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Waters Synapt Ion Mobility QToF Mass Spectrometry

Unleashing the Potential of Ion Mobility Mass Spectrometry with Waters Synapt G2-Si

Mass spectrometry has become an essential technique in a variety of scientific fields, ranging from biotechnology to environmental analysis. As a result, several types of mass spectrometry instruments have been developed to cater to specific needs. One such instrument is the Waters Synapt G2-Si, which combines quadrupole time-of-flight (QToF) mass spectrometry with ion mobility spectrometry (IMS) for advanced analytical applications. In this article, we will explore the unique features and benefits of the Waters Synapt Ion Mobility QToF Mass Spectrometry system.

Ion Mobility Spectrometry: A Versatile Technique

Ion Mobility Spectrometry is a separation technique that measures the mobility of ions in a gas phase under the influence of an electric field. IMS is particularly useful for differentiating isomers and conformers, which can be challenging with traditional mass spectrometry techniques. By combining IMS with QToF mass spectrometry, the Waters Synapt G2-Si offers increased separation power, enhanced selectivity, and improved structural information.

Advantages of the Waters Synapt G2-Si System

The Waters Synapt G2-Si system offers several advantages over conventional QToF mass spectrometers:

a. Enhanced Resolution and Sensitivity: The Synapt G2-Si features an advanced ion mobility cell, which provides higher resolution and sensitivity compared to previous generations of ion mobility mass spectrometers.

b. Improved Structural Information: Ion mobility separation enables researchers to obtain detailed structural information about analytes, such as conformational changes, isomer differentiation, and molecular interactions.

c. Faster Data Acquisition: The Synapt G2-Si's rapid data acquisition capabilities allow for the efficient analysis of complex samples, saving valuable time and resources.

d. Versatility: The system can be used in various applications, including proteomics, metabolomics, lipidomics, and drug discovery.

Key Applications of Waters Synapt Ion Mobility QToF Mass Spectrometry

The Waters Synapt G2-Si system has found use in a wide range of applications:


Synapt Ion Mobility QToF MS has become an invaluable tool for proteomics research, where it enables the identification, quantitation, and characterization of proteins and their post-translational modifications. Its ability to separate isomeric and isobaric species allows for improved peptide sequence coverage and identification of co-eluting peptides, facilitating in-depth analysis of complex protein mixtures.


In metabolomics, Synapt Ion Mobility QToF MS provides a comprehensive platform for the identification and quantification of small molecules in biological samples. Its sensitivity and selectivity allow researchers to detect low-abundance metabolites, while its high-resolution capabilities enable accurate identification of isomeric metabolites, providing insight into metabolic pathways and disease biomarkers.


Synapt Ion Mobility QToF MS plays a significant role in pharmaceutical research, from drug discovery to quality control. The technology is used to characterize drug candidates, identify impurities and degradation products, and analyze protein-drug interactions. Additionally, its ability to differentiate between isomeric species is invaluable for the assessment of drug stereoisomers and their potential biological activities.

Structural Biology

The Synapt Ion Mobility QToF MS system is well-suited for structural biology applications, including the analysis of protein complexes and their conformations. The ion mobility separation allows for the determination of collision cross-sections (CCS) of ions, which can provide insights into protein structure and folding, as well as the elucidation of protein-ligand and protein-protein interactions.

Complex Mixture Analysis

The combination of ion mobility separation and high-resolution QToF MS makes the Synapt system ideal for analyzing complex mixtures. This includes environmental samples, natural products, and food analysis, where the system can help identify and quantify trace components, contaminants, and potential allergens.

Imaging Mass Spectrometry

Synapt Ion Mobility QToF MS has been successfully employed in imaging mass spectrometry (IMS), enabling the spatial distribution analysis of molecules within biological samples, such as tissues. This technique provides valuable information on molecular localization, helping to elucidate biological processes and disease progression.


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