Compound Discoverer Users Meeting at ASMS

Compound Discoverer Users Meeting on Saturday, June 3rd 2023, 9-12am at ASMS in Houston, Texas.

Registration is now open!

Compound Discoverer 3.3 SP2 released

We are happy to announce that Compound Discoverer 3.3 SP2 software is now available for download. To access your software from the download site, log in to your account here:

Enhancements in the Compound Discoverer 3.3 SP2 application

• The Spectral Libraries library includes one additional mass spectral library: the Epoxidized Soybean Oil Library

AN001586, which is a mass spectral library generated from compounds identified in epoxidized soybean oil.

• The Mass Lists library includes four new mass lists:

– Three new mass lists for the identification of PFAS compounds: PFAS_NIST, PFAS_NEG, and Chemical List PFASSTRUCT-2022-04-20

– The Food Contact Chemicals database mass list (FCCDB_2022)

• The Mass Lists library also includes two updated mass lists:

– The LipidMaps Structure Database mass list has been updated to the latest version 2023-01-11.

– The Extractables and Leachables HRAM Compound Database – 2023 Update has been expanded to 2,662


• The Compound Classes library includes the following two new compound class files for the identification of

PFAS compounds:

– PFAS Fine structure fragment_lib

– PFAS General from FluoroMatch Suite

• A new processing workflow template for identifying per- and polyfluoroalkyl substances (PFAS) has been added

to the set of templates for LC studies.

• The Transformations list includes one new transformation reaction: PFAS Chain Shortening (for PFAS


• The limit for the number of compounds that you can export to the molecular networks viewer has been

increased to 3,000.

• A new tutorial for the mapping of biological pathways using the BioCyc Genome Database Collection has been

added to the set of user guides and tutorials that you can access from the Help > Manuals menu

How to display KEGG IDs and Compound Class in the Compounds table

Compound Discoverer can display KEGG IDs or Compound Class as an additional column in the “Compounds” table for all compounds with hits in mzCloud™. To ensure desired IDs are displayed in your Compounds table, please edit the parameters of the “Assign Compound Annotation” node and select KEGG ID or Compound Class in the dropdown menu for the mzCloud Search.

BioCyc – Biological pathway mapping in Compound Discoverer

BioCyc has recently gained popularity as an excellent pathway mapping tool. The database accommodates metabolic networks for ~ 20,000 sequenced organisms across 3,105 pathways, and ~ 19,000 metabolites. Its superior informatics functions allow zoomable pathway diagrams featuring chemical structures and offer the key capability of overlaying user-obtained OMICS study results (e.g., fold change, peak area, or stable isotope labeling data) onto organism-specific metabolic pathways, producing data-oriented pathway representation and leading the way to successful biological interpretations.

Many academic organizations have institutional subscriptions  and BioCyc offers a free trial period for all Thermo Fisher Scientific users as well as a 20% discount for a one-year subscription. For more information, please visit

Attached is a tutorial showing you how to work with the BioCyc Pathways mapping feature in Compound Discoverer 3.3 service pack 2 (SP2) application.

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.