A rapid shotgun method using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) was developed for the characterization of fennel proteins. Following enzymatic digestion with trypsin, small volumes of the extract were analyzed via direct infusion in positive ion mode. For molecular identification, a dedicated bioinformatic strategy was implemented, starting from the publicly available NCBI protein database. From the 231 entries originally listed under the Foeniculum vulgare organism, only the unique, non-redundant protein sequences were retained, eliminating partial or duplicate entries that appear in the database under different identifiers. This refinement produced a curated dataset of 92 specific fennel proteins. In consideration of possible allergenic cross-reactivity—especially relevant to individuals with spice–mugwort–allergy syndrome—this protein list was expanded by adding 10 known allergenic proteins from botanically related species such as celery, parsley, carrot, birch, and mugwort. Thus, a final database of 102 protein sequences was constructed. All proteins were then in silico digested to simulate tryptic peptide fragmentation, producing a theoretical list of m/z values. These predicted values were compared to the experimental mass spectra acquired from FT-ICR-MS using a custom-developed MATLAB algorithm, designed to match signals with high accuracy. Finally, database searching in Peptide Mass Fingerprint mode was performed by using the matched m/z values as input data. A total of 70 proteins were successfully identified in the fennel extract, including 61 specific to fennel and 9 allergenic proteins from the additional reference sources. This method proves to be both time-efficient and robust for complex plant protein analysis.