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

Aug 30, 2023 | Blogs, Food / Beverage, Food and Beverage | 0 comments

Read Time: 7 minutes

On June 12, 2023, during a webinar hosted by New Food, Lin Qingsong—Principal Research Fellow and Director of the Protein and Proteomics Centre at the National University of Singapore—discussed the latest considerations related to risk assessment of alternative proteins.

Watch the webinar now >

To help SCIEX customers successfully navigate this rapidly growing field, Lin took the time to answer a wide range of questions that were submitted during and after the event, which are provided below.

  1. What are some of the safety concerns related to new alternative proteins?

As the field of alternative proteins continues to expand, there are bound to be new ingredients, compounds or processes applied to create novel foods. We need to understand that this is an ongoing process and that the important factor is having a proper framework that can be applied to any new food products. In accordance with US Food and Drug Administration (US FDA) and European Food Safety Authority (EFSA) food safety guidelines, we must identify several risks, such as allergenicity, contamination and accurate food labeling of nutritional profiles, including novel ingredients of known and unknown risk.

  1. Are there any differences in terms of protein profiling between cell cultured meat and conventional evolved meat?

It is likely that there will be differences given that cultured meat and conventional meat are produced in vastly dissimilar environments and processes. Although it is hard to say at this point what the differences might be, our lab is currently investigating this topic. We are partnering with regulatory authorities and cultured meat companies to analyze their proprietary samples following reported guidelines. So, we hope we can shed some light on this question soon.

  1. How can we address the safety risks of unknown compounds?

For novel ingredients of unknown risk, the main challenge is that they are unknown. Therefore, the only way to investigate them is to apply proper safety risk assessment protocols during product development and manufacturing and to continue research to discover compounds of concern. Untargeted analysis is a space where mass spectrometry really shines with its ability to perform.

  1. Are there any tests for investigating health risks associated with consumption of alternative proteins?

Similar to safety assessments of any other food products, tests and checks will be performed before an alternative protein product is allowed to enter the market. For known toxic compounds, these safety assessments help reduce the risk to consumers. Unfortunately, unknown toxic compounds are usually only identified when issues arise and are reported by individuals after consumption. In these cases, tests and characterizations are then performed to identify the toxic molecules and their pathology on humans.

  1. How can proteomics help address safety concerns in alternative proteins?

I think proteomics can contribute to food safety in two ways. First, untargeted proteomics can be used to profile and identify all detectable proteins for the alternative protein sample. The resulting data can help with both safety and innovation, including detecting allergens and toxic proteins, identifying bioactive proteins and pinpointing molecular pathways. Second, targeted proteomics can be used to measure the quantity of any target proteins—for example, allergens or toxic proteins—to help ensure that they are at permissible levels. So yes, proteomics can be quite useful in addressing food safety.

  1. The number of proteins detected is often an indicator of proteomics data quality. Is this a useful indicator of whether an alternative protein sample contains more good proteins (such as bioactive proteins) or bad proteins (such as allergens)?

The number of detected proteins is usually a good indicator of overall data quality, but the ability to detect specific proteins—such as allergens and bioactive proteins—depends on many other factors. For example, the protein sequence database is a critical component of the protein identification process, meaning that the protein sequences must be known before the mention of the data can occur. Conversely, this also means that if we do not have prior information on the protein sequence, then we will be unable to identify the protein, even if we detect it in the data.

  1. How does the digestibility of pea and bean protein change during an extrusion process?

In our research, we are currently focused on the identification of proteins and metabolites in alternative protein samples. However, others—for example, Patil et al., Foods 2016, 5(2), 26—have shown that extrusion may increase the digestibility of legumes.

  1. How about edible insect protein and protein isolates?

Our preliminary experiments on edible insect proteins intended for use as pet foods have indicated a food safety risk in terms of cross reactivity with seafood allergens, which concurs with what many others have shown. The prominent allergens common to both insect proteins and seafood include tropomyosin and arginine kinase isoforms.

  1. Is the risk of common infectious organisms completely eliminated with alternative proteins?

Contamination from common infectious organisms can occur in many forms along the food production process, from ingredients to manufacturing. While guidelines exist to ensure the safety of natural ingredients and proper food processing, this does not completely eliminate the possibility of contamination. It is therefore crucial to have food safety checks in place, and mass spectrometry can be extremely useful for this.

  1. Can omics be used in meat food fraud?

Omics can definitely be used in meat food fraud analysis. Proteomics approaches can be used to accurately identify meat-specific protein biomarkers, which can then be used for the detection of meat food fraud. Targeted proteomics approaches have demonstrated the ability to quantify percentage mixtures from different animal sources in meat mixtures.

  1. How do I know that alternative proteins are safe and valuable for the needs of the human body?

The safety of alternative proteins depends on using safe ingredients, following proper hazard analysis and critical control point (HACCP) procedures during manufacturing and having proper storage conditions in place. Ingredients that have never been consumed by humans are regarded as novel foods and are subject to stricter novel food regulations (for examples, refer to guidelines from the US FDA and EFSA). Novel foods are tested for levels of possible toxic and allergenic compounds against international reference values.

The value of proteins in novel foods mostly depends on their amino acid composition—for example, if the food contains most or all essential amino acids upon digestion. Another consideration is the similarity between the proportion of amino acids in the food and that of the human body, since this defines the amount of each amino acid that the body needs.

  1. Which phases need more focused risk assessment and optimization in precision fermentation?

In general, safety risk considerations related to microbial food depend on the microbe that is being used. The strain must be known to be food-safe and contain no toxic compounds. Moreover, genetic modifications (if any) must be performed according to genetically modified organism (GMO) guidelines stipulated by the US FDA and EFSA. The process must follow good manufacturing practice (GMP) and have a proper HACCP procedure in place. I am unable to comment further on the technical aspects as we do not specialize in precision fermentation.

  1. How do you optimize untargeted protein profiling?

Optimizing untargeted protein profiling can involve optimization of the protein extraction process, LC-MS data acquisition and data processing. The extraction protocol should ideally extract and solubilize most of the proteins from the sample through combinations of physical and chemical approaches. LC conditions can be optimized to enhance chromatographic separation of the peptides prior to MS analysis to improve protein detection and coverage. Data processing strategies can involve combining database searches from multiple search engines or even de novo sequencing.

  1. How are thyroid cancer biomarkers identified via combining multi-omics?

Integration of multi-omics data can bring new and deeper insight into cancer mechanisms, which can be translated into sensitive and accurate biomarkers and novel therapeutic opportunities. This is beyond the scope of the current discussion, but many resources are available that discuss the potential of multi-omics in precision medicine, such as Raufaste-Cazavieille et al., Front. Mol. Biosci. 2022, 9.

To learn more, access the on-demand webinar here >

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