Category Archives: Uncategorized

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.

New Tutorial Quick Video on “How to copy a structure from Related Structures table and save as .mol file”.

New tutorial quick video is now available on how to copy a structure from Related Structures table and save as a .mol file.

New Tutorial Quick Video on Data Processing nodes

View the new tutorial quick video on Data Processing nodes including the Mass Defect Filter node and Retention Time Aligner node.

New Resources Page

New Resources page where you can download or view scientific posters, application notes and presentations highlighting the use of Compound Discoverer for various small molecule research applications.

New Tutorial Video on Connection to mzCloud

View the new quick tutorial video on how to copy a spectrum in Compound Discoverer and paste into mzCloud for compound ID.

New tutorial video on the example study

View the new tutorial video on the example study. The example study is located on the Compound Discoverer 1.0 software media. This video will walk you through setting up study, setting up a node based processing workflow, running analysis on a sample group, results review and generating report.