Transforming small molecule identification and characterization

Go beyond with intelligence and technology

The Thermo Scientific Orbitrap ID-X Tribrid Mass Spectrometer combines industry-leading mass analyzer technology dedicated for small molecule analysis with the Thermo Scientific AcquireX intelligent MSn data acquisition strategy, to collect more meaningful data. By capturing more low-abundance analytes and leveraging streamlined data analysis and mass spectral prediction tools, the system's intuitive, automated workflow accelerates results to let you go beyond faster.


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Break your bottlenecks

small molecule compound

Addressing the "Identity Crisis" in Small Molecule Compound Identification

In this webinar we discuss a fundamental new approach to untargeted small molecule analysis involving optimized mass spectrometers, powerful new data acquisition strategies, and an arsenal of new software tools to translate high-quality Orbitrap mass spectra into more, confidently-assigned small molecule structures.

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Key benefits of Orbitrap ID-X Tribrid Mass Spectrometer

Focus on your science, not on instrument setup Collect more meaningful data, not just more data Speed, simplicity, and flexibility that match your analysis Demystify unknowns with MSn data
Profile your complex samples with the combination of Thermo Scientific Tribrid architecture, method editor templates and ready-to-use experimental parameters, which enable you to efficiently acquire data without the need for extensive user expertise. Increase profiling efficiency by automating MSn data acquisition methods with the intelligent Thermo Scientific AquireX data acquisition tool, and attain a higher number of compounds with distinguishable fragmentations that can be further analyzed. Produce information-rich MSn data on complex samples enabling fast, automated data processing. Using a comprehensive, integrated set of data analysis tools, extract high-confidence results from complex data. Identify knowns and unknowns with confidence, and elucidate structures of unknowns with LC/MS-based tools for structural elucidation, including MSn mass spectral trees, in-silico fragmentation, and precursor ion fingerprinting.

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Orbitrap ID-X ordering guide

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Learn how the Orbitrap ID-X Tribrid mass spectrometer works

See what makes the Orbitrap ID-X Tribrid mass spectrometer the preferred solution for transforming small molecule identification and characterization.

The mass spectrometer combines the quadrupole, ion trap and HRAM Thermo Scientific Orbitrap mass analyzer technology for acquiring the richest MSn data for every sample run. Dual fragmentation techniques – CID and HCD – are available at any stage of MSn, with subsequent mass analysis in either the ion trap or ultra-high resolution Orbitrap mass analyzer.

Orbitrap ID-X Tribrid MS ion path

Orbitrap ID-X Tribrid MS ion path

By capturing more low-abundance analytes and leveraging a streamlined, complete, and integrated suite of software analysis tools, the small molecule structural elucidation identification bottleneck can be significantly improved, making identification and characterization more feasible. This allows you to go beyond, faster than ever before.

The three levels of AcquireX data acquisition options enable rapid profiling across multiple samples or exhaustive sample interrogation through replicate injections. Each method increases the number of compounds sampled with distinguishable fragmentation spectra for sample and study characterization.

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Transform small molecule identification and characterization with the AcquireX acquisition tool to generate more meaningful fragmentation spectra.


Software and library solutions to streamline your data analysis

Match your analysis requirements with software that provides speed, simplicity, and flexibility and overcome challenges in full-scan MS data analysis and interpretation of small molecules

Thermo Scientific Compound Discoverer software efficiently extracts high-confidence insights from information-rich small molecule HRAM data. This mass spectrometry data analysis software offers a full suite of tools to address your challenges with small molecule data analysis. The software streamlines unknown identification, determination of real differences between samples, and elucidation of biological pathways. It serves as a hub to seamlessly connect users to the tools they need to analyze productively and confidently.

Delivering Confidence for Small Molecule Identification

In this white paper we address the challenges in small molecule identification with mass spectral libraries. mzCloud spectral libraries and mzVault software are designed to address the challenges of small molecule identification for routine and research applications.

Mass spectral libraries and databases may be required to identify unknown compounds when reference standards are not available. This is particularly true for studies in areas such as metabolomics, forensic toxicology, food & beverage, environmental emerging contaminants or extractables & leachables. Rank search more effectively with the industry-leading online mzcloud spectra fragmentation library.

Learn more about the mzCloud mass spectral library

Discover the difference that high-resolution mass spectral libraries can make when addressing the challenges of small-molecule unknown characterization and how powerful data analysis tools can make the most of these libraries by allowing you to find answers quickly and confidently to drive your decision-making process.

Supports MSn spectral ion tree searching and enables custom library creation

Confident small molecule unknown compound identification and structural elucidation can be labor intensive and time consuming. Simplify and streamline this challenge through the use of Thermo Scientific Mass Frontier software which utilizes the most high quality, fully curated experimental spectral and fragmentation libraries available to provide greater insights, understanding and confidence when turning your data into actionable knowledge.

When small molecule unknowns don't provide a spectral hit, how can we still identify them?

New Generation of Software Tools for the Identification of Compounds

Addressing the "Identity Crisis" in Small Molecule Compound Identification isn’t easy. Learn how you can use Thermo Scientific Mass Frontier software and an integrated software framework to translate high quality mass spectra into more confidently-assigned small molecule structures.

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mzLogic data analysis algorithm to easily maximize your MSn data

Cut through the confusion of dozens or hundreds of chemical database possibilities by using your real fragmentation data combined with the highest quality curated spectral library.  Leverage mzLogic to combine spectral library similarity with chemical database searching in a completely new way to leverage real world fragmentation information to propose the best candidates for true unknowns.

Maximize your real fragmentation data by combining spectral library similarity searching with chemical database searching.

High-quality MSn data provided by the Orbitrap ID-X mass spectrometer addresses the current bottleneck of compound identification by combining precursor ion fingerprinting with substructure analysis of unknown metabolites. Additional tools available for LC-MS-based structure elucidation include MSn mass spectral trees and in-silico fragmentation.

Compound annotation using MSn to demystify unknowns

Comparative MS/MS spectra for two flavonoid structrual isomers where the only structural difference is associated with aglycone substructure. The addition of the two sugar rings to the base aglycone substructure result in similar MS/MS spectral patterns prohibiting correct structural identification despite low mass errors for precursor and MS/MS product ions. Incorporation of neutral-loss triggered MS3 performs tandem mass spectral analysis and subsequent MS3 acquisition resulting in clearly defining the two isomeric compounds.

Monitor your mass spectrometry analyses anywhere, anytime.

Monitor your mass spectrometry analyses anywhere, anytime.

Using the Thermo Scientific Almanac web- and smartphone-based application gives you the ability to remotely access and manage your LC-MS systems, 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 and maximize up-time.

Key Almanac Tools

  • Instrument Connect Platform: manage your systems and data in a single location
  • Instrument Status: see what is happening in real time
  • Instrument Logbook and Events: easily see what has happened and log important information
  • Instrument Utilization Reports: evaluate system usage over time
  • Instrument Scheduler: manage system access and utilization
  • Push to Service: minimize time taken to diagnose issues
Almanac Workflow

Connect your laboratory: Always know what’s going on within your laboratory with any cloud-connected device. Maximize system utilization with long-term trending of system usage and sample throughput, through to checking data acquisition and multiple other productivity tools.

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Applications ideal for using the Orbitrap ID-X mass spectrometer

Currently, insufficient metabolome annotation limits biological interpretation of untargeted metabolomics studies. Orbitrap ID-X MS provides a streamlined approach to routinely achieve comprehensive metabolome coverage with confident compound annotations against spectral libraries and de novo structural elucidation of unknown metabolites. Orbitrap ID-X MS combines the power of HRAM Orbitrap mass analyzer technology with intelligent MSn acquisition, AcquireX, for untargeted metabolomics to address the identification bottleneck reinventing the way metabolomics is done today.

Higher efficiency - Orbitrap ID-X

Orbitrap ID-X MS delivers improved MS/MS sampling by automatically excluding background ions and focusing acquisition on true sample components. This novel, data-informed approach, Acquire X, utilizes sequential injections to interrogate more unique compounds. AcquireX increased the number of compounds with fragmentation data in human plasma (NIST SRM1950) over traditional DDA by 139% after three injections.

For Research Use Only. Not for use in diagnostic procedures.

Distribution of precursor intensity per subsequent injection

AcquireX prevents redundant fragmentation of highly abundant compounds allowing for more analytes of lower abundance to be sampled with subsequent injections. In the analysis of human plasma (NIST SRM1950), the most abundant compounds were only fragmented in injection one resulting in a 5-fold decrease in average intensity of compounds fragmented from injection 1 to injection 3.

For Research Use Only. Not for use in diagnostic procedures.

Higher quality - Orbitrap ID-X part1

Orbitrap ID-X offers multistage fragmentation (MSn) and the flexibility of complementary dissociation techniques (HCD, CID) to increase the probability of generating information-rich product ion spectra across more compound classes. Fragmentation of metabolite kynurenine illustrates the complementarity of HCD and CID.

Higher quality - Orbitrap ID-X part2

Annotation of more high quality spectra leads to improved metabolome coverage and enables comprehensive pathway annotation and functional interpretation of results. Confident annotations of metabolites in the tryptophan degradation pathway enabled detection of changes in the levels of anthranilic acid in a comparison among healthy donors and donors with Crohn's disease.

For Research Use Only. Not for use in diagnostic procedures.

Higher efficiency - Orbitrap ID-X

Orbitrap ID-X MS delivers improved MS/MS sampling by automatically excluding background ions and focusing acquisition on true sample components. This novel, data-informed approach, Acquire X, utilizes sequential injections to interrogate more unique compounds. AcquireX increased the number of compounds with fragmentation data in human plasma (NIST SRM1950) over traditional DDA by 139% after three injections.

For Research Use Only. Not for use in diagnostic procedures.

Distribution of precursor intensity per subsequent injection

AcquireX prevents redundant fragmentation of highly abundant compounds allowing for more analytes of lower abundance to be sampled with subsequent injections. In the analysis of human plasma (NIST SRM1950), the most abundant compounds were only fragmented in injection one resulting in a 5-fold decrease in average intensity of compounds fragmented from injection 1 to injection 3.

For Research Use Only. Not for use in diagnostic procedures.

Higher quality - Orbitrap ID-X part1

Orbitrap ID-X offers multistage fragmentation (MSn) and the flexibility of complementary dissociation techniques (HCD, CID) to increase the probability of generating information-rich product ion spectra across more compound classes. Fragmentation of metabolite kynurenine illustrates the complementarity of HCD and CID.

Higher quality - Orbitrap ID-X part2

Annotation of more high quality spectra leads to improved metabolome coverage and enables comprehensive pathway annotation and functional interpretation of results. Confident annotations of metabolites in the tryptophan degradation pathway enabled detection of changes in the levels of anthranilic acid in a comparison among healthy donors and donors with Crohn's disease.

For Research Use Only. Not for use in diagnostic procedures.

Featured webinar: Advanced Metabolome Annotation with Orbitrap ID-X Tribrid mass spectrometer
Featured webinar: Advanced Metabolome Annotation with Orbitrap ID-X Tribrid mass spectrometer

In this symposia Dr. Ionne Ntai discusses Advanced Metabolome Annotation with Orbitrap ID-X Tribrid mass spectrometer.

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Pharma small molecule analysis encompasses API impurity ID, metabolite ID, degradation profiling, and extractables & leachables analysis. Each of them plays a critical role and is an integral part of drug R&D and development. High resolution mass spectrometry (HRMS) has been a pivotal tool for these applications.

The Orbitrap ID-X mass spectrometer elevates the HRMS capability to a new level, with the intelligent data acquisition of AcquireX, it removes the complex matrices by automatic background exclusion, ensuring the capture of low-abundance analytes, which significantly improves the identification. The information rich MSn fragments provide in-depth structure knowledge, and facilitate identification of unknown or unexpected compounds with high confidence. Furthermore, the ready-made templates allow users to carry out the analysis with ease.

Pharma MetID, part 1
 Click to enlarge

Impurities analysis performed on the Orbitrap ID-X mass spectrometer using AcquireX data acquisition strategies. Analysis on the excipient sample, along with an analysis to determine background precursors is performed. Background precursors are automatically incorporated into an exclusion list and subsequently imported into the refined method. The exclusion list significantly decreases the number of compounds of interest targeted during standard data- dependent analysis methods resulting in more efficient MS/MS and MS3 data acquisition. The highlighted retention times indicate the measured elution times for two isomeric impurities.

Pharma MetID, part 2
 Click to enlarge

Comparative high-resolution accurate mass (HRAM) MS and MS/MS spectra acquired at the identified retention times. The full scan HRAM MS spectra show the complexity of co-eluting background ions as well as isomeric impurities highlighted (Figures 1 and 2) for the two retention times. The background ions differ significantly requiring automated exclusion list generation to increase DDA MS/MS and MS3 sampling efficiency. The comparative product ion spectra show similar fragments prohibiting structural assignment. An MS3 spectra was acquired from the m/z 704 MS/MS product ion to assign probable impurity structures.

Pharma MetID, part 3
 Click to enlarge

Plausible precursor and product ion structures were evaluated using the Fragments and Mechanisms tool in Mass Frontier 8.0 software. Two plausible structures were evaluated for fragmentation pathways to predict formation of the m/z 583.1873 product ion. The first structure has a direct pathway justifying the m/z 704 fragmenting to form the m/z 583 product ion, while the second proposed structure predicts the m/z 583.1873 fragment would originate from the m/z 601 MS/MS product ion as opposed to the alternative m/z 704 product ion structure.

The Orbitrap ID-X mass spectrometer in combination with Compound Discoverer software, AcquireX and mzLogic offers a compelling solution for the pharmaceutical industry. Learn how to address your metabolite ID challenges.

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LC-MS webinar series

LC-MS webinar series

Expand your application knowledge

Our LC-MS on-demand webinar series expands your application knowledge for pharma, biopharma, environmental, omics, food, forensics and clinical research and more. Learn how the latest high-performance mass spectrometry solutions can enable your laboratory to solve your most pressing analytical challenges, regardless of sample type. 


Monitor your system remotely from anywhere in the world

Monitor your system remotely from anywhere in the world

  • Connect your lab and boost productivity with secure remote access to your data and instruments.
  • Monitor your instrument in real-time with automatic email notifications.
  • Store data in secure accounts and share with colleagues and collaborators.

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