High-throughput multiplexed protein quantitation

High-throughput multiplexed protein quantitation

Proteomics techniques are evolving to become a highly sensitive, quantitative, and high-throughput approach to analyzing global protein dynamics within a cell, tissue or an organism. In the past decade critical advances have been made across the entire proteomics workflow, most notably the development of TMT 11plex isobaric tandem mass tag labeling combined with state-of-the-art advancements in analytical mass spectrometry, which have enabled more accurate, high-throughput quantitative proteomics.

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Learn how TMT proteomics technology and the magic of multiplexing are helping scientists follow proteins in a cell over time to better understand what makes a cell functional, why and how molecules move about in a cell and what the practical applications are to this type of work.

 


How TMT quantitative proteomics works

Tandem mass tags are isobaric chemical tags that provide multiplexing capabilities for relative quantitative proteomics analysis. This ability to perform concurrent MS analysis of multiple samples increases throughput and enables relative quantitation of up to 11 different samples derived from cells, tissues or biological fluids. The tags consist of an MS/MS reporter group, a spacer arm and an amine reactive group. The amine reactive group binds to the N- terminus of a peptide or to a lysine residue during labeling.

In relative quantitation experiments, different isobaric tags are used to label different systemic conditions. Once labeled, all samples are mixed and analyzed in a single liquid chromatography mass spectrometry (LC-MS) experiment. Because the isobaric tags possess the same chemical properties, all peptides from different TMT-labeled samples co-elute during LC separation. Once the peptides enter the mass spectrometer, they are detected simultaneously as a single and indistinguishable precursor ion peak.

How TMT quantitative proteomics works

Following fragmentation, the tags from each individual systemic condition generate a unique signature reporter ion in the low m/z area of the MS/MS spectrum. Peptide identification is achieved by matching the resulting ion peaks to those provided in fragment databases. Peptide quantitation is accomplished by comparing the intensities of the reporter ions.

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TMT quantitation product solutions

TMT quantitation product solutions
Pierce TMT 11 plex Yeast Digest Standard

A lyophilized yeast peptide mixture of four congenic strains labeled with TMT11plex reagents to monitor LC-MS/MS system performance.

EasyPep Mini MS Sample Prep Kit

Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.

TMT 11-plex isobaric label reagent set

Realize high-throughput quantitative proteomics with eleven different isobaric tadem mass tag labels. This set can be used to prepare up to eleven different peptides for parallel labeling and concurrent analysis.

Pierce High pH Reversed-Phase Peptide Fractionation Kit

Increase protein identifications by over 50% in complex peptide samples using orthogonal peptide fractionation.

Acclaim PepMap 100 C18 LC Columns

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

EASY-Spray LC Columns

With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.

EASY-nLC 1200 System

Experience performance and throughput at 1200 bar with the easy to operate nano-flow UHPLC instrument.

UltiMate 3000 RSLCnano System

Take advantage of the wide flow rate range in the Ultimate 3000 RSLCnano which gives you the flexibility you need for low flow applications.

Precision
MS2 Quantitation

Orbitrap Exploris 480 MS
Orbitrap Exploris 480 MS

Best in class MS/MS system

Ideally suited for less complex samples
interaction studies with pull-downs
Immunoprecipitations
Purified samples

Accuracy & Precision
Real-Time Search MS3 Quantitation

Orbitrap Eclipse Tribrid MS
Orbitrap Eclipse Tribrid MS

Best in class Tribrid mass spectrometer

Ideally suited for more complex samples
Whole proteome profiling
Whole cell interactomics
Subcellelar lacalization


The Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer delivers best in class TMT MS2 quantitation for multiplexed proteome analysis. By leveraging intelligent acquisition schemes such as Precursor Fit Filter and TurboTMT, proteins are quantified with the highest confidence with easy setup.

The optional Thermo Scientific FAIMS Pro Interface, the next generation ion mobility technology, can be added to boost protein/peptide quantitation efficiency further within a remarkably compact footprint.


The Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer boasts the highest resolving power of all our Orbitrap LCMS instruments (up to 500,000 @ m/z 200), achieving extreme detection limits and selectivity in full-scan MS mode. This system offers the exclusive Real-time Search for Synchronous Precursor Selection MS3 (SPS MS3) for highly accurate and precise TMT quantitation results. This unique acquisition strategy improves the ratio accuracy for TMT reporter ions and boosts sensitivity, increasing total quantified peptides. Along with the new QR5 Segmented Hyperbolic-Surface Quadrupole, ion transmission is improved on narrow isolation windows, which is crucial for minimizing interferences. The brighter ion source permits 0.4 amu isolation windows and minimizes ratio inaccuracy.

Perform protein quantitation and identification easily

Isobaric labeling experiments require both qualitative and quantitative data extraction from raw LC-MS files. Thermo Scientific Proteome Discoverer software is the most comprehensive data analysis platform for qualitative and quantitative proteomics research; it not only supports differential analysis of fragmentation data at the SPS MS3 level for protein quantitation, but also at the MS2 level for protein identification. The software offers a comprehensive data mining tool set and supports multiple search engines during peptide identification.

Pierce TMT 11 plex Yeast Digest Standard

A lyophilized yeast peptide mixture of four congenic strains labeled with TMT11plex reagents to monitor LC-MS/MS system performance.

EasyPep Mini MS Sample Prep Kit

Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.

TMT 11-plex isobaric label reagent set

Realize high-throughput quantitative proteomics with eleven different isobaric tadem mass tag labels. This set can be used to prepare up to eleven different peptides for parallel labeling and concurrent analysis.

Pierce High pH Reversed-Phase Peptide Fractionation Kit

Increase protein identifications by over 50% in complex peptide samples using orthogonal peptide fractionation.

Acclaim PepMap 100 C18 LC Columns

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

EASY-Spray LC Columns

With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.

EASY-nLC 1200 System

Experience performance and throughput at 1200 bar with the easy to operate nano-flow UHPLC instrument.

UltiMate 3000 RSLCnano System

Take advantage of the wide flow rate range in the Ultimate 3000 RSLCnano which gives you the flexibility you need for low flow applications.

Precision
MS2 Quantitation

Orbitrap Exploris 480 MS
Orbitrap Exploris 480 MS

Best in class MS/MS system

Ideally suited for less complex samples
interaction studies with pull-downs
Immunoprecipitations
Purified samples

Accuracy & Precision
Real-Time Search MS3 Quantitation

Orbitrap Eclipse Tribrid MS
Orbitrap Eclipse Tribrid MS

Best in class Tribrid mass spectrometer

Ideally suited for more complex samples
Whole proteome profiling
Whole cell interactomics
Subcellelar lacalization


The Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer delivers best in class TMT MS2 quantitation for multiplexed proteome analysis. By leveraging intelligent acquisition schemes such as Precursor Fit Filter and TurboTMT, proteins are quantified with the highest confidence with easy setup.

The optional Thermo Scientific FAIMS Pro Interface, the next generation ion mobility technology, can be added to boost protein/peptide quantitation efficiency further within a remarkably compact footprint.


The Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer boasts the highest resolving power of all our Orbitrap LCMS instruments (up to 500,000 @ m/z 200), achieving extreme detection limits and selectivity in full-scan MS mode. This system offers the exclusive Real-time Search for Synchronous Precursor Selection MS3 (SPS MS3) for highly accurate and precise TMT quantitation results. This unique acquisition strategy improves the ratio accuracy for TMT reporter ions and boosts sensitivity, increasing total quantified peptides. Along with the new QR5 Segmented Hyperbolic-Surface Quadrupole, ion transmission is improved on narrow isolation windows, which is crucial for minimizing interferences. The brighter ion source permits 0.4 amu isolation windows and minimizes ratio inaccuracy.

Perform protein quantitation and identification easily

Isobaric labeling experiments require both qualitative and quantitative data extraction from raw LC-MS files. Thermo Scientific Proteome Discoverer software is the most comprehensive data analysis platform for qualitative and quantitative proteomics research; it not only supports differential analysis of fragmentation data at the SPS MS3 level for protein quantitation, but also at the MS2 level for protein identification. The software offers a comprehensive data mining tool set and supports multiple search engines during peptide identification.

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Tandem mass tag mass spectrometry advancements for highest quantitative results

Increase Throughput Icon
Increase Accuracy and Precision
Increase Proteome Coverage

Our Orbitrap LCMS based TMT quantitation solutions are the most published in the industry compared to other isobaric tagging applications. (See Resources section below for articles and documents.) To obtain the most complete quantitative profiles we have delivered improvements that enable the highest quantitative accuracy and precision to meet research goals.

Recent improvements have been made both in terms of technology and performance of mass spectrometry as well as taking advantage of intelligent acquisition and algorithms that more intelligently pull out real quality data from raw spectra. Together with TMT reagents, they deliver the industry’s gold standard for the identification and quantitation of thousands of proteins from multiplexed samples in a single run that is the most accurate, precise and cost effective for functional biology studies.

Turbo TMT

TurboTMT intelligent acquisition based on novel ΦSDM spectral processing increases resolution to baseline resolve TMT reporter ion isotopologues and speeds up spectral acquisition for TMT 11plex experiments, thereby increasing throughput for identification of quantifiable peptides.

Precursor Fit Filter

The Precursor Fit Filter algorithm reduces co-isolated ion interferences that can mask true differences in protein abundance. Precursors are selected on highest specificity within the isolated window resulting in highest MS/MS quality for better quantitative accuracy and proteome depth.

Real-Time Search data acquisition improves experimental speed and quantitation accuracy

Real-Time Search improves experimental speed and quantification accuracy when combined with the advanced SPS MS3 experimental approach. With Real-Time Search data acquisition, MS3 scans are only triggered if a peptide-spectrum match (PSM) is identified from the preceding MS2. This reduces the number of MS3 events, increases the precursor sampling rate and results in a greater number of quantified peptides; improving experimental speed. With the aid of the Real-Time Search data acquisition strategy, the Orbitrap Eclipse Tribrid MS selects only those fragment ions that correspond to the identified PSM for quantification in the MS3 scan, resulting in improved quantitation accuracy.

Real-time search data acquisition
FAIMS Pro Interface

Adding the FAIMS Pro interface to the workflow increases precursor selectivity, reduces interference, and gas-phase fractionation resulting in greater accuracy in TMT peptide quantification.

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TMT quantitation workflow

The Thermo Scientific Tandem Mass Tag multiplexing workflow with unique intelligent acquisition management delivers best in class quantification for multiplexed proteome analysis. By leveraging intelligent acquisition schemes built into HRAM Orbitrap MS we enable life scientists to quantify proteins with the highest confidence without sacrificing proteome coverage or depth and with easy set up.

In combination with TMT reagents, we deliver three complete Orbitrap MS workflows that include sample preparation for the identification and quantitation of thousands of proteins from multiplexed samples in a single run that is the most accurate, precise and cost effective for functional biology studies. Each workflow is optimized for highest quantitative accuracy/precision, coverage depth and minimizing co-ion interference and ratio compression

Thermo Scientific TMT MS2 multiplexing workflow with unique intelligent acquisition management delivers best in class quantitation for multiplexed proteome analysis yielding unrivaled confidence in discovery proteomics experiments with no compromise in coverage or depth. This TMT MS2 workflow using the Orbitrap Exploris 480 mass spectrometer utilizes intelligent acquisition schemes (TurboTMT mode, PrecursorFit filter) to deliver the highest number of quantifiable peptides for multiplexed proteome analysis. In combination with TMT reagents, and the FAIMS Pro Interface, the Orbitrap Exploris 480 MS is the only dedicated MS/MS system with resolving power that can perform TMT 11plex experiments yielding unrivaled confidence in discovery proteomics experiments with no compromise in coverage or depth.

TMT MS2 Workflow with FAIMS Pro Interface

The FAIMS Pro Interface reduces co-ion interference and improves quantitative accuracy.

TMT MS2 with FAIMS reduces interference, improves accuracy

Thermo Scientific SPS MS3 multiplexing workflow on Orbitrap Tribrid mass spectrometers provides a unique, unmatched capability to accurately measure the subtle changes in proteome for multiplexed proteome analysis.

TMT SPS MS3 Workflow

The use of SPS MS3 compared to MS2 dramatically increases the reporter ion signal intensity and improves the ratio accuracy, due to improved counting statistics, leading to a significant increase in the number of quantified peptides. Following MS2 , SPS enables the simultaneous isolation of up to 20 MS2 fragment ions that undergo higher energy collisional dissociation (HCD) fragmentation with the MS3 fragments detected in the Orbitrap analyzer. This technique further minimizes co-ion interference and ratio compression compared to MS2.

Classic SPS MS3

TMT Real-Time Search SPS MS3 Workflow

Thermo Scientific TMT Real-Time Search for SPS MS3 multiplexing workflow with unique intelligent acquisition delivers unrivalled quantitation for multiplexed proteome analysis that is the most accurate, precise and cost effective for functional biology studies, and it is exclusive to the Orbitrap Eclipse Tribrid MS.

TMT Real-Time Search SPS MS3 Workflow

The implementation of Real-Time Search for SPS enables significant improvements to specificity, accuracy and analytical performance for TMT experiments. This approach relies on searching MS/MS spectra in real time against a user provided database and only performing SPS for identified spectra, thereby eliminating MS3 acquisition for unidentified spectra. This translates to increased sampling of precursors, resulting in 30-50% more identified peptides and increased accuracy in quantitation. Data indicates that the Real-Time Search for SPS MS3 workflow provides dramatic performance improvements for quantitative multiplexed experiments.

Real Time Search SPS MS3

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Free ebook: TMT is opening doors to a whole new view of biology with mass spectrometry

Free ebook: TMT is opening doors to a whole new view of biology with mass spectrometry

Advanced TMT quantitation workflows are making it possible to sensitively detect rare peptide species, to identify differences between healthy and diseased tissue, and conduct sophisticated surveys of the cellular proteome. This ebook provides an overview of TMT technology, and offers five case studies that illustrate some of the cutting-edge applications for which these reagents are being used.

Download eBook