Comprehensive characterization of raw and processed quinoa from conventional and organic farming by label-free shotgun proteomics

Quinoa, a dicotyledonous plant native to the Andes, is recognized as a high-quality food due to its outstanding nutritional properties, including complete proteins. However, there is a lack of information on how the proteomic profile of raw quinoa is influenced by processing methods such as boiling and extrusion, as well as by conventional and organic farming conditions. Here, proteins from both raw (seeds and grains) and processed (boiled and extruded) white quinoa cultivated under conventional and organic farming were extracted, trypsinized, and analyzed by nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS). The mass spectra data were then scrutinized against a dedicated quinoa database from The National Center for Biotechnology Information via MaxQuant/Andromeda, leading to the identification and quantification of 1,796 proteins. Finally, qualitative and quantitative data interpretation tools were employed for data inspection and visualization, unveiling for the first time, similarities and differences at the proteomic level among the studied samples.