Alternative proteins testing

Alternative protein testing is fundamental to the research and development of novel foods, which include those derived from cellular agriculture, precision fermentation and plant- and insect-based products. Drawing on our extensive expertise in life sciences and food testing, we deliver cutting-edge technology to advance your alternative protein R&D.

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Explore the latest and trending topics

Journal article: Identification and screening of umami peptides from skipjack tuna (Katsuwonus pelamis) hydrolysates using EAD/CID based micro-UPLC-QTOF-MS and the molecular interaction with T1R1/T1R3 taste receptor

Taste plays a crucial role in consumer acceptance of alternative protein products. In this study, potential umami peptides were identified using collision-induced dissociation (CID) and electron-activated dissociation (EAD) MS/MS fragmentation techniques. These findings are pivotal for developing savory flavors in various food products, enhancing their appeal and market viability.

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Omics in the rapidly developing field of alternative proteins: Innovation and safety

Watch this on-demand webinar to hear from Dr Lin Qingsong, Principal Research Fellow, Director, Protein and Proteomics Centre, National University of Singapore and be informed about up-to-date risk assessment considerations of alternative proteins.

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Testing tomorrow's proteins today

Developing alternative protein products with high-value nutritional profiles, that are also safe for consumption, starts with the right equipment.

High-resolution mass spectrometry (HRMS) is used for proteomics and metabolomics approaches to understand changes in prototype cell-lines or cell culture media. Post-translational modifications and changes in protein expression have been highlighted as new allergen risks and HRMS is used for discovery proteomics to look for new proteolytic peptides as markers for allergenic proteins. HRMS can also be used to look for unwanted secondary metabolites from cell-lines in bioreactors as well as extractables and leachables and potentially harmful residues.

Nominal mass spectrometry is commonly used for lipidomics approaches, targeted screening of cell culture media components in production as well as allergen testing and residue testing. Plant-based foods can contain a variety of natural toxins as well as pesticides. Cell-cultured foods may contain processing contaminants, growth factors, veterinary drugs and more. SCIEX technology can answer a multitude of questions that arise from product development with alternative proteins.

Metabolomics: Designed with non-statisticians in mind and intuitively developed, MarkerView software distills complex datasets quickly.

Cell culture media analysis (CCMA): SCIEX CCMA methods by triple quadrupole and high resolution QTOF systems offer high sensitivity, selectivity, and robustness for the identification and quantification of over 110 compounds.

Lipidomics: SelexION technology can be used to greatly reduce isobaric interferences in lipid analyses. It uses a discrete, lipid class-specific compensation voltage (CoV) to filter ions into the mass spectrometer and prevents precursor lipid isobars from contributing to MS/MS spectra. This results in unparalleled selectivity, a general reduction in noise.

Workflows:

Non-targeted metabolomics Discovery proteomics Targeted proteomics

Non-targeted metabolomics

Non-targeted metabolomics seeks to identify metabolites and turn them into biological answers. SCIEX solutions focus on generating comprehensive datasets containing large amounts of information through unique approaches such as data-independent acquisition (DIA) using SWATH DIA or alternative fragmentation using electron-activated dissociation (EAD). Discover methodologies and solutions for identifying new and unknown metabolites and comparatively quantifying across complex samples and matrices:

Explore the metabolome with high sensitivity, expanding metabolite coverage
Enable fast, accurate identification and quantitation using sensitive, robust and reproducible technologies
Perform large-scale experiments with powerful, high-throughput workflows and solutions
Enable comprehensive target characterization and structural elucidation with election associated dissociation (EAD) technology

Resources for Non-targeted metabolomics in alternative protein testing

Solution

Non-targeted metabolomics

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ZenoTOF 7600+ system

The SCIEX ZenoTOF 7600+ system is a Zeno trap-enabled QTOF engineered with the added specificity of the scanning quadrupole dimension to enhance speed, depth and certainty in quantitative measurements.

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MarkerView software

Designed with non-statisticians in mind and intuitively developed, MarkerView software does the heavy lifting so you can focus on high-value decisions like reviewing trends and differences in targeted or untargeted mass spec workflows. Distill complex datasets quickly, find statistically significant differences and reveal key insights faster. MarkerView software is now integrated into the SCIEX OS ecosystem.

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SCIEX Triple Quad 6500+ system

Delivering the perfect balance of speed, performance, and sensitivity for your most challenges analytes.

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PA 800 Plus system

Characterize therapeutic molecules with confidence with the kit-based system.

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Unlocking Food Quality and Safety with Discovery Proteomics

Mass spectrometry (MS)-based discovery proteomics is increasingly being adopted in food and beverage testing as a powerful tool for comprehensive, untargeted protein profiling. Leveraging high-resolution LC-MS/MS platforms, this approach enables the identification and relative quantification of thousands of proteins in complex food matrices without prior knowledge of the proteome.

In food safety and quality control, discovery proteomics facilitates:

Allergen detection and characterization beyond conventional ELISA or PCR-based methods, enabling identification of isoforms and post-translational modifications (PTMs) that may influence allergenicity.
Authentication and traceability of food products by generating protein fingerprints that distinguish between species, geographic origin, or production methods (e.g., grass-fed vs. grain-fed beef).
Detection of adulterants and contaminants, including undeclared proteins from other species or processing residues.
Monitoring of fermentation and spoilage processes, particularly in beverages like wine, beer, and kombucha, by profiling microbial proteomes and metabolic enzymes.
Assessment of processing effects such as heat-induced protein denaturation, Maillard reaction products, and proteolytic degradation.

By enabling hypothesis-free exploration of the proteome, discovery proteomics supports the development of targeted assays, biomarker discovery, and systems-level understanding of food composition and transformation. When integrated with bioinformatics pipelines and spectral libraries, this approach enhances reproducibility and regulatory compliance in food testing workflows.

Example publications

Solution

Discovery Proteomics

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ZenoTOF 8600 system

The newest accurate mass platform with sensitivity levels up to 10x greater than existing SCIEX technology. This translates not only into the lower limits of quantitation but also into new enabled approaches to making biologically relevant discoveries that can be proved by the data.

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ZenoTOF 7600+ system

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MarkerView software

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Precision Protein Quantification in Food Testing with Targeted Proteomics

Targeted proteomics, powered by mass spectrometry (MS), is a robust and highly specific approach for the quantitative analysis of predefined proteins and peptides in complex food and beverage matrices. Utilizing techniques such as Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), and Parallel Reaction Monitoring (PRM), this method enables reproducible, high-throughput quantification with excellent sensitivity and selectivity.

In food and beverage testing, targeted proteomics is widely applied for:

Quantitative allergen detection: Enables precise measurement of trace-level allergenic proteins (e.g., casein, gluten, peanut proteins) with greater specificity than immunoassays, even in thermally processed or hydrolyzed products.
Verification of food authenticity: Confirms species identity in meat, fish, and dairy products by targeting species-specific peptide markers, supporting efforts to combat food fraud and mislabeling.
Monitoring of fermentation and bioprocessing: Tracks key enzymes and microbial proteins involved in fermentation (e.g., in beer, wine, yogurt), providing insights into process consistency and product quality.
Assessment of protein degradation and modification: Quantifies proteolytic fragments or PTMs (e.g., oxidation, glycation) that arise during storage, processing, or spoilage.
Compliance with regulatory thresholds: Supports quantitative reporting of contaminants or allergens in accordance with global food safety standards (e.g., EU, FDA, Codex).

By leveraging stable isotope-labeled internal standards and optimized LC-MS/MS workflows, targeted proteomics delivers high-confidence quantitation with minimal matrix interference. This makes it an indispensable tool for routine food testing laboratories, R&D groups, and regulatory agencies seeking to ensure product integrity, safety, and traceability.