SYNAPT XS

SYNAPT XS 

Ultimate flexibility for deeper discovery

Ultimate flexibility for deeper discovery

In the arena of scientific discovery, the slow pace of advancement and escalating costs of research can prove to be a challenge. Unlike competitor systems with restricted inlet options, scan function limitations, or requiring multiple platforms, only Waters offers an all-encompassing high-performing LC-MS solution, the SYNAPT XS mass spectrometer, for ultimate flexibility and greater freedom of analytical choice – supporting scientific creativity and technical success for any application.

  • Novel technology building blocks deliver cutting-edge analytical performance
  • SONAR and HDMSE provide a unique toolkit for interrogating complex mixtures
  • Ion mobility multiplies peak capacity and selectivity of analysis
  • CCS measurements increase security of compound identification
  • Deeper discovery in Mass Spectrometry Imaging with Full Spectrum Molecular Imaging enabled by DESI XS and MALDI
The Waters SYNAPT XS offers flexibility and freedom of analytical choice with an extensive range of chromatographic inlets. SYNAPT XS

Overview

  • Serve the broadest range of applications with the most extensive range of chromatograph inlets for ultimate flexibility 
  • Attain fragment ion information for every detectable component for unambiguous confirmation of compound identity with DIA modes SONAR, MSE, and HDMSE 
  • Generate rich fragmentation data from highly complex samples in all acquisition modes including DDA
  • Simplify and streamline the mass spectral imaging workflow and deliver multi-layered, information-rich data with multiple imaging techniques and accompanying High Definition Imaging (HDI) Software
  • Achieve automated higher order structure determination thorough confident identification, intact mass analysis, and best-in-class reproducibility
  • Enhance MS/MS possibilities using complementary fragmentation techniques with high resolution and accurate mass measurements

Recommended Use: For deeper discovery by aligning complimentary workflows on a single Ion mobility enabled time-of-flight mass spectrometer with the flexibility of multiple ion sources and acquisition modes.

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Cutting edge performance with novel technology

With technology building blocks inherited from the Waters Advanced Mass Spectrometry SELECT SERIES, advanced innovation is built-in, ensuring scientists using this platform are at the cutting edge of mass spectrometry while retaining the ease of use and established end-to-end workflows for which the SYNAPT is well known.

  • StepWave XS - Redesigned segmented quadrupole transfer optics provide enhanced sensitivity for challenging compounds while further improving levels of analytical robustness.
  • Extended ToF - Delivers UPLC-compatible mass resolution, matrix-tolerant dynamic range, and quantitative results for the most complex samples, while offering superior specifications to previous SYNAPT models.

Interrogate complex mixtures with a unique toolkit

A complete analytical strategy requires the combination of appropriate complementary techniques to see the bigger picture. With both SONAR and IMS-based data independent acquisition (DIA) modes of operation on the SYNAPT XS, the discovery analyst is in a unique position to interrogate complex mixtures by complementary mechanisms. Both types of acquisition increase analytical peak capacity, providing ‘clean and clear’ fragmentation data, but based on different molecular properties. This provides a truly unique investigative toolbox for the in-depth interrogation of complex mixtures.

Discover more with ion mobility and CSS measurement

Conventional mass spectrometers separate components based on m/z. The SYNAPT XS also allows separation of molecules according to their size, shape, and charge during ion mobility experiments as a function of their collisional cross section (CCS). As well as ion mobility offering an additional dimension of resolution, multiplying peak capacity, and selectivity of analysis the measurement of CCS offers additional molecular identifiers. The measured CCS of an ion can be used to help confirm an ion’s identity or investigate its structure. The inclusion of ion mobility significantly increases the extent and confidence with which a scientist can profile complex mixtures and complex molecules – dramatically enhancing sample definition.

Achieve ultra-confident structural characterization of components

Time aligned parallel (TAP) fragmentation is an acquisition mode unique to the T-Wave IMS design. It permits users to take the advantage of the TriWave configuration, which allows the pre-IMS T-Wave and post-IMS T-Wave to operate as two separate collision cells. The resultant CID-IMS-CID instrumental operation helps to provide ultra-confident structural characterization of components. TAP fragmentation provides a distinct advantage for building a complete structure, through superior fragment ion coverage, sensitivity, and accuracy compared to traditional MSn or MS/MS techniques.

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Obtain chemical information directly from a wide range of surfaces with Desorption Electrospray Ionization (DESI) mass spectrometry imaging with the DESI XS, a breakthrough MS ion source.

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SYNAPT XS

The SYNAPT™ XS is a high-resolution, ion mobility-enabled mass spectrometer designed to empower scientific discovery with unmatched analytical flexibility. Built for laboratories that demand deeper insight from increasingly complex samples, the SYNAPT XS combines advanced acquisition modes, ion mobility separation, and broad inlet compatibility into a single, integrated platform. It is ideally suited for discovery-driven applications across omics, structural biology, pharmaceutical development, materials science, and mass spectrometry imaging.

At the heart of the SYNAPT XS is the flexibility to adapt to any analytical challenge. The system supports an extensive range of chromatographic inlets and multiple ionization sources, allowing users to align complementary workflows on a single instrument. From LC-MS to imaging techniques like DESI XS and MALDI, the SYNAPT XS seamlessly transitions between methods—enhancing productivity and extending application reach.

Key performance technologies include StepWave™ XS, a redesigned segmented quadrupole transfer optic that delivers enhanced sensitivity and robustness for challenging compounds, and the Extended Time-of-Flight (ToF) analyzer, offering high resolution, broad dynamic range, and accurate quantitation. Inheriting innovation from Waters' SELECT SERIES, the SYNAPT XS ensures top-tier analytical performance while retaining the ease of use and workflow familiarity the SYNAPT line is known for.

For in-depth sample interrogation, the SYNAPT XS offers both SONAR™ and HDMSE (high-definition MSE) acquisition modes—delivering clean, unambiguous fragmentation data even from complex mixtures. These data-independent acquisition (DIA) modes allow for fragment ion generation of every detectable component, increasing confidence in compound identification and significantly boosting peak capacity and selectivity.

A key differentiator of the SYNAPT XS is its integration of ion mobility separation, which introduces an additional dimension of molecular resolution by separating ions based on their size, shape, and charge. This enables scientists to multiply analytical peak capacity, separate co-eluting species, and measure collisional cross-section (CCS) values to improve structural insight. CCS values act as molecular fingerprints, supporting the confirmation of compound identity and structural characterization in a way not possible with mass-to-charge (m/z) separation alone.

Further extending structural analysis capabilities, the SYNAPT XS offers Time-Aligned Parallel (TAP) Fragmentation, a mode enabled by its unique TriWave configuration. TAP fragmentation utilizes both pre- and post-ion mobility collision cells to generate highly informative fragment ion data, allowing users to build complete structural profiles of components with greater sensitivity and specificity than traditional MS/MS or MSⁿ techniques.

Designed for scientists who need to extract maximum information from every sample, the SYNAPT XS enables high-definition mass spectrometry imaging, detailed mixture profiling, and advanced structure-function studies—all within one platform. With its modular architecture, exceptional data quality, and wide-ranging application compatibility, the SYNAPT XS is built to accelerate the pace of scientific discovery while supporting the creativity and adaptability of modern research demands.

FAQs

What types of samples and applications is the SYNAPT XS best suited for?
The SYNAPT XS is designed for research environments that require detailed analysis of complex or information-rich samples. It is well suited for omics applications (proteomics, metabolomics, lipidomics), pharmaceutical R&D, biotherapeutic characterization, structural biology, materials science, and mass spectrometry imaging. Its broad inlet compatibility and high-resolution ion mobility separation make it especially valuable for samples with co-eluting or structurally similar components. The system's ability to generate accurate mass and fragmentation data across multiple acquisition modes allows researchers to confidently profile unknowns, quantify trace-level compounds, and characterize large biomolecules, all within a single platform.

What are SONAR and HDMSE acquisition modes, and how are they used?
SONAR and HDMSE are advanced data-independent acquisition (DIA) modes available on the SYNAPT XS, offering enhanced capabilities for analyzing complex mixtures. SONAR continuously scans the quadrupole mass range during each acquisition cycle, enabling the separation of co-eluting precursor ions and the generation of cleaner, more confident fragment ion assignments. HDMSE, by contrast, couples traditional MSE acquisition with ion mobility separation, providing an additional layer of resolution by separating ions based on size, shape, and charge before fragmentation. Both modes allow users to collect comprehensive fragment ion data for every detectable component in a sample—without the need for predefined inclusion lists—making them ideal for untargeted screening, structural confirmation, and in-depth sample profiling.

What is Time-Aligned Parallel (TAP) Fragmentation, and why is it important?
Time-Aligned Parallel (TAP) Fragmentation is a unique acquisition mode enabled by the SYNAPT XS's TriWave™ ion mobility configuration. TAP uses both the pre-ion mobility and post-ion mobility collision cells in a coordinated manner, allowing ions to be fragmented before and after ion mobility separation. This configuration improves fragment ion coverage, structural detail, and analytical confidence. By leveraging two collision stages in a single scan cycle, TAP enables scientists to generate complementary fragmentation spectra, revealing more about the structure and connectivity of complex molecules. This mode is particularly valuable for structural characterization, enabling superior performance compared to conventional MS/MS or MSⁿ techniques. TAP is especially useful in applications requiring detailed molecular insight, such as biotherapeutic analysis, natural product characterization, and advanced small molecule research.