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Matrix-assisted laser-desorption and ionization time-of-flight mass spectroscopy (MALDI-TOF MS) is a flexible technique for the analysis of protein-containing biological samples. Simple and inexpensive methods have previously been developed for MALDI-TOF MS sample preparation that are able to discriminate between <i>Impatiens</i> species that are closely related and also between regional biotypes of the invasive weed <i>Impatiens glandulifera</i> (Himalayan balsam) with leaf material and also seed material. The current article investigates whether MALDI-TOF MS, through acid-soluble protein &#8216;fingerprinting&#8217;, can be used to analyze plant seeds that result from intensive commercial plant-breeding activity. As an initial proof-of-concept study, tomato seeds from eleven seed-catalogue varieties (F1 Pink Baby Plum, F1 Fantasio, F1 Lizzano, F1 Sungold, F1 Tumbler, Faworyt, Golden Sunrise, Hundreds and Thousands, Indigo Rose, Moneymaker, and Red Alert), listed as <i>Solanum lycopersicum</i> or under the synonym <i>Lycopersicon esculentum</i> were analyzed using MALDI-TOF MS. Whilst peak-rich and highly-reproducible spectra were obtained, with very high Bruker comparison scores and low MALDI-TOF MS variance, sample-preparation variance, and seed-to-seed variance, the spectral differences between varieties were only slightly greater than the above combined variances, indicating very close similarity between all eleven varieties studied. These results are discussed in comparison with those previously observed with the naturally-evolving invasive species <i>I. glandulifera</i>.