The post-harvest processing of coffee beans leads to a wide range of reactions involving proteins. The formation of crosslinks between proteins and phenolic compounds present in high concentrations of coffee beans represents one of the most challenging and still not fully characterized reactions. The aim of this work was to assess the presence of products from such reactions in coffee samples, focusing on the adducts between cysteine and chlorogenic acids (CQAs). For this purpose, 19 green and 15 roasted coffee samples of the Coffea arabica, Coffea canephora, and Coffea liberica varieties were selected for this study and basically characterized. Then, targeted liquid chromatography mass spectrometry (LC-MS/MS) methods were developed to assess the formation of adducts between CQA and cysteine, glutathione, and N-acetylcysteine as the amino acid and peptide models, and quantified such adducts in coffee samples. The results of the characterization showed a heterogeneous distribution of the protein content (8.7–14.6%), caffeine (0.57–2.62 g/100 g), and antioxidant capacity (2–4.5 g ascorbic acid/100 g) in Arabica, Canephora, and Liberica samples. Glutamic acid, arginine, and proline were found to be the major amino acids, while 5-CQA (38–76%), 3-CQA (4–13%), and 4-CQA (4–13%) were the most abundant CQA derivatives of all coffee varieties. The model experiments for adduct formation demonstrated that cysteine binds to CQA via thiol groups and 5-CQA initially isomerizes to 3- and 4-CQA, depending on the conditions, allowing cysteine to bind to two different sites on 3-, 4- or 5-CQA molecules, thus, forming six different Cys-CQA adducts with m/z 476. The reaction was more favored at pH 9, and the adducts proved to be stable up to 90 °C for 10 min and up to 28 days at room temperature. The relative quantification of adducts showed peak area values ranging from 1100 to 3000 in green coffee bean samples, while no adducts were detected in roasted coffee beans. Overall, this work was the first attempt to demonstrate the presence of Cys-CQA adducts in coffee beans and paves the way for further investigations of such adduct formation at the protein level.

For many years, coffee has maintained its place in Turkey as Turkish coffee (i.e., boiled, finely ground, unfiltered), and has become globally recognized. However, in recent years, especially for young people, filter coffee has become more popular, instead of Turkish coffee. As is generally known today, climatic conditions and processing techniques have an impact on the constituents of coffee. It is also thought that the finer grinding of Turkish coffee may affect the variability of the coffee contents. The mentioned popularity of the coffee beverage is also causing an increased interest in its nutritional and functional properties as well as its chemical constituents. Therefore, an analytical determination of the coffee ingredients is essential. Taste may be the most important criterion for coffee consumption for most consumers, but the health benefits should not be underestimated. Coffee has an antioxidant effect due to the phenolic compounds present, such as chlorogenic acid. It is also known to prevent cellular damage, which has led to increased interest in its antioxidant properties. The aim of this study was to investigate the total chlorogenic acids (CQAs), caffeine and antioxidant capacities of coffees commonly consumed in Turkey. For this purpose, three green and three roasted coffee samples of the Coffea arabica, Coffea canephora and Coffea liberica varieties were selected for this study and characterized. Different targeted mass spectrometry (LC-MS/MS) methods were developed to encompass the above-mentioned ingredients. The roasting process significantly increased the caffeine content in three roasted samples compared to green coffees. These values ranged from 1.2 g per 100 g dry mass (DM) in green coffees to 2.6 g per 100 g DM in roasted coffees. It could be shown that the most dominant CQA contained was 5-CQA. While the amount of CQA in green coffees is approximately 49–64%, it decreases down to 33–41%, by isomer conversion partly, to 4-CQA and 3-CQA in the roasting process. The highest value was found at 3.5 g/100 g DM. The highest value for the antioxidation capacity was 4.4 g ascorbic acid equivalents/100 g DM roasted coffee and the lowest value was 2.4 g/100 g DM in green coffee. This study was the first attempt to demonstrate the presence of different CQAs, caffeine and antioxidation capacity in coffee beans from the market in Turkey and needs to be followed up further with a larger sample size in future studies.