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Accelerating ScienceAnalyteGuru / Metabolomics / Why Compound Discoverer 3.4 Software is Worth Your Attention!

Why Compound Discoverer 3.4 Software is Worth Your Attention!

By Zoe Julian, Product Marketing Manager for software, Thermo Fisher Scientific 06.24.2025

Have you explored what’s new in Thermo Scientific Compound Discoverer software, version 3.4?

In case you missed it, earlier this year we released version 3.4 – bringing new capabilities to small molecule researchers. Get ready to elevate your compound identification and analysis experience with this new version packed with groundbreaking features and enhancements.

Here’s a look at some of the key updates and why you should be excited:

1. LipidSearch (MKI) is now integrated

The new LipidSearch (MKI) node simplifies lipid identification, making it faster and more accurate. And here’s the best part: you don’t need to install separate software!

2. Improved quality control for small molecule experiments

A new QC node leverages internal standards to automatically detect and group in-source fragments, ensuring accurate and reliable results.

3. Improved compound identification

Connect to the latest version of the mzCloud Spectral database (2.0), which includes over 16.5 million spectra, 32,000 MSn trees and extensive metadata such as compound classes and CAS numbers. Providing deeper insight and better identification confidence.

4. Performance boost

Experience up to 8x faster processing speeds for various nodes, including alignment, detecting compounds, fill gaps, and mzLogic, ensuring that your data analysis is completed in record time.

5. New spectral library and mass list parameters

Now, you can use different sets of parameters for various spectral libraries or mass lists, allowing for precise matching and prioritization.

6. Smarter feature detection and component assembly

Separate feature detection and component assembly for greater flexibility and performance. New nodes streamline the creation of grouped feature tables and efficiently group ions and in-source fragments.

7. New molecular networking capabilities

Inject seed compounds (a compound of interest that is not present in the data set) into your molecular networks to form clusters with related compounds, helping you interpret complex networks more effectively. This feature is particularly useful for PFAS-related studies!

8. Seamless Integration with the Thermo Scientific Ardia Platform

Connect to the Ardia Platform for direct raw data access and result file uploads, streamlining your workflow and enabling easy sharing of result files!

Excited to learn more?

Take a look at our webinar where we dive deep into these new features and demonstrate how Compound Discoverer 3.4 Software can elevate your workflows, including pesticides.   

Stay ahead with Compound Discoverer Software —where innovation meets precision!

Visit us on LinkedIn: #CompoundDiscoverer #SmallMolecules #Software

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Zoe Julian

Zoe Julian is a Product Marketing Manager for Chromatography and Mass Spectrometry software at Thermo Fisher Scientific. With over 12 years' experience of working with chromatography and mass spectrometry techniques with a background in GC and GC-MS(/MS) organic environmental analysis, she has helped many laboratories and industries improve their workflows through a unique understanding of their challenges. Transitioning to a focus on Chromeleon CDS she has shown customers how software solutions can improve their productivity and support their day-to-day operations.
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