Designed for small-molecule analysis

The Thermo Scientific Orbitrap IQ-X Tribrid mass spectrometer is designed to reveal complex chemical structures for compound identification and structure elucidation of small molecules. The system combines industry-leading mass analyzer technology with intelligent automation with real-time decision making, intuitive software, and remote, hands-free calibration, to address the complexities of small-molecule identification and characterization so you can confidently collect more meaningful data.

Look inside the novel
Orbitrap IQ-X Tribrid
mass spectrometer


 From acquisition to analysis, the system lets you detect and characterize more low-abundance analytes in complex matrices for structure elucidation and unknown compound annotation. This is enabled by intelligent data acquisition using Real-Time spectral library searching and Thermo Scientific AcquireX workflows to reveal more compounds with certainty.

Highlights of Orbitrap IQ-X Tribrid mass spectrometer

Automation, easy-to-use software to simplify setup and data acquisition

Instrument control software with pre-built templates and ready-to-use experimental parameters are designed to help you quickly profile your complex samples. Automated instrument calibration using dedicated Auto-Ready ion source hardware ensures the instrument is ready to go when you are set.

Intelligent acquisition to collect more meaningful data

The intelligent Real-Time Library Search and AcquireX data acquisition tool automates MSⁿ data acquisition and increases profiling efficiency to help you obtain a higher number of compounds with distinguishable fragmentations to empower deeper analysis.

"Metabolomics and proteomics both use mass spectrometers, but the analytical workflows are quite different, so having an instrument like the Orbitrap IQ-X Tribrid MS that is specifically dedicated to metabolomics and small molecules is very useful because it has been ideally optimized."

Dr Gary J. Patti,


Professor of Chemistry, Michael and Tana Powell

Washington University School of Medicine in St. Louis

Data analysis tools to empower speed, flexibility and deeper analysis

A comprehensive, integrated set of data acquisition and analysis tools enables you to confidently and quickly produce information-rich MSⁿ data from complex samples.

LC-MS companion software tools for structural elucidation illuminate MSⁿ data

LC-MS software tools including MSⁿ mass spectral trees, novel spectral prediction techniques, in-silico fragmentation modeling, and precursor ion fingerprinting assist you to identify knowns and elucidate structures of unknown unknowns.

"This system utilizes Real-Time Spectral Library Searching that enables us to take an MS², compare it to a library, and immediately know whether we have fully characterized the molecules. And if we haven’t, then we can harness the power of the ion trap to perform MSⁿ so that we can fully elucidate that structure in real-time."

Joshua Coon,


Thomas and Margaret Pyle Chair at the Morgridge Institute for Research Professor,

Biomolecular Chemistry and Chemistry University of Wisconsin, Madison

Hardware and data acquisition technology

Instrument hardware design and an efficient, comprehensive data acquisition workflow makes the Orbitrap IQ-X Tribrid mass spectrometer the preferred solution for performing small-molecule identification, characterization, and quantitation.

Instrument hardware design and intelligent data acquisition

Proven Tribrid architecture combines a quadrupole, linear ion trap, and Thermo Scientific Orbitrap HRAM technologies to acquire the rich MSⁿ data from every sample. Multiple fragmentation techniques: — Collision-induced dissociation (CID), Higher-energy collisional dissociation (HCD), and optional Ultraviolet photodissociation (UVPD)— are available at any stage of MSⁿ, with subsequent mass analysis in either the ion trap or ultra-high resolution Orbitrap mass analyzer.

The Orbitrap IQ-X Tribrid MS ion path schematic

Throughout the Orbitrap IQ-X Tribrid MS, best-in-class technologies deliver solid results. The Auto-Ready ion source standardizes calibration with dedicated hardware to support consistent performance over time. The Thermo Scientific EASY-IC ion source uses a second ion source to generate specific calibrant ions to provide real-time adjustment of the instrument’s mass accuracy to less than 1 ppm, enabling corrections for scan-to-scan variations and superior mass accuracy. The advanced quadrupole technology includes a segmented quadrupole mass filter which enables higher transmission at narrower isolation width down to 0.4 m/z, improving sensitivity and selectivity. The ultra-high field Orbitrap analyzer can achieve resolutions up to 500,000 at m/z 200 distinguishing between ions of interest and interfering ions with optional resolving power up to 1,000,000 (1M) resolution for fine isotope structure. The dual-pressure linear ion trap provides MSⁿ rates of up to 45Hz and sensitive mass analysis of three complementary fragmentation types: CID, HCD and optional UVPD.

Real-Time Library Search enables on-the-fly spectral matching for higher confident identification

Real-Time Library Search technology provides on-the-fly spectral searching against a local and customizable mzVault library to allow for decision-based triggering of MSⁿ scans. Using this intelligent technique increases confidence in metabolite identification and characterization and improves structural analysis of isomeric species. 


The Met-IQ data acquisition specifically uses Real-Time Library Search technology to enable selective detection and characterization of unknown compounds that are structurally related to known compounds, such as drug metabolites to pro-drugs.

AcquireX data acquisition technology for more meaningful data

The AcquireX workflow captures more low-abundance analytes with an integrated suite of software analysis tools to improve small-molecule structural elucidation identification. Using the AcquireX data acquisition tool significantly streamlines the workflow, reducing bottlenecks and making both identification and characterization faster and more feasible.

AcquireX data acquisition supports five workflows to maximize flexibility for your experiments. Data acquisition options enable rapid profiling across multiple samples and exhaustive sample interrogation through replicate injections. Each method improves the quality and the number of compounds sampled with distinguishable fragmentation spectra for sample and study characterization.

AcquireX Intelligent Data Acquisition Workflow

Download this Smart Note to learn the ways in which AcquireX data acquisition can help you address the challenges of small-molecule study and characterize your samples with fragment-rich spectral data while improving lab efficiency.

Enabling software and tools for mass spectrometry data analysis

Combining Real-Time Library Search with AcquireX data acquisition workflows and other enabling tools delivers a dramatic reduction in the number of compounds without MSⁿ spectra and a significant increase in the number of compounds identified. Using Thermo Scientific Compound Discoverer software in combination with a range of spectral libraries (Thermo Scientific mzCloud mass spectral fragmentation library), compound databases, and ranking tools (Thermo Scientific mzLogic algorithm) significantly aids identification and characterization of unknowns. The use of spectral library fragmentation information and structural databases provides higher confidence in assignments for more compounds in less time.

Compound Discoverer software extracts insights from information-rich small-molecule HRAM data

Compound Discoverer mass spectrometry data analysis 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

Learn more about how we address the challenges in small-molecule identification with mass spectral libraries. The mzCloud spectral libraries and Thermo Scientific mzVault software are designed to address the challenges of small-molecule identification for routine and research applications.

Mass spectral libraries and ranking tools

The mzCloud compound databases and mzLogic algorithm ranking tools aid unknown putative identification to help you find answers quickly and drive decision making. The tools are readily available online and comprise an extensive mass spectral fragmentation library as well as structural databases.

Mass Frontier spectral interpretation software

Thermo Scientific Mass Frontier software supports MSⁿ spectral ion tree searching and enables custom library creation. The software utilizes high quality, fully curated experimental spectral and fragmentation libraries to provide greater insights, understanding, and confidence when turning your data into actionable knowledge.

Compound annotation using MSⁿ data

Compound annotation using high-quality MSⁿ data provided by the Orbitrap IQ-X Tribrid mass spectrometer combines precursor ion fingerprinting with substructure analysis of unknown metabolites to address common bottlenecks in compound identification. Additional tools available for LC-MS-based structure elucidation include MSⁿ mass spectral trees and in-silico fragmentation.

The above image shows comparative MS/MS spectra for two flavonoid structural 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 that prohibit 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 that result in a clear definition of the two isomeric compounds.

Remote monitoring and Connect Cloud Platform

Remotely access and manage your system with Almanac Instrument Monitoring

Monitor your mass spectrometry analyses anywhere, anytime using the Thermo Scientific Almanac web- and smartphone-based application. 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.

Connect your laboratory to drive more insights from your data

Thermo Fisher Connect Platform is part of our full suite of digital capabilities for secure, cloud-based data storage, scientific analysis apps and peer collaboration tools. In addition, our asset management tools allow you to remotely schedule time on your lab’s instruments and monitor your run via your mobile device.

Using Thermo Fisher Connect, it’s easy to connect, save and synchronize your files to your secure, personal account, which includes 1 TB of free storage. Peer and document collaboration tools enable secure group collaboration.

Small-molecule characterization and identification clouding your decision making?

Learn more about how cloud-based technologies, including mass spectrometry analysis software, are becoming more prevalent in laboratories.



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