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Mass spectrometry
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Calibration solutions,
standards and solvents
Ready-to-use liquid formulations that can quickly calibrate Thermo Scientific LC-MS instrumentation.
Data acquisition
Data analysis
Thermo Scientific Proteome Discoverer software simplifies a wide range of proteomics workflows and is recommended for quantitative analysis of TMT-based data. The software has improved data processing capabilities for handling large data sets and is enabled with study management tools.
- A new user interface for adding reporter ion isotopic distributions
- Ability to account for reporter ion isotopic impurities for TMT10plex and TMT11plex reagents
- Implementation of TMT quantification based on S/N values
- Protein and peptide quantification based on the sum of S/N values
- New methods for normalization and scaling for peptide and protein abundance values
A demo version of Proteome Discoverer software is available free of charge.
Almanac web-based monitoring and management monitors your mass spectrometry analyses anywhere, anytime. Its web- and smartphone-based application gives you the ability to remotely access and manage your LC-MS systems, maximizing up time and freeing you to focus on other important tasks during your day. Check real-time system status and acquisitions, set up automated e-mails to notify you of a completed acquisition or error, schedule instrument access, monitor utilization, or send service files to aid in system diagnostics.
Unless stated otherwise, Proteome Discoverer software would be recommended for each of the workflows below.
The below workflows are not relevant for the Thermo Scientific Orbitrap ID-X Tribrid Mass Spectrometer and Orbitrap IQ-X Tribrid MS, as these instruments are dedicated to small molecule analysis.
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
This 84-page handbook provides helpful hints and troubleshooting for preparation of samples from a variety of sources for MS analysis.
Amine-reactive Thermo Scientific TMT10plex Isobaric Mass Tag Labeling Reagent Set plus TMT11-131C increases sample multiplexing from 10-plex to 11-plex, enabling even greater throughput for protein identification and quantitative analysis by tandem mass spectrometry (MS).
Sample labeling for TMT-based quantitation
Protein extracts isolated from cells or tissues are reduced, alkylated and digested overnight. Samples are labeled with the TMT Reagents and then mixed before sample fractionation and clean-up. Labeled samples are analyzed by high resolution Orbitrap LC-MS/MS to identify peptides and quantify reporter ion relative abundance. See the
User's Guide for a step-by-step TMT labeling procedure for intact proteins as well as peptides including preparing whole cell protein extracts, protein digestion, and peptide labeling.
Increase protein identification from LC/MS analysis through orthogonal peptide fractionation of complex peptide samples.
Free webinar: Sample prep reagents for improved proteome depth, quantification and throughput
Simplifying Complexity: New MS Reagents that Improve Proteome Depth, Quantification, and Throughput
This webinar focuses on an optimized proteomics sample preparation workflow for isobaric tags and highlights new tools for fractionation, sample throughput, accurate quantitation.
Trapping column
Obtain high resolution separations of low abundant peptides in complex proteomic samples using the Acclaim PepMap 100 C18 columns with their high loading capacity.
Separator column
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
The Thermo Scientific Pierce TMT11plex Yeast Digest Standard is a lyophilized yeast peptide mixture of four congenic strains labeled with TMT11plex reagents to monitor LC-MS/MS system performance for Tandem Mass Tag (TMT) quantitation.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
This 84-page handbook provides helpful hints and troubleshooting for preparation of samples from a variety of sources for MS analysis.
Amine-reactive Thermo Scientific TMT10plex Isobaric Mass Tag Labeling Reagent Set plus TMT11-131C increases sample multiplexing from 10-plex to 11-plex, enabling even greater throughput for protein identification and quantitative analysis by tandem mass spectrometry (MS).
Sample labeling for TMT-based quantitation
Protein extracts isolated from cells or tissues are reduced, alkylated and digested overnight. Samples are labeled with the TMT Reagents and then mixed before sample fractionation and clean-up. Labeled samples are analyzed by high resolution Orbitrap LC-MS/MS to identify peptides and quantify reporter ion relative abundance. See the
User's Guide for a step-by-step TMT labeling procedure for intact proteins as well as peptides including preparing whole cell protein extracts, protein digestion, and peptide labeling.
Increase protein identification from LC/MS analysis through orthogonal peptide fractionation of complex peptide samples.
Free webinar: Sample prep reagents for improved proteome depth, quantification and throughput
Simplifying Complexity: New MS Reagents that Improve Proteome Depth, Quantification, and Throughput
This webinar focuses on an optimized proteomics sample preparation workflow for isobaric tags and highlights new tools for fractionation, sample throughput, accurate quantitation.
Trapping column
Obtain high resolution separations of low abundant peptides in complex proteomic samples using the Acclaim PepMap 100 C18 columns with their high loading capacity.
Separator column
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
The Thermo Scientific Pierce TMT11plex Yeast Digest Standard is a lyophilized yeast peptide mixture of four congenic strains labeled with TMT11plex reagents to monitor LC-MS/MS system performance for Tandem Mass Tag (TMT) quantitation.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Mass spec analysis of TMT labeled samples
What is synchronous precursor selection?
The SPS method begins with selection of the parent ion in the MS scan, followed by its isolation in the quadrupole and fragmentation by collisionally induced dissociation (CID) in the ion trap. Following fragmentation, SPS enables simultaneous isolation of up to 20 MS2 fragment ions. A select group of MS2 fragment ions are then transferred back into the ion routing multipole (IRM) where they undergo higher energy collisional dissociation (HCD) fragmentation, with the MS3 fragments then detected in the Orbitrap analyzer.
The use of SPS 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.
Watch this free webinar to learn more
Robust classification of stem cell protein location by SPS-MS
3
Kathryn Lilley from University of Cambridge describes hyperLOPIT; a spatial proteomics method which enables the characterization of protein subcellular localization.
Click image to enlarge
Technical resources
Technology
Phosphopeptide and TMT
Cancer proteomics
Other applications
Thermo Scientific Pierce Trypsin/Lys-C protease mix, MS-Grade, is a mass spectrometry (MS)-grade serine endoproteinase mixture of trypsin and LysC that can be used for concurrent digestion of proteins for more efficient digestion than with trypsin alone.
The Thermo Scientific High-Select TiO2 Phosphopeptide Enrichment Kit enables efficient enrichment of phosphorylated peptides from complex and fractionated protein digests for analysis by mass spectrometry (MS). (This product replaces Cat. No. 88301.)
The Thermo Scientific High-Select Fe-NTA Phosphopeptide Enrichment Kit enables efficient enrichment of phosphorylated peptides from complex and fractionated protein digests for analysis by mass spectrometry (MS). (This product replaces Cat. No. 88300.)
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Thermo Scientific Pierce Trypsin/Lys-C protease mix, MS-Grade, is a mass spectrometry (MS)-grade serine endoproteinase mixture of trypsin and LysC that can be used for concurrent digestion of proteins for more efficient digestion than with trypsin alone.
The Thermo Scientific High-Select TiO2 Phosphopeptide Enrichment Kit enables efficient enrichment of phosphorylated peptides from complex and fractionated protein digests for analysis by mass spectrometry (MS). (This product replaces Cat. No. 88301.)
The Thermo Scientific High-Select Fe-NTA Phosphopeptide Enrichment Kit enables efficient enrichment of phosphorylated peptides from complex and fractionated protein digests for analysis by mass spectrometry (MS). (This product replaces Cat. No. 88300.)
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Technical resources
General
TMT phosphopeptide analysis
Thermo Scientific MS-grade crosslinkers are available in multiple different linker lengths, MS-cleavabilitiy and deuterium isotope labels.
After size-exclusion chromatography to separate the crosslinked complex, digest using MS grade proteolytic enzyme.
Utilize this serine protease for its selectivity which enables reproducible protein digestion and mass-spectrometry based protein identification.
Use this MS-grade serine protease in tandem with trypsin for enhanced digestion.
Increase protein identification by over 50% in complex peptide samples using orthogonal peptide fractionation.
Simplifying complexity: New MS reagents that improve proteome depth, quantification, and throughput
This webinar focuses on an optimized proteomics sample preparation workflow for isobaric tags and highlights new tools for fractionation, sample throughput, accurate quantitation.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Thermo Scientific MS-grade crosslinkers are available in multiple different linker lengths, MS-cleavabilitiy and deuterium isotope labels.
After size-exclusion chromatography to separate the crosslinked complex, digest using MS grade proteolytic enzyme.
Utilize this serine protease for its selectivity which enables reproducible protein digestion and mass-spectrometry based protein identification.
Use this MS-grade serine protease in tandem with trypsin for enhanced digestion.
Increase protein identification by over 50% in complex peptide samples using orthogonal peptide fractionation.
Simplifying complexity: New MS reagents that improve proteome depth, quantification, and throughput
This webinar focuses on an optimized proteomics sample preparation workflow for isobaric tags and highlights new tools for fractionation, sample throughput, accurate quantitation.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Technical resources
General
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
Separate low abundance peptides in complex samples using the Acclaim PepMap LC columns.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
The Thermo Scientific Pierce Peptide Retention Time Calibration Mixture enables reversed phase liquid chromatography (LC) and mass spectrometry (LC-MS) users to optimize and confirm correct operation of their equipment.
The Thermo Scientific Pierce HeLa Protein Digest Standard is a highly validated mammalian protein digest that may be used as a quality control sample for mass spectrometry (MS) analysis of complex proteomic samples.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
Separate low abundance peptides in complex samples using the Acclaim PepMap LC columns.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
The Thermo Scientific Pierce Peptide Retention Time Calibration Mixture enables reversed phase liquid chromatography (LC) and mass spectrometry (LC-MS) users to optimize and confirm correct operation of their equipment.
The Thermo Scientific Pierce HeLa Protein Digest Standard is a highly validated mammalian protein digest that may be used as a quality control sample for mass spectrometry (MS) analysis of complex proteomic samples.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Technical resources
General
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
Separate low abundance peptides in complex samples using the Acclaim PepMap LC columns.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
<li><span class="icon-lt-pdf"></span><a href="https://assets.thermofisher.com/TFS-Assets/CMD/posters/PN-64761-Recombinant-Proteins-ASMS2016-PN64761-EN.pdf" target="_blank">Poster Note: Development of Mass Spectrometry-Based Methods for Quality Assessment of Recombinant Proteins</a></li>
The Thermo Scientific Pierce HeLa Protein Digest Standard is a highly validated mammalian protein digest that may be used as a quality control sample for mass spectrometry (MS) analysis of complex proteomic samples.
The Thermo Scientific Pierce Peptide Retention Time Calibration Mixture enables reversed phase liquid chromatography (LC) and mass spectrometry (LC-MS) users to optimize and confirm correct operation of their equipment.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
Separate low abundance peptides in complex samples using the Acclaim PepMap LC columns.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
<li><span class="icon-lt-pdf"></span><a href="https://assets.thermofisher.com/TFS-Assets/CMD/posters/PN-64761-Recombinant-Proteins-ASMS2016-PN64761-EN.pdf" target="_blank">Poster Note: Development of Mass Spectrometry-Based Methods for Quality Assessment of Recombinant Proteins</a></li>
The Thermo Scientific Pierce HeLa Protein Digest Standard is a highly validated mammalian protein digest that may be used as a quality control sample for mass spectrometry (MS) analysis of complex proteomic samples.
The Thermo Scientific Pierce Peptide Retention Time Calibration Mixture enables reversed phase liquid chromatography (LC) and mass spectrometry (LC-MS) users to optimize and confirm correct operation of their equipment.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Technical resources
General
The Thermo Scientific SureQuant kits enable multiplex immunoprecipitation to mass spectrometry (mIP-MS) for the simultaneous enrichment and quantitation of multiple proteins.
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
Thermo Scientific Heavy Peptide AQUA Custom Synthesis Service provides isotopically labeled, AQUA-grade peptides for the relative and absolute quantitation of proteins at very low concentrations in complex protein mixtures.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
Separate low abundance peptides in complex samples using the Acclaim PepMap LC columns.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
* Only available for Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer.
The Thermo Scientific SureQuant kits enable multiplex immunoprecipitation to mass spectrometry (mIP-MS) for the simultaneous enrichment and quantitation of multiple proteins.
Prepare your samples in less than 3 hours using pre-formulated reagents for analysis by mass spectrometry.
Thermo Scientific Heavy Peptide AQUA Custom Synthesis Service provides isotopically labeled, AQUA-grade peptides for the relative and absolute quantitation of proteins at very low concentrations in complex protein mixtures.
With its outstanding peak capacity, the EASY-Spray C18 LC columns enable comprehensive proteome characterization.
Separate low abundance peptides in complex samples using the Acclaim PepMap LC columns.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
* Only available for Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer.
Technical resources
Used as a QC standard for method development and intact protein mass measurements, the Pierce Intact Protein Standard Mix is a mixture of recombinant proteins.
Compared to other bead-based columns, ProSwift RP-4H LC columns deliver superior resolution and faster separations.
PepSwift Monolithic Capillary LC Columns are based on a polystyrene divinylbenzene copolymer, the monolithic structure offers a high-quality alternative to traditional microparticulate sorbents, providing important advantages to the chromatographic separation. High-sensitivity proteomics and biotech applications are easily performed using these columns.
Run fast protein separations at high linear velocities with these reversed-phase monolith columns which deliver the outstanding resolving power of nonporous analytical media combined with faster separations and analysis than other bead-based columns.
Ensure robust nano and capillary flow LC-MS with EASY-Spray LC Columns. The integrated column/emitter design eliminates dead volume and is temperature-controlled for maximum reliability and performance. Rigorously tested to ensure maximum quality, these columns are designed for maximum simplicity and ease-of-use.
MAbPac RP columns for high-performance reversed-phase (RP) HPLC and LC/MS characterization of monoclonal antibodies (mAbs), fragments, variants, antibody drug conjugates (ADCs), PEGylated proteins, and bispecific proteins. These columns have excellent resolution, long column lifetime, and low carry-over. The surface chemistry, particle size, and pore size, have been optimized for high resolution separations.
These proven LC systems will provide you with the versatility and ruggedness your laboratory requires all the way from method development to routine analysis.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
For high-end UHPLC applications, use the Vanquish Horizon UHPLC system to achieve the highest sensitivity and precision, while spending less time on maintenance and set up.
Access the extensive workflows in BioPharma Finder software to interpret and visualize results to get to the answers you need faster.
Perform comprehensive analysis of top-down and middle-down proteomics data with these data tools featuring robust search engines for proteoform characterization.
Used as a QC standard for method development and intact protein mass measurements, the Pierce Intact Protein Standard Mix is a mixture of recombinant proteins.
Compared to other bead-based columns, ProSwift RP-4H LC columns deliver superior resolution and faster separations.
PepSwift Monolithic Capillary LC Columns are based on a polystyrene divinylbenzene copolymer, the monolithic structure offers a high-quality alternative to traditional microparticulate sorbents, providing important advantages to the chromatographic separation. High-sensitivity proteomics and biotech applications are easily performed using these columns.
Run fast protein separations at high linear velocities with these reversed-phase monolith columns which deliver the outstanding resolving power of nonporous analytical media combined with faster separations and analysis than other bead-based columns.
Ensure robust nano and capillary flow LC-MS with EASY-Spray LC Columns. The integrated column/emitter design eliminates dead volume and is temperature-controlled for maximum reliability and performance. Rigorously tested to ensure maximum quality, these columns are designed for maximum simplicity and ease-of-use.
MAbPac RP columns for high-performance reversed-phase (RP) HPLC and LC/MS characterization of monoclonal antibodies (mAbs), fragments, variants, antibody drug conjugates (ADCs), PEGylated proteins, and bispecific proteins. These columns have excellent resolution, long column lifetime, and low carry-over. The surface chemistry, particle size, and pore size, have been optimized for high resolution separations.
These proven LC systems will provide you with the versatility and ruggedness your laboratory requires all the way from method development to routine analysis.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
For high-end UHPLC applications, use the Vanquish Horizon UHPLC system to achieve the highest sensitivity and precision, while spending less time on maintenance and set up.
Access the extensive workflows in BioPharma Finder software to interpret and visualize results to get to the answers you need faster.
Perform comprehensive analysis of top-down and middle-down proteomics data with these data tools featuring robust search engines for proteoform characterization.
Technical resources
Achieve exceptional peak shape and resolution for your HPLC and LC/MS applications with Hypersil GOLD HPLC columns. These endcapped, ultrapure, silica-based columns deliver significant reduction in peak tailing using generic gradients with C18 selectivity. With their excellent resolution, efficiency, and sensitivity, Hypersil GOLD columns give you confidence in the accuracy and quality of your analytical data.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Access the extensive workflows in BioPharma Finder software to interpret and visualize results to get to the answers you need faster.
Achieve exceptional peak shape and resolution for your HPLC and LC/MS applications with Hypersil GOLD HPLC columns. These endcapped, ultrapure, silica-based columns deliver significant reduction in peak tailing using generic gradients with C18 selectivity. With their excellent resolution, efficiency, and sensitivity, Hypersil GOLD columns give you confidence in the accuracy and quality of your analytical data.
Achieve maximum resolution and sensitivity for LC-MS analysis of complex mixtures with nano-, capillary-, and micro-flow UHPLC.
Access the extensive workflows in BioPharma Finder software to interpret and visualize results to get to the answers you need faster.
Used as a QC standard for method development and intact protein mass measurements, the Pierce Intact Protein Standard Mix is a mixture of recombinant proteins.
MAbPac SEC-1 size exclusion chromatography HPLC columns for high-resolution separation of monoclonal antibody (mAb) analysis and large proteins, These size-exclusion chromatography (SEC) columns provide superior performance, even under nondenaturing conditions, and in high- and low-salt mobile phases and volatile eluents.
MAbPac SCX-10 LC Columns for high-resolution, high efficiency analysis of monoclonal antibodies (mAbs) and associated variants. The unique nonporous pellicular resin provides the resolving power to separate mAb variants that differ by as little as one charged residue. A hydrophilic layer surrounds the polymeric beads and eliminates hydrophobic interactions with the resin, resulting in very efficient peaks. A proprietary grafted cation-exchange surface provides pH selectivity control for high-resolution separations.
These proven LC systems will provide you with the versatility and ruggedness your laboratory requires all the way from method development to routine analysis.
For high-end UHPLC applications, use the Vanquish Horizon UHPLC system to achieve the highest sensitivity and precision, while spending less time on maintenance and set up.
Access the extensive workflows in BioPharma Finder software to interpret and visualize results to get to the answers you need faster.
Perform comprehensive analysis of top-down and middle-down proteomics data with these data tools featuring robust search engines for proteoform characterization.
Used as a QC standard for method development and intact protein mass measurements, the Pierce Intact Protein Standard Mix is a mixture of recombinant proteins.
MAbPac SEC-1 size exclusion chromatography HPLC columns for high-resolution separation of monoclonal antibody (mAb) analysis and large proteins, These size-exclusion chromatography (SEC) columns provide superior performance, even under nondenaturing conditions, and in high- and low-salt mobile phases and volatile eluents.
MAbPac SCX-10 LC Columns for high-resolution, high efficiency analysis of monoclonal antibodies (mAbs) and associated variants. The unique nonporous pellicular resin provides the resolving power to separate mAb variants that differ by as little as one charged residue. A hydrophilic layer surrounds the polymeric beads and eliminates hydrophobic interactions with the resin, resulting in very efficient peaks. A proprietary grafted cation-exchange surface provides pH selectivity control for high-resolution separations.
These proven LC systems will provide you with the versatility and ruggedness your laboratory requires all the way from method development to routine analysis.
For high-end UHPLC applications, use the Vanquish Horizon UHPLC system to achieve the highest sensitivity and precision, while spending less time on maintenance and set up.
Access the extensive workflows in BioPharma Finder software to interpret and visualize results to get to the answers you need faster.
Perform comprehensive analysis of top-down and middle-down proteomics data with these data tools featuring robust search engines for proteoform characterization.
Technical resources
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