Plant metabolomics, lipidomics, ionomics, fluxomics, and peptidomics are essential approaches for exploring how plants respond to epigenetic, pathological, and environmental stimuli through comprehensive chemical profiling. Over the past decades, significant progress has been made in protocols and methodologies to address the challenges in sample collection and extraction. Despite these advancements, sample preparation remains intricate, with ongoing debates about the most effective strategies. This review emphasizes the importance of clear research questions and well-designed experiments to minimize complexity, save time, and enhance reproducibility. It provides an overview of the key steps in these fields, including harvesting, drying, extraction, and data pre-acquisition for major analytical platforms. By discussing best practices and common challenges, this review aims to streamline methods and promote more consistent and reliable research outcomes.

The main bioactive compounds in coffee beans affecting beverage quality include trigonelline, 5-caffeoylquinic acid (5-CQA), and caffeine. Despite the use of various analytical techniques, there is a need for a faster and more accessible alternative to the costly and complex methods used in routine coffee composition analysis. This study aimed to optimize and validate a high-performance liquid chromatography with ultraviolet detection (HPLC-UV-DAD) method for the simultaneous quantification of these three bioactive compounds in five Coffea arabica cultivars (Yellow Catuai, Guesha, Arara, Red Catuai, and Laurina). The evaluated parameters included linearity, accuracy, robustness, precision, limit of quantification, and detection. The proposed method met the criteria of the analytical validation figures of merit, being considered to be fast and effective for determining these compounds. In addition, the study of the concentration of these compounds in the different coffee cultivars showed significant differences, with the Laurina cultivar having the lowest concentration of caffeine (7.9 mg g^–1). Between raw and roasted beans, there were significant variations in the degradation rates of 5-CQA and trigonelline, with the highest for 5-CQA in the Arara cultivar (62.59%) and the highest for trigonelline (28.76%) in the Laurina cultivar. The speed and simplicity of the method can be used to investigate the contribution of these bioactives to the sensory characteristics of the drink and their possible health benefits.

Caffeic and ferulic acids are critical phenolic compounds in coffee beans, known for their antioxidant properties and influence on coffee’s acidity. This study developed and validated a rapid and simple analytical method to quantify these acids in raw and roasted coffee extracts using high-performance liquid chromatography with a violet detector (HPLC-UV). Parameters such as linearity, accuracy, precision, robustness, limit of quantification, and detection were analyzed. The two acids were quantified in five Coffea arabica cultivars (Red catucai, Siriema, IPR 98, Yellow catuai, and Yellow catucai), and the results were within the standards recommended by ANVISA and INMETRO. The concentrations of caffeic acid ranged from 1.43 to 1.93 mg/g in roasted grains and from 0.16 to 0.38 mg/g in raw grains; for ferulic acid, the concentrations ranged from 0.13 to 0.16 mg/g in raw grains and from 0.27 to 0.50 mg/g in roasted grains. According to the Tukey test, only cultivar IPR 98 showed a statistically significant difference in roasted grains. The proposed method offers a rapid and accurate analysis, contributing to the study of bioactive properties and the relationship between beverage quality and the presence of these compounds in coffee beans.