Category Archives: Uncategorized

Added two new Scripting nodes

Two new scripting nodes were added. 1. A script to export the Compounds table with multiple ions for each compound instead of the reference ion. 2. A script with custom calculations for PFAS analysis (for more details on this node please also see here).

Compound Discoverer software Users Meeting in Bremen- Registration is open now!

We are excited to welcome you in person to Bremen, Germany again for the Proteome Discoverer & Compound Discoverer software Users Meeting from 12-13 December, 2022.

Please follow the link here for online registration.

Compound Discoverer Workshop at the Metabolomics Society meeting

Join us at the 18th International Conference of the Metabolomics Society Meeting. We’ll have a Compound Discoverer Workshop on Sunday, 19 June 2022 | 09:00 – 11:00 [CEST] at the Sercotel Sorolla Palace. You can sign up for the workshop here.

Upcoming Webinar on May 17th : Probing Metabolite Utilization and Growth in Pathogenic Microbes

The high resolution accurate mass measurements that Orbitrap mass spectrometers provide are particularly valuable for metabolomic tracing experiments, termed “fluxomics” or “stable isotope labeling”. In these experiments scientists introduce stable isotope labeled compounds to create metabolic roadmaps to understand biological pathways and perturbations to systems. A major challenge is to interpret the results of these experiments, but Compound Discoverer software provides unique capabilities to determine isotopic enrichment in an untargeted fashion by leveraging the high resolution accurate mass data generated by Orbitrap instruments. Compound Discoverer software provides easy to interpret results through multiple powerful visualizations including isotopologue distribution charts and customizable overlays of labeling onto biochemical pathways through Metabolika. This powerful approach is an excellent complement to standard untargeted metabolomics and our differentiated products provides unique abilities and insights.

Please register here.

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.


Here are all available links.

Exciting additions to an exciting software, CD 3.2 update-20210303 1005-1

Starting your journey with Compound Discoverer-20210311 0936-1

Data visualization and statistical analysis in CD 3.2-20210316 0939-1

Acquisition strategies to get the most out of Compound Discoverer-20210323 1003-1

Unfortunately the identification part could not be recorded.

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