Improving the proteome coverage of Daphnia magna ‐ implications for future ecotoxicoproteomics studies

Abstract

Aquatic pollution is an increasing problem and requires extensive research efforts to understand associated consequences and to find suitable solutions. The crustacean Daphnia is a keystone species in lacustrine ecosystems by connecting primary producers with higher trophic levels. Therefore, Daphnia is perfectly suitable to investigate biological effects of freshwater pollution and is frequently used as an important model organism in ecotoxicology. The field of ecotoxicoproteomics has become increasingly prevalent, as proteins are important for an organism's physiology and respond rapidly to changing environmental conditions. However, one obstacle in proteome analysis of Daphnia is highly abundant proteins like vitellogenin, decreasing the analytical depth of proteome analysis. To improve proteome coverage in Daphnia, we established an easy‐to‐use procedure based on the LC‐MS/MS of whole daphnids and the dissected Daphnia gut, which is the main tissue getting in contact with soluble and particulate pollutants, separately. Using a comprehensive spectral library, generated by gas‐phase fractionation and a data‐independent acquisition method, we identified 4621 and 5233 protein groups at high confidence (false discovery rate < 0.01) in Daphnia and Daphnia gut samples, respectively. By combining both datasets, a proteome coverage of 6027 proteins was achieved, demonstrating the effectiveness of our approach.

Daphnia as a versatile model system in ecology and evolution

“…Only seven studies of the entire data set analyzed whole-transcriptome expression profiles (using RNA-seq). Besides RNA-seq, proteomics is also rapidly developing for Daphnia as a powerful research tool [ 122 ].…”

Protecting our environment, a motivating outdoor game for proteomics!

“…In this issue of Proteomics , Wilde and collaborators [8] propose the use of tandem mass spectrometry operated in data‐independent analysis mode to obtain comprehensive coverage of the proteome of the crustacean Daphnia magna , a miniaturized relevant model for aquatic ecotoxicology [9]. It has been demonstrated that this sophisticated method applies well to such species, even if the biological material is only available in limited quantity and the dynamic range of the proteome is quite unfavorable.…”