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Rationale: Quantification of small molecules by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) is challenging yet attractive, due to micro‐scale procedural simplicity, high throughput and lack of memory effects. Since these features are important while analyzing trace elements in quality control schemes, MALDI‐TOFMS was used for the determination of copper (Cu) and lead (Pb) in tequila with quantification carried out by partial least squares regression (PLS2) and by univariate calibration (UC). Methods: In the proposed procedure, Bi(III) was added as internal standard (IS), diethyldithiocarbamate complexes were formed (pH 7.4) and extracted into chloroform; after solvent evaporation and re‐constitution in acetonitrile, the sample was co‐crystallized with α‐cyano‐4‐hydroxycinnamic acid on a steel target. From the acquired mass spectra, UC was performed using IS‐normalized signals of the monoisotopic ions of analytes, and the m/z range 350–513 was used for PLS2. Accuracy was tested by recovery experiments and by inductively coupled plasma (ICP)‐MS analysis. Results: When compared with direct analyte signal measurements, application of IS yielded enhanced analytical performance using either UC or PLS2; the method quantification limits were: 11.1 μg L−1, 23.4 μg L−1 for Cu and 89.8 μg L−1, 97.1 μg L−1 for Pb, respectively. In tequila, MALDI‐TOFMS and ICP‐MS provided consistent results for Cu (165–2599 μg L−1); Pb was not detected in any sample by MALDI‐TOFMS, yet recoveries obtained after standard addition were indicative of acceptable accuracy (400 μg L−1 Pb added; recoveries: 91.2–108% for UC and 98.8–120% for PLS2). Conclusions: New experimental evidence has been provided supporting the inclusion of trace metals quantification within a range of MALDI‐TOFMS applications. Slightly better results were obtained for UC as compared with PLS2 yet both methods can be recommended for testing the compliance of Cu and Pb levels with Official Mexican Norm. Of note, while using PLS2, there is no need for signal integration nor for IS normalization. [ABSTRACT FROM AUTHOR]