The complete small molecule identification and characterization solution

Integrated solutions for small molecule research

Elevate your small molecule mass spectrometry research with Thermo Scientific Compound Discoverer 2.1 software, which offers a full suite of tools to address small molecule differential analysis, identification, and pathway mapping. Our latest version of Compound Discoverer features retention time alignment, unknown peak detection, statistical tools and visualizations, integrated compound identification, ChemSpider, and an automated mzCloud library search. It is also the only analysis software that fully utilizes data generated by high-resolution accurate-mass Thermo Scientific Orbitrap mass spectrometers.

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See how it works

Compound Discoverer 2.1 solves challenges in different research fields

Metabolomics Environmental and food safety Pharma MetID Forensic toxicology
Calculate statistical differences between multiple sample sets. Identify impurities, metabolites and degradation products in complex samples. Analyze the metabolic fate and structural composition of food impurities and degradation products. Detect environmental contaminants in soil and water. Identify related components in biological samples and determine their structures to quickly isolate metabolites of interest.

Detect unknown metabolites of drugs of abuse and structurally related designer drugs.

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Benefits of Compound Discoverer 2.1 software

Enable fast component identification

Identify compounds using the mzCloud online fragmentation library without leaving the Compound Discoverer software platform. Couple your analysis with molecular weight or formula-based ChemSpider or user-created database searches.

Simplify your labeling and annotation

Automatic annotation of relevant components enables modification sites to be quickly located using color-coded MS2 and MSn fragments. This simplifies the determination of metabolite structures, impurities, degradents, and related components.

Determine statistical significance

Take advantage of interactive visualization options, including principal component analysis (PCA) scores, loading and trend plots, differential “volcano plots,” partial least square discriminant analysis (PLS-DA) S-plot, and study-wide biological pathway maps.

Customize data processing

Take control of your data processing with custom workflows, flexible visualization, grouping tools, and interactively linked displays. Visualize trends quickly and identify peaks of interest throughout multiple sample groups. Determine which comparisons and statistical analyses will be performed later.


Compound Discoverer – What are the benefits of upgrading?

What are the benefits of upgrading from 2.0 to 2.1?

  • Improved identifications: elemental composition prediction based on fine isotopic pattern (MS1) and MS/MS, mzVault local library search and mzCloud similarity search
  • QC-based area correction at the compound level
  • Automatic compound annotation and batch FISh Scoring on all structure proposals (i.e., all ChemSpider hits) for an unknown compound
  • New nodes for searching BioCyc and Compound Class Scoring (flags and scores unknown compounds based on common fragments)

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Contact us

We’re here to help you maximize your free trial of Compound Discoverer software. Contact us if you would like more information on how to use it, or if you’d like to have a representative contact you.

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