# The Applications of MALDI-TOF MS in the Diagnosis of Microbiological Food Contamination
## 3 Applications in Food Microbiology
### Authentication and Traceability  
Authentication and traceability are critical components of food quality assurance, regulatory compliance, and supply chain transparency. Food authentication refers to the verification of the origin, species, or production methods of food products, while traceability involves the systematic tracking of food through all stages of production, processing, and distribution. Both are essential to combat food fraud, ensure labeling accuracy, protect regional designations (e.g., Protected Designation of Origin, PDO), and respond swiftly to food safety incidents [105; 113; 114]. MALDI-TOF MS has emerged as a valuable analytical tool in supporting both authentication and traceability efforts in food systems. Its ability to generate species- or strain-specific proteomic fingerprints allows for the discrimination of microbial communities associated with specific foods, production environments, or geographic regions. These microbial signatures, often referred to as \"microbiomes\" or \"microbial terroirs,\" can act as biological indicators of product origin and production history [5; 103]. One of the most promising applications of MALDI-TOF MS in this context is the identification and differentiation of microbial populations in fermented and processed foods. Fermentation processes, whether natural or starter culture-driven, result in complex and relatively stable microbial consortia that can be characteristic of specific production methods or regions. For example, MALDI-TOF MS has been used to differentiate _Lactobacillus_ and _Streptococcus_ species in cheeses produced in different regions, or to identify unique yeast strains in traditional sourdoughs, beers, or wines, enabling verification of artisanal or protected-status products [111; 115; 116]. In addition to product authentication, MALDI-TOF MS supports traceability by enabling the monitoring of microbial contaminants or environmental isolates throughout the food production chain. By constructing a microbial fingerprint database specific to a facility, raw material, or processing step, it is possible to rapidly trace sources of contamination or spoilage. This is especially valuable in ready-to-eat foods or minimally processed products, where microbial control is paramount and the identification of contamination sources must be both rapid and precise [105; 108; 113]. Furthermore, strain-level typing using MALDI-TOF MS has been investigated as a method for tracking pathogen outbreaks. Although MALDI-TOF MS is less discriminatory than WGS or pulsed-field gel electrophoresis (PFGE), recent advances in spectral analysis algorithms and the development of strain-specific biomarker libraries have improved its utility in epidemiological investigations. It can serve as a rapid preliminary screening tool to identify potential outbreak clones before confirmatory genotyping methods are applied [117; 118; 119; 120]. MALDI-TOF MS has also demonstrated value in verifying the authenticity of probiotic products. In this context, it is used to confirm that marketed strains match the label claim and that no undesired or potentially harmful microbial species are present. This application is increasingly important, given the growing consumer demand for functional foods, the regulatory need to substantiate probiotic efficacy, and safety [3; 111]. However, successful deployment of MALDI-TOF MS for authentication and traceability requires robust and curated databases, as well as standardized protocols for sample handling and data interpretation. Matrix effects, especially in complex food substrates, can hinder spectral quality and affect identification reliability. Thus, continuous development of food-specific spectral libraries, combined with metadata such as geographic origin and production details, is essential for maximizing the discriminatory power of the technology.