New Omics Research Platform Solution from Waters, powered by Nonlinear Dynamics

This post refers to the TransOmics™ Informatics range of software, which has since been superseded by the Progenesis QI range, which represents the merging of Waters’ TransOmics™ Informatics into Nonlinear Dynamics’ existing Progenesis software. All of the features described, however, remain relevant. A fuller description of the new products can be found here.


The Nonlinear Support Team

After several months working behind the scenes it is exciting to be able to share with you that Waters Corporation and Nonlinear Dynamics are working towards an exclusive OEM agreement, which would provide a new ‘Omics Research Platform Solution for Waters’ customers. The news was announced as part of Waters’ press briefing at the 60th ASMS Conference in Vancouver, Canada.

While we continue to develop and support the Progenesis™ range of software for our own customers, the final OEM agreement will combine Waters expertise in instrumentation with ours in data analysis software. The result? A new research platform solution for users of ACQUITY®/nanoACQUITY UPLC® separations and the SYNAPT® G2-S HDMS™.

Waters’ innovations in data-independent LC and ion mobility mass spectrometry (IMS) allow you to generate a comprehensive data set, in a single experiment, from very complex samples. This data can be mined exhaustively and repeatedly over an extended period. Our contribution is in providing the informatics element necessary to analyse and visualise these data sets.

Together with Waters we are working on two new products. The first, called Waters TransOmics™ Informatics for Proteomics, would combine features of Progenesis LC-MS and ProteinLynx™ Global SERVER 3.0 for HDMS data. The second, Waters TransOmics™ Informatics for Metabolomics, would combine features of Progenesis CoMet and MarkerLynx™ XS for HDMS data.


The collaboration will provide the Omics Research Platform Solution for relative quantitative analysis
across both proteomics and metabolomics discovery research.

Latest UPLC/MS technology combined with cutting-edge informatics

The UPLC®/IMS/MSE or ‘data independent’ mode of acquisition provides unprecedented duty cycle, peak capacity and dynamic range to profile either proteins or metabolites. In addition, ion mobility can separate two co-eluting peptides of similar mass thus preventing co-fragmentation. This eliminates mixed-spectra and increases the number of ‘searchable peptide spectra’. The result is comprehensive quantitative AND qualitative data from the same experiment.

HDMSeUPLC CSH C18/MSE separation in positive electrospray ionization mode from rat plasma lipid extract. Co-eluting chromatographic peaks are further separated by ion mobility, which both simplifies and enhances lipid identification

The TransOmics™Informatics will provide an easy-to-use, common workflow for relative quantification and identification of metabolomics or proteomics data generated by this latest MS-technology. It incorporates many of the features developed for Progenesis™, already in use today, including:

  • Peak modelling and ion intensity maps displayed during data import
  • Precursor ion alignment algorithm and co-detection
  • Complete datasets containing no missing values that allow you to get reliable results from multivariate statistical tools such as the PCA, Correlation Analysis and Power Analysis included
  • Ability to compare any number of groups within the same experiment
  • MS/MS spectra can be identified by MASCOT with identifications automatically associated with quantified precursor ions and quantify at the protein level
  • Compatibility with Thermo, Agilent, ABSciex and Bruker data

However, features unique to The TransOmics™ Informatics include:

  • Analysis and visualization of large-scale ion mobility data
  • Ability to measure Hi3 absolute quantification as part of the proteomics workflow


Example of visualising ion mobility mass spectrometry separating two co-eluting peptides of similar mass  as part of the TransOmics™ Informatics workflow.

To find out more about the new Omics Research Platform Solution you can visit Water’s website.

Solutions for the future

The new Waters Omics Research Platform Solution is designed to facilitate relative quantitative analysis across multiple discovery areas. This is the first step towards building knowledge of the interplay between molecules at the protein, metabolite, and lipid levels.

This is essential to understand the underlying biology of an organism or a specific disease state for researchers in the pharmaceutical and life sciences, food, and clinical research areas. So, this has the potential to support ‘omics researchers across many fields into the future.

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