My Compound Discoverer

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.

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.

We are excited to invite you to an exclusive webinar where we’ll showcase all of the new features implemented into the software, and share a customer application in the field of pesticide analysis.

Join us:  📅 March 27, 2024     ⏰ 8am PDT, 11am EDT, 5pm CET    🌐 Register now

Here’s what you can expect: 

Speakers:
– Julio César Espana Amórtegui, PhD, National Food Institute at the Danish Technical University
– Dr. Ralf Tautenhahn, Manager, Product Applications, Thermo Fisher Scientific

Discover New Features: Learn about the powerful new updates to Compound Discoverer Software. Whether you’re looking to improve your speed, accuracy, or data interpretation, these updates are designed to enhance your user experience and provide greater flexibility. Highlights include;

• New LipidSearch (MKI) node
• Automatically detect and group in-source fragments
• QC for small molecule experiments using internal standards
• mzCloud™ 2.0 connectivity for improved compound identification
• Performance improvements – up to 8x faster!
• And connectivity to the Ardia Platform   

Real-world Application: Hear directly from Julio Espana, PhD (National Food Institute of Denmark), who will present their cutting-edge research on the occurrence of adjuvant residues from pesticide formulations on harvested crops. Learn how they identified complex polymers using a nontargeted method and a customized Kendrick mass defect approach implemented in Compound Discoverer software. See how tailored visualization tools were utilized to highlight charge states and homologous series of ethoxylated units, effectively identifying the ‘needle in the haystack’ 

Practical Tips: Gain valuable insights that you can apply directly to your own work. Whether you’re new to Compound Discoverer software or an experienced user, you’ll leave with actionable strategies to enhance your workflows. 

Live Q&A: Have specific questions or challenges? Get expert advice in the live Q&A session to help you make the most of the software. 

Don’t miss this opportunity to learn from the experts and hear how Compound Discoverer Software can provide you with even more!  Register now 

We’ve been asked about this many times. Now it is finally happening! In this upcoming webinar we will give an introduction on how to develop scripting nodes for Compound Discoverer. Learn how to seamlessly integrate your existing in-house software, allowing you to export, read, and process result tables, and directly return the results as new columns or tables within the Compound Discoverer software. You can register here.

Our annual Compound Discoverer Users Meeting will be on December 9 and 10th, 2024 at the Atlantic Hotel in Bremen, Germany. You can register here. In response to your feedback from last year, we are planning to have additional training sessions for new users on Monday morning, right before the actual meeting, which will start around noon. Please see below for a preliminary agenda.

Whitney Stutts, Ph.D (Research Assistant Professor, Molecular and Structural Biochemistry, North Carolina State University) will be presenting at the Thermo Fisher Scientific breakfast workshop at ASMS on Monday, June 3rd (7 – 8 a.m. PDT | Anaheim Marriott | Platinum Ballroom 9) : Reporting compound annotation confidence in Compound Discoverer using automated scoring. You can still register here. Don’t miss it!