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Compound Discoverer & Proteome Discoverer Users Meeting 2019

The registration is now open for our annual Users Meeting in Germany. We are looking forward to see you in Bremen!


Compound Discoverer 3.1 released

Compound Discoverer 3.1 has just been released!  New features include :

  • Molecular Networks to interactively explore relationships between compounds based on transformations and spectral similarity
  • Scripting node to embed scripts—for example, Python or R scripts—in workflows
  • Mass Defect Plot for Compounds and Expected Compounds
  • Search mzCloud node:
    • Supports automatic searches of multiple spectral libraries
    • Supports the new “Autoprocessed” mzCloud library
    • Displays the fragment structure for matching peaks

Download a free demo from here.

Compound Discoverer Users meeting at ASMS


Registration for the Compound Discoverer Users meeting at ASMS 2019 is now open.

Updated E&L Unknown Workflow Templates Due To Recent ChemSpider Change

ChemSpider recently removed PubChem as a data source. Therefore, PubChem is no longer available in the Search ChemSpider node.

Please click links below to download the updated E&L unknown workflow templates:
CD 3.0: Resources – CD 3.0 page
CD 2.1: Resources – CD 2.1 page
CD 2.0: Resources – CD 2.0 page

Compound Discoverer 3.0 wins Innovation Award


We are very happy that Compound Discoverer 3.0 was named among the Top 15 Innovations of 2018 by The Analytical Scientist  !

Compound Discoverer 3.0 released

Compound Discoverer 3.0 has been released!

Some of the major new features added in Compound Discoverer 3.0 include:

  • Untargeted stable isotopic label analysis (isotopic or metabolic flux analysis).
  • mzLogicTM algorithm – a new approach to rank order chemical database putative candidates leveraging the >2 million real reference spectra from mzCloud.
  • Partial reprocessing of workflows
  • MetabolikaTM pathways

Download a free demo from here.

For more information, brochures and videos please also visit

Proteome Discoverer & Compound Discoverer Users Meeting 2018

Registration is now open for our annual Users Meeting in Bremen!



Service Pack (SP1) Released for Compound Discoverer 2.1!

For current Compound Discoverer 2.1 users:
To download the service pack, log into Flexera and download the service pack and installation instructions from TMO-Prospects account | Demo | Compound Discoverer 2.1 SP1 Upgrade From 2.1.

For current Compound Discoverer 2.0 users:
The electronic upgrade to Compound Discoverer 2.1 SP1 is free! Log into Flexera and download 2.1 SP1 from TMO-Prospects account | Demo | Compound Discoverer 2.1 SP1 Demo and Upgrade From 2.0.

For current Compound Discoverer 1.0 users:
Contact your Thermo sales person to purchase the Compound Discoverer 2.1 SP1 Upgrade From 1.0. To try out the 2.1 SP1 demo version for 60 days, use the instructions for new users below.

For new users:
To download the Compound Discoverer 2.1 SP1 Demo (CD 2.1 SP1 Demo), go to the Thermo Scientific Software Portal (Flexera) and download it from the “Compound Discoverer 2.1 SP1 Demo and Upgrade From 2.0” folder. Use the instructions for CD 2.1 SP1 Demo.

Click here for full instructions.

mzCloud in Compound Discoverer 2.1


Compound Discoverer now supports batch searching against the mzCloudTM spectral library ( including spectral similarity searching in version 2.1! Increase the structure information available for structure interpretation of previously unidentified compounds.

Click here for more.

Three New Tutorial Quick Videos Are Available For Viewing

Three new tutorial quick video have been added:
1. Use Custom Explanations to elucidate structure and run FISh Scoring on the fly for expected or unknown compounds.
2. How to correlate specialized traces (UV, PDA, analog traces or pattern traces) to MS peaks.
3. How to report manual peaks with correlated MS peaks.