Interest in targeted profiling of quercetin glycoconjugates occurring in edible foodstuffs continues to expand because of their recognized beneficial health effects. Quercetin derivatives encompass several thousands of chemically distinguishable compounds, among which there are several compounds with different glycosylations and acylations. Since reference standards and dedicated databases are not available, the mass spectrometric identification of quercetin glycoconjugates is challenging. A targeted liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) was applied for screening quercetin glycoconjugates in edible peperoni di Senise peppers (Capsicum annuum L.), protected by the European Union with the mark PGI (i.e., Protected Geographical Indication), and cultivated in Basilicata (Southern Italy). Chromatographic separation was accomplished by reversed-phase liquid chromatography (RPLC) using water/acetonitrile as the mobile phase and detection was performed on a linear ion trap mass spectrometer fitted with an electrospray ionization (ESI) source operating in negative ion mode. A correlation between experimental RP chromatographic retention time and those predicted by partition coefficients (log P) along with MS/MS data and an in-house developed database (named QUEdb) provided deep coverage for sixteen quercetin glycoconjugates. Among them, eleven quercetin glycoconjugates were already described in the literature and five were reported for the first time. These last acyl glycosidic quercetin derivatives were tentatively identified as quercetin-(galloyl-rhamnoside)-hexoside, [CHO] at m/z 761.1; quercetin-(sinapoyl-hexoside)-rhamnoside, [CHO] at m/z 815.4; quercetin-(galloyl-caffeoyl-hexoside)-rhamnoside, [CHO] at m/z 923.0; quercetin-(feruloyl-hexoside)-rhamnoside, [CHO] at m/z 785.1; and quercetin-(succinyl-rhamnoside)-rhamnoside, [CHO] at m/z 693.1. Graphical abstract.