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

## TL;DR

This study uses proteomics to compare how processing and farming methods affect the protein content and diversity in quinoa.

## Contribution

The study is the first to use label-free shotgun proteomics to analyze quinoa proteins under different processing and farming conditions.

## Key findings

- Boiling and extrusion reduced total protein content and diversity in quinoa.
- Organic farming increased protein diversity, especially translation-related proteins.
- Conventional farming showed higher abundance of catalytic and enzymatic proteins.

## Abstract

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.