Gas chromatography coupled to mass spectrometry analysis of volatiles, sugars, organic acids and aminoacids in Valencia Late orange juice and reliability of the Automated Mass Spectral Deconvolution and Identification System for their automatic identification and quantification

► Volatile and polar compounds of orange juices were analyzed by GC–MS. ► AMDIS settings and MS operational parameters were appropriately optimized. ► Accuracy of automated AMDIS analysis was corroborated by manual data processing. ► AMDIS analysis is valid to perform multiple metabolite determinations. Neutral volatiles and non-volatile polar compounds (sugars, organics acids and aminoacids) present in Valencia Late orange juice have been analysed by Gas Chromatography coupled to Mass Spectrometry (GC–MS). Before analysis, the neutral volatiles have been extracted by Headspace-Solid Phase Microextraction (HS-SPME), and the non-volatile polar compounds have been transformed to their corresponding volatile trimethylsilyl (TMS) derivatives. From the resulting raw GC–MS data files, the reliability of the Automated Mass Spectral Deconvolution and Identification System (AMDIS) to perform accurate identification and quantification of the compounds present in the sample has been tested. Hence, both raw GC–MS data files have been processed automatically by using AMDIS and manually by using Xcalibur™, the manufacturer's data processing software for the GC–MS platform used. Results indicate that the reliability of AMDIS for accurate identification and quantification of the compounds present in the sample strongly depends on a number of operational settings, for both the MS and AMDIS, which must be optimized for the particular type of assayed sample. After optimization of these settings, AMDIS and Xcalibur™ yield practically the same results. A total of 85 volatiles and 22 polar compounds have been identified and quantified in Valencia Late orange juice.