus a full range of products and resources to assist you along the entire workflow. Regardless of which technique you decide is best, know that we’re here to help, so never hesitate to contact one of our technical experts for assistance as you make decisions about how to approach your work.
TSQ Altis Triple Quadrupole Mass Spectrometer
Orbitrap Exploris 480 Mass Spectrometer
Orbitrap Exploris 240 Mass Spectrometer
Orbitrap Eclipse Tribrid Mass Spectrometer
|Ideal use based on type of experiment, application||High-throughput targeted quantitation on specific, well-characterized proteins||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, it accelerates your path to large-scale studies, delivering proven high data quality and time savings, so you can go beyond faster to actionable outcomes.||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, it 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.||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, it accelerates your path to new, impactful results, so you can drive your science beyond today’s discovery.|
|Workflow types supported|
Quantitative proteomics applications, workflows and product solutions
Quantitative discovery proteomics using mass spectrometry seeks to identify and characterize as many proteins as possible across a broad dynamic range while also measuring the relative protein abundance changes happening in multiple sample sets. This is also referred to as untargeted proteomics experiments.
View the workflow from sample preparation to mass spectrometry and data analysis, plus our recommended products for each step by clicking on the links in the table below.
|Tandem Mass Tag (TMT) Quantitation||Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)||Label-Free Quantitation (LFQ)|
|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 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.|
|Samples per LC-MS||1-16||1-3||1|
|Workflow & Products||Workflow & Products||Workflow & Products|
White Paper: 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.
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
Quantitative targeted proteomics using mass spectrometry is used to determine relative or absolute abundances of peptides representing the proteins of interest with a high degree of accuracy and sensitivity. Frequently applied to large sample sets, and often used on target peptides selected through analysis of data from earlier discovery experiments, it allows profiling of hundreds of targets in a single experiment.
|SureQuant Internal Standard (IS) Targeted Quantitation||Parallel Reaction Monitoring (PRM)||Selected Reaction Monitoring (SRM)||Selected Ion Monitoring (SIM)|
|Key benefit||Sensitivity and efficiency||High selectivity||Highest sensitivity||Flexibility|
|A new paradigm for absolute quantitation of target proteins building on the PRM approach, enabling reliable detection and quantification of hundreds to thousands of targets in a wide range of samples while maintaining speed, sensitivity, and overall performance.||Utilizing the built-in Orbitrap mass analyzer in our newest instruments, it detects all target product ions in parallel using one, concerted high resolution mass analysis, most suitable for quantifying tens to hundreds of targets in complex matrices.||Performed on a triple quadrupole, it’s the gold standard for reliable, more routine, targeted quantitation, relative or absolute, and is ideally suited for analyzing and quantifying large numbers of samples.||Isolates a selected peptide ion characteristic of the targeted protein; only the selected target is transferred to the analyzer for detection, no fragmentation, simple method set up, most suitable for quantifying tens of proteins in samples of medium complexity.|
|Samples per LC-MS||1||1||1||1|
|Accuracy||Very good||Very good||Very good||Very good|
|Workflow & products|
Choosing between label-free quantification proteomics (LFQ) or TMT proteomics
Making the decision to use a label or label-free method for your quantitative proteomics experiment largely depends on a few key factors: sample size, time, and cost.
Learn how modern proteomics researchers are striving to close the gap between qualitative and quantitative techniques to ensure all identified proteins are quantified with high precision and accuracy to gain real, significant biological insights based on how proteins function and respond to changes in their environment. Also see visual representations and diagrams for some popular quantitative proteomics workflows and techniques.