Discovery Proteomics

Discovery Proteomics

Accurately detect, identify, and measure proteins differentially expressed in disease states and biological, metabolic, and signaling processes with Waters flexible discovery proteomics solutions. Waters helps scientists obtain high quality results to confidently understand the functional role of proteins to feed the proteomic translational pipeline.

Accurately detect, identify, and measure proteins differentially expressed in disease states and biological, metabolic, and signaling processes with Waters flexible discovery proteomics solutions. Waters helps scientists obtain high quality results to confidently understand the functional role of proteins to feed the proteomic translational pipeline.

Overview

Discovery proteomics helps scientists understand the important functional roles these complex macromolecules play. Accurately identifying proteins differentially expressed in disease states can be potentially translated to functional biomarkers. Proteomics is also an important component of systems biology approaches, and multi-omics analysis helps validate findings to better understand metabolic and signaling processes.

To more accurately understand the proteome, Waters pioneered Data Independent Acquisition (DIA) strategies to improve the quantitative analysis of ‘bottom-up’ non-labeled proteomics methods while generating peptide fragment spectra for all detectible species. With Waters high resolution mass spectrometry technologies, high peak capacity chromatography systems, Progenesis Software, and DIA methods, your lab can dig even deeper into the proteome.

Applications

Accurate identification of the proteins differentially expressed in disease states can be potentially translated to functional biomarkers given appropriate validation studies. Learn about Waters expertise with protein biomarker discovery with these application notes.

Accurate identification of the proteins differentially expressed in disease states can be potentially translated to functional biomarkers given appropriate validation studies. Learn about Waters expertise with protein biomarker discovery with these application notes.

Application Notes

White Paper: Considerations for Selecting the Optimal Stationary Phases for Proteomic Trap-and-Elute Nanochromatography

Understand the importance of selecting a relevant nanocolumn and trap while developing a trap-and-elute nanoLC method. This white paper sheds light on how Waters nanoEase m/z Nanocolumns and Traps deliver unsurpassed chromatographic resolution, enabling seamless integration to alleviate challenging analyses in the laboratory.

Understand the importance of selecting a relevant nanocolumn and trap while developing a trap-and-elute nanoLC method. This white paper sheds light on how Waters nanoEase m/z Nanocolumns and Traps deliver unsurpassed chromatographic resolution, enabling seamless integration to alleviate challenging analyses in the laboratory.
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Solutions

Waters LC-MS systems offer absolute performance in separation and sensitivity for discovery proteomics workflows.

Ultimate power, ultimate performance. Redefine the boundaries of science.

Ultimate power, ultimate performance. Redefine the boundaries of science.
SELECT SERIES Cyclic IMS

Combine novel cyclic ion mobility separation with state-of-the-art high performance, time-of-flight mass spectrometry with SELECT SERIES Cyclic IMS to extend the benefits of routine ion mobility and achieve variable, high-resolution separations.

  • Protein Biomarker Discovery

Without discovery, decisions are made in the dark.

Without discovery, decisions are made in the dark.
SYNAPT XS High Resolution Mass Spectrometer

Obtain ultimate flexibility to support scientific creativity and technical success for discovery metabolomics applications with SYNAPT XS, for cutting-edge analytical performance with SONAR and HDMSE to interrogate complex mixtures.

  • Protein Biomarker Discovery

Let your LC inlet do the work for your nano- to micro-scale separations.

Let your LC inlet do the work for your nano- to micro-scale separations.
ACQUITY M-Class System

Achieve the sensitivity of micro- and nanoflow liquid chromatography with UPLC technology when you equip your lab with the ACQUITY UPLC M-Class System, delivering the usability of an analytical-scale UPLC system.

  • Protein Biomarker Discovery

Expand the dynamic range of your analysis with 2D separations.

Expand the dynamic range of your analysis with 2D separations.
ACQUITY UPLC M-Class System with 2D Technology

Streamline the 2D-LC separation process with the ACQUITY UPLC M-Class System with 2D Technology that offers highly intuitive menu-driven method setup, standardized separation chemistries, and intelligent valve operation for better chromatographic resolution of complex proteomic samples.

  • Protein Biomarker Discovery

Waters software streamlines data acquisition, processing, and reporting discovery proteomics analysis results.

Discover the changing proteins in your samples

Discover the changing proteins in your samples
Progenesis QI for Proteomics

Discover the presence of proteins in your complex samples using label-free analysis with Waters Progenesis QI for Proteomics. Evaluate the quality of your LC-MS data with quality control (QC) metrics using highly visual guided workflows.

  • Protein Biomarker Discovery

Quality consumables to support your success. 

Enhance the quality of in-solution enzymatic protein digestions 

Enhance the quality of in-solution enzymatic protein digestions 
RapiGest SF Surfactant

Overcome MS compatibility and time-consuming proteolytic digestion issues with Waters RapiGest SF Surfactant, enabling same-day digestions and simplified analysis to radically enhance your testing efficiency.

  • Protein Biomarker Discovery

Benchmark and validate your protein columns with ease 

Benchmark and validate your protein columns with ease 
Protein Standards

Run your protein analysis easily and confidently with Waters Protein Standards, prepackaged in Waters vials, and allow direct solubilization while minimizing sample loss and discrepancies. 

  • Protein Biomarker Discovery

Generate high-quality peptide and protein separations

Generate high-quality peptide and protein separations
Nano and MicroFlow LC-MS Columns

Reproducibly generate peptide and protein separations with Waters Ethylene-Bridged Hybrid (BEH), Charged Surface Hybrid (CSH), and High Strength Silica (HSS) peptide and protein nano columns for highly efficient separations with an increased number of peak identifications.

  • Protein Biomarker Discovery

Your success is just a click away

Your success is just a click away
Waters Global Services

Optimize your laboratory's productivity and success with Waters Global Services to maintain peak system performance, minimize down time, address application challenges, and support stringent compliance requirements.

  • Protein Biomarker Discovery

Make science more accessible with Waters Capital

Make science more accessible with Waters Capital
Payment Solutions

Maximize resources and minimize risk with payment options from Waters Capital, including upgrading aging equipment, getting customized support, and bundling services into one monthly payment.

  • Protein Biomarker Discovery

The data speaks for itself

The data speaks for itself
Multivariate statistical analysis of the high throughput proteomic data. Unsupervised principal component analysis (A) shows clear separation between healthy controls and breast cancer subjects. The corresponding heatmap (B), highlights clear regions of differential protein expression between the two cohorts. The under- and over-expression of ApoA2 and LRG1, respectively, are provided as examples (C). The box-whisker plots indicate significant differences and tight  conservation of the data within each group.
Fragment ions overlapping on the m/z scale but which exhibit different charge states (1+ and 2+) can be separated by IMS. As can be seen, the singly charged ion is much smaller in the no WE spectrum. When using WE, ions of different charge states can be extracted, effectively removing interferences, and then be identified with more confidence in subsequent database searches.
Sequence Coverage reproducibility for 12 E. Coli proteins, 5% CVs are routinely observed.
Protein overview for the three cohorts. Venn diagram indicates that most of the proteins overlap between conditions (A), while box-whisker plots show the technical reproducibility of the SONAR technique in terms of %CV (B) and protein sequence coverage (C).

Webinars and Resources

  • Brochure

The SELECT SERIES Cyclic IMS

The SELECT SERIES Cyclic IMS
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Learn more about Waters Discovery Proteomics.

Learn more about Waters Discovery Proteomics.
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