My Compound Discoverer

We are delighted to invite you to our annual user meetings, taking place 7 – 10 December 2026 in Bremen, Germany.

These meetings are designed to help you make the most of your software — whether you’re new to Compound Discoverer or looking to expand your expertise. You’ll hear real-world case studies, explore cutting-edge workflows, and gain practical insights from Thermo Fisher Scientific experts and fellow users.

This year’s program builds on the success of previous user meetings and includes:

• Two days of interactive sessions, user presentations, and best practice discussions
• Optional two full training days to strengthen your skills from beginner to expert
• A group networking dinner
• Optional 1-2-1 discussions with experts (sign up at the event)

Our scientists, developers, and partners will be there to share the latest developments and answer your questions. Don’t miss this opportunity to learn, connect, and grow with the community.

More information and registration page can be found here.

What is going to happen:

The legacy mzCloud will be going offline in March of 2027.  This is a result of the end of life of Microsoft Silverlight upon which the legacy website was built.  This does NOT affect the new mzCloud library.

What is the impact:

Web users – little to no impact, sign up to or continue to use the new mzCloud site (www.mzCloud.org) where new library content is added throughout the year.

Compound Discoverer – Users on Compound Discoverer 3.4 or later will be unaffected as you can already search the new mzCloud online from these new versions.  Users on older Compound Discoverer versions will either need to update to a new version of Compound Discoverer or use the offline mzCloud libraries in mzVault format which will allow you to continue to access the curated MS2 data from mzCloud in an offline format.

Microsoft and Silverlight are trademarks of Microsoft Corporation.

A new scripting node was developed that assigns annotation confidence levels based on the widely adopted Schymanski et al. scoring scheme. Please see https://pubs.acs.org/doi/10.1021/acs.analchem.5c03229 for more details.

The scripting node for Compound Discoverer 3.3, 3.4 and 3.5 can be downloaded here https://mycompounddiscoverer.com/annotation-confidence-scoring/ .

At the Compound Discoverer Users Meeting this year, Prof. Lee Ferguson (Duke University) presented the integration of the SIRIUS software into Compound Discoverer via a customized processing node. You can find a recording of his presentation here, and the slide deck can be downloaded here.

The CDSirius node developed by Prof. Ferguson can be downloaded here. The accompanying website also provides detailed installation instructions and explanations of all node parameters.

The SIRIUS software is free for academic use (account registration required); however, a commercial license is required for business and other non-academic users.

We are happy to announce that Compound Discoverer 3.5 has been released. You can download it from here. Here is an overview of some of the new capabilities in CD3.5:

• In-silico fragmentation (“FISh Scoring”) uses a new algorithm with increased coverage for negative ionization mode and increased speed of fragmentation.
• Apply PFAS Scoring node for PFAS prioritization.
• PFAS Plot shows the normalized mass defect (MD/C) versus normalized mass (m/C), with option for CF₂-transformed.
• The top-level Formulas table consolidates detected or predicted formulas from all annotation sources within a workflow.
• You can now export a Compounds table to the Thermo Scientific™ Chromeleon™ Chromatography Data System (CDS).
• You can now export a GC/EI Compounds table to Chromeleon.
• New targeted stable isotope labeling workflow
• The user interface now scales the font size used in most charts and views in CD.
• Internal Loss Search:
  – Lists & Libraries > Neutral Losses. New option to select neutral loss between the precursor and a fragment or between two fragments.
  – The Search Neutral Losses node now also reports internal loss.
• Added 17 neutral losses that are characteristic for PFAS
• and more.

For details, please see the Release Notes.

A slide deck with an overview of the new features in 3.5 release can be found below.

11/06/2025, 8am PT . You can register here.

PFAS contamination presents unique challenges, especially when it comes to detecting unknowns in complex samples. In this webinar, we’ll demonstrate how Thermo Scientific™ Compound Discoverer™ version 3.5 software introduces powerful new tools to streamline non-targeted PFAS analysis, enhance confidence in identification, and simplify data interpretation.

•    Apply advanced Compound Discoverer 3.5 software features to improve non-targeted PFAS detection

•    Confidently identify and annotate unknown PFAS in challenging matrices

•    Streamline data processing and reporting for faster decision-making

Registration is now open for the annual Compound Discoverer & Proteome Discoverer Users Meeting, Dec 9-11. Join us in Bremen, Germany !

• An optional full training day to strengthen your skills
• Two days of interactive sessions, user presentations, and best practice discussions
• A group networking dinner
• An optional guided tour of our Bremen factory or 1-2-1 discussions with experts  (sign up at the event)

Please use this link to register.

We’re pleased to announce that our annual Thermo Scientific™ Compound Discoverer™ and Proteome Discoverer™ Software User Meetings will be held in Bremen, Germany, from 9th – 11th December 2025. 

Following the huge success of last year’s meeting and ½-day pre-training, we are excited to offer an optional full training day before the 2-day user meeting. Meet other users, hear about real-world applications, and explore new software developments with Thermo Fisher experts. 

The two meetings will run in parallel. 

Tuesday 9th December | Optional training day 

• Get a solid grounding in the use of Compound Discoverer or Proteome Discoverer software 
• Learn experimental design and data processing best practices 
• Discover tips and tricks to enhance your use of the software  

Wednesday 10th – Thursday 11th December | User meeting 

• Learn about current developments and new technologies in recent releases 
• Hear from other users about their experiences and learnings 
• Interact with Thermo Fisher experts and learn how to get the most out of your data  
• Networking dinner (Wednesday evening)  
• Optional guided factory tour (Thursday afternoon)  

Save the date now — registration details coming soon! 
9-11 December 2025 | Atlantic Grand Hotel | Bremen, Germany 

Help us plan your perfect meeting — please take a moment to answer our quick survey  

Any questions? Email analyze.eu@thermofisher.com  

We look forward to seeing you in Bremen! 

Version 6.0 of the PyEDS toolkit by Martin Strohalm was released recently.

The PyEDS is a Python library providing collection of utilities to conveniently access and display results from Thermo Discoverer software like Compound Discoverer or Proteome Discoverer. Although the data are stored in open format already (SQLite database), reading complex hierarchies is still not a trivial task and requires certain knowledge of internal mechanisms. Using PyEDS, all the hard work is done automatically, so you can focus more on your research instead of how to read the data.

The PyEDS library provides several tools to read data (pyeds.EDS), displaying tables metadata (pyeds.Summary) as well as displaying actual data in nicely formatted tables (pyeds.Review). In addition, a set of utilities is now available to simplify custom scripting nodes (pyeds.scripting).

import pyeds

# open result file using 'with' statement
with pyeds.EDS("examples/data.cdResult") as eds:
    
    # read top 10 most abundant compounds in specific RT range
    items_iter = eds.Read("Compounds",
        query = "RetentionTime > 3.8 AND RetentionTime < 4.1 AND Name != ''",
        order = "MaxArea",
        desc = True,
        limit = 10)
    
    # print some properties
    for item in items_iter:
        print(item.Name, item.Formula, item.RetentionTime)

…
Noroxycodone-d3 C17 H16 D3 N O4 3.8511594324229588
6-(1,2-Dihydroxypentyl)-4-methoxy-5,6-dihydropyran-2-one C11 H18 O5 3.8892103560637996
Striatisporolide A C11 H16 O4 3.8904788953324587
PEG n6 C12 H26 O7 3.8514281937047308
1,3-Butyleneglycol dimethacrylate C12 H18 O4 4.062345800093047
8-Epideoxyloganic acid C16 H24 O9 3.967517173120096
Propan-2-yl 2-hydroxy-4-methylsulfanylbutanoate C8 H16 O3 S 4.064400409011077
Striatisporolide A C11 H16 O4 4.09791974254791

import pyeds

# open result file using 'with' statement
with pyeds.Summary("examples/data.cdResult") as summary:
    
    # show full info
    summary.ShowAll()

The example above will open your web-browser and display a graphical, interactive network of all the information stored in your result file and how the tables are linked together. You can click on any of the nodes and it will show detailed information about all the data (columns) stored in the selected table.

We are very happy to announce that Compound Discoverer 3.4 has been released. You can download it from here. Here is a short overview of new capabilities in CD3.4:

• Can be connected to Thermo Scientific™ Ardia™ Platform for direct raw data access and result file upload
• Includes LipidSearch node for simplified lipid identification 
• QC for small molecule experiments using internal standards
• Automatically detects and groups in-source fragments
• Connects to mzCloud™ 2.0 for improved compound identification
• Performance improvements, up to 8x faster

For more details, please see the Release Notes and visit the webinar shown in the post below. A recording of the webinar is available.

FAQ:

• No need to uninstall your existing Compound Discoverer software. You can install CD3.4 in parallel to any other CD version on your PC.
• The LipidSearch node in CD3.4 does not require the LipidSearch standalone software to be installed.