Author Archives: Ralf Tautenhahn

Compound Discoverer 3.3 released

Compound Discoverer version 3.3 has just been released. New features in this version include:

  • New peak detection algorithm
  • Peak rating calculation and filter
  • New method for retention time alignment
  • Searches entire MSn spectral trees against the mzCloud spectral library
  • Improvements for Molecular Networking, and more.

You can download your trial version of CD3.3 from here.

Second Compound Discoverer™ Webinar Series 2021

Dear Orbitrap users,
We are running a new series of webinars to familiarize our user-base with more functions in Thermo Fisher Scientific™ Compound Discoverer™ software.
The sessions will vary in topics and suitability to your level of experience. You are welcome to register, and forward to your colleagues, in any or all of the sessions below.
Each session is described briefly here and in detail in the registration link. You may directly register via the link provided for each session. You need to fill a short registration form for each session, but you can save your answers and spare a few clicks if you intend to register for more than one session.
The series will be presented by Elizabeth Crawford, Vincent Jespers and Anas Kamleh.

QF1 for Compound Discoverer 3.2

QuickFix 1 for Compound Discoverer 3.2 is now available for download : .

It primarily fixes the problem with invalid structures in the Natural Products Atlas Mass List, which sometimes caused a “Cannot create structure from given MOL string” error.  We also made a small change in the Mass List Editor to make sure we don’t see this problem again with other mass lists.

Willing to improve your knowledge and experience with Compound Discoverer software? These webinars are for you!

Wednesday March 3rd 11.00 CET: Exciting additions to
an exciting software, CD 3.2 update
Go to and register.

Thursday March 11th 10.30 CET: Starting your journey
with Compound Discoverer
Go to and register.

Tuesday March 16th 10.30 CET: Data visualization and
statistical analysis in CD 3.2
Go to and register.

Wednesday March 17th 10.30 CET: Compound
Identification tools in CD 3.2
Go to and register.

Tuesday March 23th 11.00 CET: Acquisition strategies
to get the most out of Compound Discoverer
Go to and register.

Compound Discoverer 3.2 released

Compound Discoverer 3.2 has been released. New features include:

  • Processing capability for GC-Orbitrap data
  • Neutral loss searches
  • Custom tags for annotating and filtering result table entries
  • Support for importing structures from SDF files
  • Support for importing the information for a study from an Excel spreadsheet, including the names and location of the input files, their sample types, and their study factor values.
  • New Apply Missing Value Imputation node that is available as an alternative to the Gap Filling node
  • New Apply SERRF QC Correction node for QC-based correction of batch effects that uses the Systematic Error Removal using Random Forests method described by Fan et al.
  • […] for more details on new features and enhancements please see the Release Notes that come with the software.

Compound Discoverer 3.2 can be downloaded from here.

Virtual Software Workshops

Data to knowledge with extensive Mass spectral library resources – mzCloud combined with Thermo Scientific instrument solutions

19th Nov 1pm ET – Tim Stratton

GC-Orbi, CD: Gain new impactful insights for your analysis with Thermo Scientific GC-Orbitrap MS and Compound Discoverer 3.2 software

30th Nov 1pm ET – Xin Zheng, Jason Cole


Compound Discoverer 3.2 – The Ultimate Toolbox to Analyze Untargeted Metabolomics Data

Compound Discoverer is an integrated software platform to handle all your metabolomics data analysis needs including statistics for comparative analysis, unknown annotations, data visualization, pathway mapping, and stable isotope labeling. In this presentation, we will discuss some of the challenges in metabolomics data analysis and take a closer look at the unique tools and flexible workflows in Compound Discoverer that help streamline the data analysis and get results faster. This presentation also includes a preview of the new features in the upcoming version 3.2.

Oct 2, 2020 12:30 PM CDT at the Virtual Users Meeting

Virtual Mass Spec Users Meeting is Open for Registration

New Scripting Nodes

A couple new scripting nodes can be found here.

  • Adding an m/z column to the Compounds table
  • Adding m/z and Delta Mass [ppm] columns to the Expected Compounds table
  • Calculate O/C and H/C ratios in the Compounds table
  •  Show KEGG IDs (top mzCloud hit) in the Compounds table 

Your feedback and requests for additional scripting nodes are welcome!

Working from home

We appreciate that many people are transitioning to working from home and would like to do what we can to ease that transition. We realize that you may need access to data processing software, which is currently licensed on a lab-based computer. We would like to remind you that you can download fully functioning versions of our software from to load on a remote-based computer. You will get an automatic 60-day trial license (no license key needed), which we will extend as needed during this challenging period. To extend a license, please send an email to