Negative-ion mode matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) was used for the characterization of storage, neutral oligosaccharides extracted from Jerusalem artichoke, red onion, and wheat. The oligosaccharides from the real samples were analyzed with 2,4,6-trihydroxyacetophenone as the most convenient matrix that was selected in advance with the standard carbohydrate samples (inulin and maltooligosaccharides). The oligosaccharides from Jerusalem artichoke and red onion (similarly as inulin) produced [M - H](-) peaks as the main distribution, which reflects their nonreducing composition. On the contrary, the cross-ring fragmentations [M - H - 120](-) formed the main distribution in the mass spectra of hydrolyzed wheat starch similarly to reducing maltooligosaccharides and dextrans. The negative-ion mode MALDI-TOF MS is capable of recognizing reducing and nonreducing oligosaccharides. Such a simple differentiation of malto or inulin type of oligosaccharides is not possible in the positive-ion mode.