The consequences of sample pooling in proteomics: An empirical study

Abstract

Pooling of samples in proteomics experiments might help overcome resource constraints when many individuals are analysed. The measured biological variation should be reduced giving increased power to detect treatment differences. Pooling has been advocated in microarray work but there are few tests of its potential in proteomics. In this study, we examine three issues on which the success of the pooling approach might hinge and provide evidence that: (i) the protein expression in a pool matches the mean expression of the individuals making up the pool for the majority of proteins, although for some proteins the pool expression is different; (ii) the biological variance between pools is reduced compared with that between individuals, as predicted in theory, but this reduction is not as large as expected. A practical consequence of this is that power could be reduced; (iii) proteins detectable in individual samples are usually but not always visible when samples are pooled. We conclude that pooling of samples in proteomics work is a valid and potentially valuable procedure but consideration should be given to these issues in experimental design.

Upregulation of Calprotectin and Downregulation of Retinol Binding Protein in the Serum of Workers with Trichloroethylene‐induced Hypersensitivity Dermatitis

“…Underlying sample pooling strategies is a biological averaging assumption that the measures taken for the pool are equal to the average of the measures taken for individuals 33) . Based on the above assumption, pooling reduces variability by minimizing individual variation, but this is only suitable for experiments when the focus is not on the individual but rather on characteristics of the population 34,35) . The pooling approach in proteomics has been advocated and widely used in studies in vitro [33][34][35][36][37] and in vivo 38) .…”

“…Based on the above assumption, pooling reduces variability by minimizing individual variation, but this is only suitable for experiments when the focus is not on the individual but rather on characteristics of the population 34,35) . The pooling approach in proteomics has been advocated and widely used in studies in vitro [33][34][35][36][37] and in vivo 38) . Considering the corticosteroid therapy given the THD patients, although there was only a trace dose of corticosteroid in the last application and a 1-2 wk interval between the last application and the second collection of blood samples, doubts might arise about the specificity of the altered proteins to THD.…”

Mild osmotic stress in intertidal gastropods Littorina saxatilis and Littorina obtusata (Mollusca: Caenogastropoda): a proteomic analysis

“…The soft body was withdrawn from the shell and put into a cold lytic buffer (25 mM tris pH 8.5, 7 M urea, 2 M thiourea, 4 % CHAPS). Several individuals (3 males and 3 females) were pooled in 1 ml of the lytic buffer (to improve reliability of samples, Diz et al, 2009). Two replicates were made for every experimental time point.…”

Comparative Proteomic Analysis of Rat Bronchoalveolar Lavage Fluid after Exposure to Zinc Oxide Nanoparticles

“…30) us, two pooled BALF samples from four control and six exposed rats were subjected to 2-DE analysis. e conditions for 2-DE analysis used in this study followed the reported by Magi et al with slight modi cations.…”