A high-performance liquid chromatography tandem mass spectrometry method has been developed and validated to quantify alternariol, alternariol monomethyl ether, tenuazonic acid, altenuene, altertoxin I, and tentoxin, and implemented to better understand the risks associated with Alternaria contamination of tomatoes and fate of the toxins during processing. This method has been developed for routine use, by reducing the cost, duration, and complexity of manipulations. Limits of quantification were below EU recommendations 2022/553, reaching 1.2-3.7 µg kg^-1 for alternariol and alternariol monomethyl ether and 9.4-18.4 µg kg^-1 for tenuazonic acid depending on the matrix. Apparent recovery ranged between 85 and 103%, and intraday repeatability was <15%. Different Alternaria strains isolated from tomatoes were assessed for their toxin production profiles, and the impact of processing operations on Alternaria toxins naturally occurring in tomatoes was evaluated on a pilot scale. Tenuazonic acid was the predominant toxin produced by Alternaria strains and contaminating tomatoes. Processing operations did not reduce toxin accumulation, which demonstrates its thermostability. Additionally, tomato skin and seeds residues, which are reused for different applications, was 2.6 times more contaminated than tomato pulp.

Alternaria alternata is a common postharvest mold affecting tomato products, including cherry tomatoes, and causing their contamination with mycotoxins. When consumers encounter moldy fruits, some may remove the visibly contaminated part and consume the rest, to reduce waste. However, the extent to which A. alternata toxins migrate beyond visible fungal growth remains unclear, potentially posing health risks. This study investigated (i) the within-fruit migration of A. alternata in cherry tomatoes together with the associated mycotoxin production, and (ii) the diffusion of purified Alternaria toxins in tomatoes in the absence of any fungal activity. Toxins were quantified using LC-MS/MS, while fungal colonization was assessed through visual inspection and DNA quantification across fruit sections. In the absence of fungal growth, toxins remained largely confined to the spiking site and were degraded over time. In contrast, in inoculated samples, Alternaria DNA was detected at notable levels even in sections lacking visible fungal growth, while Alternaria toxins were found both in these regions and in lower fruit sections where fungal DNA was below the qPCR detection limit. These findings highlight the limitations of relying solely on visual inspection to assess food safety. A consumer recommendation is proposed to help minimize health risks while reducing food waste.