Register for the Compound Discoverer Users Meeting and CD/PD Node Development Workshop on June 2nd at ASMS 2018

Registration for the Compound Discoverer Users meeting and the CD/PD Node Development Workshop is now live.   These workshops run in parallel, so remember to register for only one.

Click here to register.

Registration is first come first serve, so register soon.

Compound Discoverer Users Meeting and Node Workshop on June 2nd at ASMS 2018

The Compound Discoverer User Meeting and Node Workshop at ASMS 2018 will be on Saturday, June 2nd. More details including registration page will come later. Please note: the node workshop is for developers and by invite only! Thank you for your interest!

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.

Welcome to Compound Discoverer

We’re excited to share the latest evolution of Thermo Fisher Scientific Compound Discoverer with the new version 2.1 (CD 2.1), our unique application for small molecule research applications in LC- HRAM MS. With Compound Discoverer 2.1 we’ve continued to improve and added even more capabilities for both “known parent” and “unknown parent” (untargeted) analysis.

In Compound Discoverer 2.1 we’ve added or improved features relevant to all applications.  Here’s just a few of the improvements or additions you’ll see in CD 2.1:

  • Easily generate potential transformation products from multiple starting compounds at once.
  • Addition of both Similarity searching and handling of stepped collision energy searching in mzCloud!
  • New normalization capabilities – Pooled QC Normalization.
  • Enhanced elemental composition calculation utilizing both very high resolution MS1 and MS/MS fragmentation data.
  • Better user control of compound annotation
  • Make better use of database matches with in silico fragmentation ranking of hits.
  • Connectivity to BioCyc for pathway visualization
  • Search local fragmentation spectral libraries in mzVault.


On this site, you will find several training and quick start videos to help you get going with Compound Discoverer 2.1 as well as options to provide feedback and get additional help with questions you may have.


– The Compound Discoverer Team

Compound Discoverer at ASMS 2018

We’re happy to announce that we will again be hosting a pair of day long training events at ASMS 2018. These two parallel sessions will allow attendees to learn more about Compound Discoverer.  Watch here for more on how to register for one of the sessions as we get closer to ASMS

– The Compound Discoverer Team

Thermo Scientific Compound Discoverer Software Users’ Meeting
Discover powerful new features in Compound Discoverer 3.0 software.  Hear from distinguished guest speakers who will discuss their experiences with Compound Discoverer software.  Get training on using the tools in Compound Discoverer for advanced workflows in a wide range of applications.

Thermo Scientific Compound Discoverer and Proteome Discoverer Software Node Development Workshop
This is a great opportunity to learn how to create your own processing nodes for use in the Discoverer platform.  Meet our software developers and get your most vexing questions answered in a day long developer workshop.


New Tips and Posters for CD 2.1

Check out the new content available under Resources → CD 2.1 to find links for recent posters using Compound Discoverer 2.1 and for quick tips.

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.