Author Archives: Tim Stratton

Compound Discoverer 2.1 Released! Get your Demo here.

For current Compound Discoverer 2.0 users:
The electronic upgrade to Compound Discoverer 2.1 is free! Follow the download instructions below and use the instructions for the CD 2.0 to CD 2.1 upgrade.

For new users:
To download the Compound Discoverer 2.1 Demo (CD 2.1 demo), go to the Thermo Scientific Software Portal (Flexera) and download it from the “Compound Discoverer 2.1 Demo” folder.


Click here for full instructions.

Compound Discoverer at ASMS 2017

Thanks to everyone who was able to join us at this years Compound Discoverer Users Meeting and parallel Node Developer Workshop at ASMS this year!

We’ve already heard great feedback from several people and, because of that, we plan to make these meetings a regular occurrence and improve them even more in the future.

— The Compound Discoverer Team

mzCloud in Compound Discoverer 2.0


Compound Discoverer now supports batch searching against the mzCloudTM spectral library ( in version 2.0!

Click here for more.

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