Minimum variance optimized Fisher ratio analysis of comprehensive two-dimensional gas chromatography/mass spectrometry data: Study of the pacu fish metabolome

Integration of rice and fish farming, e.g., pacu fish in Argentina, has raised concern that herbicides used for rice paddies may adversely affect the fish metabolome. To study this issue, tile-based Fisher ratio (F-ratio) analysis was applied to comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC xGC-TOFMS) data of pacu fish raised in an integrated rice-fish farming system (farmed class) versus fish raised in tanks (tank-raised class) to discover class-distinguishing analytes. Fratio analysis resulted in hit lists initially dominated by artifact peaks from the sample derivatization process, as well as some redundant hits. These challenges were addressed by developing an automated artifact removal algorithm and an improvement to redundant hit removal in the tile-based F-ratio analysis using a pooled farmed fish sample, either spiked with 29 metabolites (spiked class) or unspiked (i.e., the background serving as the control class). Of the 29 spiked metabolites, 23 were discovered by standard F-ratio analysis, improving to 28 discovered using control-normalized F-ratio analysis. Standard and control-normalized F-ratio hit lists initially with 185 and 246 hits, were reduced to 56 and 49 hits, respectively, after artifact removal and removing redundant hits. Next, we returned to the F-ratio analysis of the farmed fish versus the control fish. Here, we introduce a minimum variance optimized (MVO) F-ratio calculation ( MVO F-ratio) that provides a comprehensive hit list ranking. The initial MVO F-ratio analysis hit list of 537 hits was reduced to 110 hits following artifact removal. Of the 110 hits, 70 expressed a concentration ratio statistically different than 1 ( p < 0.05). The MVO F-ratio hit list discovered more true positives compared to the standard, tank-normalized, and farm-normalized F-ratio hit lists, providing the combination of results from the farm-normalized and tank-normalized hit lists. A majority of analytes (54 out of 70) important for normal biological functioning of pacu fish were significantly downregulated in the farmed fish, suggesting the integrated farming system may negatively impact pacu fish quality. (c) 2022 Elsevier B.V. All rights reserved.

Automated summary

This study compared pacu fish raised in an integrated rice-fish farming system with those raised in tanks using F-ratio analysis, and discovered the impact of farming methods on the fish's metabolome. Despite challenges such as artifact peaks and redundant hits, improved analysis methods and artifact removal led to accurate results. The findings suggest that the integrated farming system may negatively affect the quality of pacu fish.