At MSACL 2025, a Thermo Fisher Scientific–sponsored workshop led by Qin Fu addressed one of the most persistent challenges in proteomics: how to efficiently and reproducibly translate biomarker discoveries into clinically meaningful assays. Drawing on experience spanning academia and industry—including prior work in Jennifer Van Eyk’s lab—Fu shared practical insights into building a scalable, end-to-end biomarker discovery-to-validation pipeline.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Accelerating_Biomarker_Discovery_and_Validation_From_Discovery_to_Clinical_Utility_9558364cf2.jpg" alt="Thermo Fisher Scientific: Accelerating Biomarker Discovery and Validation: From Discovery to Clinical Utility" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Accelerating_Biomarker_Discovery_and_Validation_From_Discovery_to_Clinical_Utility_9558364cf2.jpg 245w," sizes="100vw" width="1024" height="512">The session highlighted how emerging mass spectrometry technologies, automation, and informatics are reshaping biomarker research—reducing complexity, improving reproducibility, and accelerating the path to clinical utility.<h3>The three tiers of biomarker assays</h3>The workshop opened with a review of the widely accepted three-tier framework that guides biomarker development from early discovery through clinical validation:<h4>Tier 3 – discovery</h4>Exploratory, untargeted workflows such as data-dependent acquisition (DDA) and data-independent acquisition (DIA). These approaches prioritize breadth, enabling the identification of large-magnitude biological changes across hundreds to thousands of analytes, typically with low-to-moderate precision and without internal standards.<h4>Tier 2 – verification</h4>Research-grade targeted assays, including parallel reaction monitoring (PRM) and multiple reaction monitoring (MRM). These methods focus on tens to hundreds of analytes, delivering improved precision and repeatability to confirm trends observed during discovery.<h4>Tier 1 – validation</h4>Clinically validated assays designed to meet rigorous quality and regulatory standards. These workflows incorporate internal standards and strict quality controls to ensure quantitative reproducibility suitable for clinical and translational use.Each tier represents a critical step toward ensuring that biomarker candidates can ultimately deliver reliable patient benefit.<h3>The central challenge: from sample to signal</h3>Reliable biomarker development depends on consistency across the entire analytical workflow—from biological sample preparation to mass spectrometry data acquisition and downstream analysis. Every step introduces potential sources of variability, and minimizing this analytical noise while preserving biological signal is essential.Automation emerged as a central theme of the workshop. Beyond improving throughput, automation fundamentally enhances reproducibility. Robotic sample preparation reduces variability associated with digestion, pipetting, and handling—enabling consistent performance across hundreds or thousands of samples, a scale that is difficult to achieve manually.<h3>Technological innovation powering a paradigm shift</h3>Recent advances in mass spectrometry are enabling researchers to bridge the gap between discovery and validation more efficiently than ever before. The workshop highlighted several Thermo Fisher Scientific platforms driving this shift:<ul><li>Thermo Scientific Orbitrap Astral mass spectrometer Optimized for discovery workflows, the Astral system delivers rapid acquisition and deep proteome coverage while maintaining high precision across large cohorts.</li><li>Thermo Scientific Stellar platform Designed for high-throughput targeted quantification, the Stellar platform supports scalable PRM workflows. Features such as PRM Conductor enable adaptive retention time tracking, which is essential for robust performance in large studies.</li><li>Thermo Scientific OptaSpray Ion Source (under evaluation) A hands-free ionization source designed to deliver consistent spray performance with simplified maintenance, supporting reproducibility across thousands of injections.</li></ul>Together, these technologies create a smoother continuum across assay tiers, shortening timelines and reducing barriers to clinical translation.<h3>Case study: Inflammatory bowel disease (IBD) cohort</h3>A key highlight of the presentation was a large-scale biomarker study in inflammatory bowel disease (IBD). The team conducted a 500-sample discovery analysis, followed by validation in a 1,000-sample cohort. Discovery was performed using the Orbitrap Astral system, while targeted validation employed the Stellar platform.This integrated approach successfully confirmed established biomarkers such as C-reactive protein (CRP) while also identifying novel protein candidates with strong translational potential. Importantly, these markers demonstrated consistency across discovery and validation data sets—underscoring the power of advanced instrumentation combined with robust workflows and informatics.<h3>From high quantity to high quality</h3>Historically, biomarker discovery has involved a tradeoff between throughput and data quality. The workshop demonstrated that this compromise is no longer necessary. By integrating automated sample preparation, optimized informatics, and next-generation mass spectrometry, researchers can now generate high-quality, high-throughput data that is both scalable and reproducible.This shift enables faster discovery while increasing confidence that candidate biomarkers are ready for downstream validation and clinical follow-up.<h3>The future of biomarker translation</h3>The workshop concluded on an optimistic note. Innovations in proteomics are fundamentally transforming biomarker development—shortening timelines, reducing costs, and accelerating the transition from discovery to clinical application.By integrating platforms such as Orbitrap Astral, Stellar, and OptaSpray, Thermo Fisher Scientific is helping advance a new era of translational biomarker science—where precision, scalability, and reliability work together to deliver meaningful clinical impact.Watch the full workshop recording to <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=ziyffQzZTwk">explore the data, workflows, and results behind this end-to-end approach to biomarker discovery and validation.</a><h3>Intended use disclaimer</h3>General Laboratory Equipment – Not For Diagnostic Procedures. Thermo Scientific general laboratory equipment, consumables, and software are intended for research, academic, and industrial use only. These products are not designed, validated, or approved for in vitro diagnostic or clinical use. Use of these products for diagnostic purposes may result in inaccurate results and potential health and safety risks.<h3>Resources</h3>Workshop &amp; educational content<ul><li>MSACL 2025 workshop recording: <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=ziyffQzZTwk">Accelerating Biomarker Discovery and Validation</a></li><li>Other MSACL workshop recordings coming soon</li></ul>Thermo Fisher Scientific Product Pages<ul><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2207">Thermo Scientific TSQ Certis Mass Spectrometer</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/836">Thermo Scientific Orbitrap Astral Mass Spectrometer</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149">Thermo Scientific Stellar Mass Spectrometer</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/order/catalog/product/B51004132">Thermo Scientific OptaSpray Ion Source</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs.html">Mass spectrometer affordability programs</a> (Refurbished MS, trade-in, financing/ leasing)</li></ul>Peer-Reviewed Literature<ul><li>Baker ES et al. <a target="_blank" rel="noopener noreferrer" href="https://europepmc.org/article/MED/22943415">Mass spectrometry for translational proteomics: progress and clinical implications.</a> Genome Medicine (2012).</li><li>Fu Q et al. <a target="_blank" rel="noopener noreferrer" href="https://academic.oup.com/clinchem/article/62/1/198/5611803">An Empirical Approach to Signature Peptide Choice for Selected Reaction Monitoring.</a> Clinical Chemistry (2016).</li><li>Fu Q et al. <a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1002/mas.21750">Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis.</a> Mass Spectrometry Reviews (2023).</li><li>Fu Q et al. <a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1021/acs.jproteome.7b00623">Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry.</a> Journal of Proteome Research (2018).</li><li>Fu Q et al. <a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1002/anie.202409446">A Proteomics Pipeline for Generating Clinical Grade Biomarker Candidates from DIA-MS Discovery.</a> Angewandte Chemie International Edition (2024).</li><li>Fu Q et al. <a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1002/anie.202507610">Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort.</a> Angewandte Chemie International Edition (2025).</li></ul><blockquote>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#Omics #BiomarkerDiscovery #MassSpectrometry #ClinicalResearch</blockquote>

Accelerating Biomarker Discovery and Validation: From Discovery to Clinical Utility

Interlaboratory comparisons (ILCs) have been used for more than a century and many important concepts are linked to them. This leaflet addresses the basic terminology of ILCs, why some colloquial terms can be misleading or misunderstood, and the importance of harmonisation.&nbsp;An ‘ILC’ is the organisation, performance and evaluation of measurements or tests on the same or similar items by two or more laboratories in accordance with predetermined conditions [1]. ILCs have a variety of overall – and detailed – objectives, the three most common [2] being:<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Eurachem_Let_s_call_a_PT_scheme_a_PT_scheme_3_9993b9fb0f.jpg" alt="Eurachem: Let’s call a PT scheme a PT scheme" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Eurachem_Let_s_call_a_PT_scheme_a_PT_scheme_3_9993b9fb0f.jpg 245w," sizes="100vw" width="1516" height="472"><h4>Some comparisons have special names&nbsp;</h4>The evaluation of participant (laboratory, organisation or individual) performance is typically referred to as ‘proficiency testing’ (PT) or ‘external quality assessment’ [1]. When the main objective is evaluating the performance of, for example, a candidate standard method, the ILC is often called a ‘method performance study’ or a ‘collaborative study’ [2, 3]. The former is quite clear whereas wording such as “collaborative” and “cooperative” just stresses joint effort. A project aimed at producing a new certified reference material may involve several laboratories conducting analyses on agreed properties [4]. Not surprisingly, this work is sometimes labelled as a ‘material certification study’. Special ILCs used to demonstrate measurement capabilities of National Metrology Institutes are called ‘key comparisons’, ‘supplementary comparisons’, and ‘pilot studies’ [5].&nbsp;<h4>Some terms can be confusing&nbsp;</h4>Other terms for ILCs, including ‘ring test’, ‘round robin’ and ‘circle analysis’, are common in the literature. They have, however, been used for different objectives and different designs and may be ambiguous or understood differently by laboratory staff. The use of these terms may, for example, imply a specific way of distributing the ILC sample. ISO/IEC 17043 uses ‘sequential scheme’, for a PT where a unique item is transferred between the participants and ‘simultaneous scheme’, in which similar items from a batch are distributed simultaneously to the participants [1].&nbsp;Terms like ‘measurement audit’, ‘interlaboratory testing scheme’, ‘measurement comparison scheme’, ‘rapid performance evaluation scheme’ and ‘intercalibration’ may not correctly reflect the category of laboratory involved, or the type of work participants do during the ILC.&nbsp;When in 1994 the IUPAC defined and described three major types of ‘interlaboratory studies’, the word ‘study’ was preferred to synonyms such as ‘trial’, ‘exercise’, ‘test’, ‘evaluation’ or ‘check’ [2].<h4>Let’s try to harmonise&nbsp;</h4>Many laboratory staff are unaware of official terms related to ILCs but recognise the acronym PT and words like ‘ring test’. Ideally, we would use a common scientific language, but harmonisation is time consuming. Terms appear and disappear and definitions change. The same term can be defined differently, even in different international standards. Lack of standards and guidelines in local languages can cause confusion and contribute to spreading of less appropriate terms.&nbsp;<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Eurachem_Let_s_call_a_PT_scheme_a_PT_scheme_2_820043ce8b.jpg" alt="Eurachem: Let’s call a PT scheme a PT scheme" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Eurachem_Let_s_call_a_PT_scheme_a_PT_scheme_2_820043ce8b.jpg 234w," sizes="100vw" width="1006" height="671">Much confusion can be avoided by clear reference to relevant standards and sectoral guides. ISO/ IEC 17043 [1] and ISO 13528 [6] contain many important concepts related to PT schemes and other ILCs. Some of these are also incorporated into ISO/IEC 17025 [7]. Additional useful, and free, tools are the Eurachem PT Guide [8] and the ISO online browsing platform [9].&nbsp;In writing guidance and instructions, remember that the term ‘interlaboratory comparison’ has a broad meaning and can be used for all cases described above. Sometimes this is clear enough for the reader. In other cases, use acknowledged terms that reflect the detailed objective of the ILC. Let’s call a PT scheme a PT scheme!

Let’s call a PT scheme a PT scheme!

The countdown is on for one of the world’s leading conferences dedicated to food analysis. The 12th International Symposium on Recent Advances in Food Analysis (RAFA 2026), taking place in Prague from 3–6 November 2026, is approaching two important milestones: the Early Bird registration deadline and the deadline for oral abstract submissions, both ending on 30 June 2026. Researchers, analysts, industry professionals, regulators, and students are encouraged to secure their participation at a reduced registration rate and take advantage of the opportunity to present their latest scientific results to the international food analysis community.RAFA 2026 will once again bring together leading experts from academia, industry, and regulatory organizations to discuss the latest developments in food safety, authenticity, contaminants, non-target screening, PFAS, microplastics, food contact materials, artificial intelligence, and advanced analytical technologies. The preliminary program already features an outstanding lineup of internationally recognized speakers addressing some of the most pressing challenges in modern food analysis and food safety.<h3>Registration</h3><blockquote>👉<a target="_blank" rel="noopener noreferrer" href="https://rafa.easyevent.eu/tickets/">Register to attend RAFA 2026!</a>Early-bird registration until 30 June, 2026</blockquote>After successful submission of your registration, you will receive by e-mail (i) an automatic confirmation of receipt indicating the total amount of payment due (either for bank transfer or for on-line payment by card), (ii) login to Member section where you can administrate your profile, submit your abstracts, and from September 2026 register for satellite events, workshops and seminars. If it will not be delivered within a few minutes after submission of your registration please contact us at RAFA2026@vscht.cz.As soon as payment of registration fee is processed, you will also receive by e-mail (iii) confirmation of payment.<h4>Registration Fees</h4><ul><li>Smart rate (Until 30 June, 2026): € 655</li><li>Regular registration (Until 30 September, 2026): € 855</li><li>Late registration (From 1 October, 2026): € 955</li><li>Student rate*&nbsp;<ul><li>Until 30 June, 2026: € 465</li><li>From 1 July, 2026: € 605</li></ul></li></ul>* The proof of student status (e.g. copy of a student identify card) is requested as an attachment of the registration form.<h5>The regular registration fee will include:</h5><ul><li>Attendance at all scientific sessions, workshops, seminars, vendor seminars and other satellite events</li><li>Access to the poster and exhibition area</li><li>Conference kit (name badge, conference bag, conference documents, certificate of participation, certificate of presentation on request)</li><li>Final programme</li><li>E-Book of Abstracts</li><li>Coffee breaks</li><li>Buffet luncheons</li><li>Welcome drink</li></ul>In the registration form you can register free of charge for the welcome drink and you can also order ticket(s) for the conference dinner (€ 85).Please note that your registration is firm when your payment has been received.<h3>Abstract submission</h3><blockquote>👉<a target="_blank" rel="noopener noreferrer" href="https://rafa.easyevent.eu/tickets/">Submit your ABSTRACT HERE!</a>In order to submit an abstract, you must first register to attend RAFA 2026. After registration you will receive an access to the Member section where you can submit your abstract(s).</blockquote>&nbsp;After successful submission of your abstract you will receive an automatic confirmation of receipt of submitted abstract via e-mail. If it will not be delivered within a few minutes after submission of your abstract please check at first your spam box-mail and then contact us at RAFA2026@vscht.cz.Please ensure that your abstract does not contain spelling, grammatical or scientific errors. Even though modifications of your submitted abstract will be allowed in the Abstract section of the Member section until the deadline for the abstract submission, please be confident on the lack of errors in your final version prior to starting the submission process.The abstract will be reproduced exactly as submitted. No proofreading will be done, although some corrections may be requested by the reviewers.If you need to withdraw your abstract, a written statement reflecting the reasons for this decision must be sent to RAFA2026@vscht.cz no later than September 30, 2026.<h4>Important notice:</h4><blockquote>1 registered participant can submit no more than 2 abstracts.</blockquote>To apply for a young scientist’s oral presentation, as an indication please respect the rule that you should be born in 1991 or later.The text of the abstract should be limited to 3000 characters including spaces. Tables and pictures are not allowed.Abstracts of oral presentations and posters will be included into the "e-Book of Abstracts" only after receipt of the conference registration fee. Any payment of the registration fee has to be received until September 30, 2026, otherwise contribution(s) will not be included into the e-Book of Abstracts and the Conference programme.<h3>Program</h3><h4>Invited Speakers</h4><h5>Food allergen risk assessment: Past, present, future</h5><ul><li>Ben Remington from Remington Consulting Group B.V., Utrecht, the Netherlands &amp; University of Nebraska, USA</li></ul>Food allergy and allergen management are global public health issues, and consumer protection depends on transparent and trustworthy labelling. While 30 years of scientific advances show that low level exposures, or reference doses, are unlikely to trigger reactions in most allergic individuals, harmonized and globally aligned regulations are still needed to promote consistent allergen risk assessment and labelling decisions. This presentation will discuss the landscape of allergen risk assessment, global policy developments, current research and future needs in the area.<h5>Unmasking hidden adulteration in honey: Strategies for detecting and characterizing honeys produced from sugar-fed colonies</h5><ul><li>Oscar Nuñez Burcio from University of Barcelona, Barcelona, Spain</li></ul>From hive to jar, not all honey tells the same story. This presentation addresses hidden adulteration associated with sugar-fed bee colonies, highlighting implications for authenticity, production practices, and the need for a more precise characterization of honey to ensure consumer trust.<h5>Analytical and toxicological methods for safety of food contact materials</h5><ul><li>Erich Leitner from Graz University of Technology, Institute of Analytical Chemistry and Food Chemistry, Graz, Austria</li></ul>Food packaging plays a critical role in protecting and preserving food throughout the supply chain. All packaging materials intended to come into contact with food must comply with strict EU safety rules. Due to increased complexity of packaging solutions, lowering legal limits and increasing numbers of target compounds, we also have to adapt the strategies used to verify and guarantee the safety of these materials.<h5>Data-driven strategies to reduce complexity in non-target HRMS analysis of food samples</h5><ul><li>Anneli Kruve from Stockholm University, Stockholm, Sweden</li></ul>LC/HRMS based non-target screening can detect hundreds to thousands of chemical features in complex food and environmental samples. Investigating all of these in detail is practically impossible, so which ones to focus on? Novel computational tools developed in computational mass spectrometry allow predicting the toxicity and concentration of the detected chemical features even if these have not yet been fully structurally elucidated. Combining these predictions enables us to focus on the chemical features possessing high risk.<h5>Role of AI in the identification of emerging food systems risks</h5><ul><li>Ákos Bernard Jóźwiak from Syreon Research Institute, Budapest, Hungary</li></ul>AI-assisted evidence synthesis – spanning curated scientific evidence, exposome data, and network analysis – is the backbone of next-generation emerging chemical food safety risk identification, enabling earlier signals and more resilient surveillance systems.<h5>Challenges of microplastics analysis in the context of food safety</h5><ul><li>Dorte Herzke from Norwegian Institute of Public Health, Oslo, Norway</li></ul>Food and food packaging are major sources of micro- and nanoplastic exposure. Plastics used in processing, storage, and packaging can release particles through heat, abrasion, and degradation. Small particles below 2 µm may cross gut barriers and carry chemicals, highlighting the need for robust and sensitive measurement methods.<h5>Never-ending analytical challenges in PFAS analysis of food</h5><ul><li>Darina Dvořáková from University of Chemistry and Technology Prague, Prague, Czechia</li></ul>Exploring and monitoring PFAS in food requires advanced strategies. Combining targeted, suspect, and non-target HRMS analysis, determination of total fluorine and sum parameters, and novel sensors provides new insights into PFAS occurrence and supports food safety monitoring.<h5>An overview of the latest scientific knowledge on process contaminants in food for appropriate risk management measures</h5><ul><li>Thierry Delatour from Nestlé Research, Lausanne, Switzerland.</li></ul>Recent scientific findings related to acrylamide and furans formation, occurrence and analytical methods in food provide important insights for risk management.

Deadline for RAFA 2026 Early Registration and Oral Abstract Submission is approaching

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RAFA provides an overview of contemporary trends in ANALYTICAL & BIOANALYTICAL STRATEGIES IN FOOD QUALITY AND SAFETY CONTROL and discusses CHALLENGES / NOVEL APPROACHES IN FOOD AND NATURAL PRODUCTS ANALYSIS.

Recent Advances in Food Analysis (RAFA)

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Accelerating Biomarker Discovery and Validation: From Discovery to Clinical Utility

Deadline for RAFA 2026 Early Registration and Oral Abstract Submission is approaching

Let’s call a PT scheme a PT scheme!