Golden standard isolation techniques, which are based on the phenotypic and genotypic characteristics of the microorganisms, are the commonly used method for identifying foodborne pathogens. Foodborne pathogen isolates can be quickly, precisely, and economically identified using novel proteomics analysis techniques. The aim of this study was to assess the efficacy, sensitivity, and dependability of Salmonella species recovered from animal-based food using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). In total, 215 samples were gathered from supermarkets, and retail stores in the Al Qalyubia Governorate of Egypt, including raw chicken breast, breaded chicken, shrimp, tilapia, seabass, mullet, and mackerel fish. The result revealed that Salmonella isolates were recovered and detected in 24 samples based on the morphological characteristics. MALDI-TOF MS was used to assess all Salmonella isolates. In contrast to traditional identification, MADI-TOF MS identified only 19 isolates as Salmonella enterica with a 99 % confidence value. This study found that MALDI-TOF MS is a quick and inexpensive technology for identifying Salmonella species that could be used as an alternate tool in the food analysis laboratory for routine identification of foodborne pathogen isolates. Further study is needed to validate the MALDI-TOF MS approach, and expanding the MS instrument’s database would increase identification accuracy.