Comprehensive Characterization of Raw and Processed Quinoa from Conventional and Organic Farming by Label-Free Shotgun Proteomics

Quinoa is widely recognized for its exceptional nutritional
properties,
particularly its complete protein content. This study, for the first
time, investigates the effects of processing methods (boiling and
extrusion) and farming conditions (conventional and organic) on the
proteomic profile. Following a label-free shotgun proteomics approach,
a total of 1796 proteins were identified and quantified across all
quinoa samples. Regarding processing, both boiling and extrusion produced
protein extracts with lower total protein content, with the number
of identified proteins decreasing from 1695 in raw quinoa to 957 in
processed quinoa. Boiling led to a reduction in protein diversity
and expression, while extrusion, which involves high temperatures
and pressures, specifically decreased the abundance of high molecular
mass proteins. Concerning cultivation practices, organic farming was
associated with a broader protein diversity, especially proteins related
to translation (28 vs 5%), while conventional farming showed a higher
abundance of catalytic and enzymatic proteins (67 vs 46%). These findings
highlight the distinct proteomic changes induced by different processing
methods and farming conditions, offering valuable insights to manage
quinoa’s nutritional, bioactive, and functional properties
across various production practices.