Author Archives: Tim Stratton

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.

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