Genetic variation that is expressed only under specific environmental conditions can contribute to additional adverse effects of inbreeding if environmental conditions change. We present a proteomic characterization of a conditional lethal found in an inbred line of Drosophila melanogaster. The lethal effect is apparent as a large increase in early mortality at the restrictive temperature (29 degrees C) as opposed to normal survival at the permissive temperature (20 degrees C). The increased mortality in response to the restrictive temperature is probably caused by a single recessive major locus. A quantitative trait locus (QTL) region segregating variation affecting the lethal effect has been identified, allowing for a separation of primary/causal effects and secondary consequences in the proteome expression patterns observed. In this study, the proteomic response to the restrictive temperature in the lethal-line (L-line) was compared with the response in an inbred-control-line (IC-line) and an outbred-control-line (OC-line). Quantitative protein changes were detected using isobaric tags for relative and absolute quantitation (iTRAQ) two-dimensional liquid chromatography-tandem mass spectrometry. In all, 45 proteins were found to be significantly differently regulated in response to the restrictive temperature in the L-line as compared with the IC-line. No proteins were significantly differently regulated between the IC-line and the OC-line, verifying that differential protein regulation was specific to a genetic defect in the L-line. Proteins associated with oxidative phosphorylation and mitochondria were significantly overrepresented within the list of differentially expressed proteins. Proteins related to muscle contraction were also found to be differentially expressed in the L-line in response to the restrictive temperature, supporting phenotypic observations of moribund muscle hyper-contraction.