2. Effectiveness in Database Retrieval: Our first practical focus was on the real-world application of molecular identification through database search. We evaluated all nine matching and padding combinations for their ability to correctly identify spectra within the HMDB dataset. While a 100% retrieval rate was achieved in ideal conditions, the performance varied when introducing systematic and random noise into the spectra. Zero-padding emerged as the most robust padding strategy, particularly under conditions of random noise, whereas MinSum was the most reliable matching algorithm for systematic peak shifts.