Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements in the nanos transcript. A comprehensive mass-spectrometric analysis of the repressor complex identified known and unanticipated components. Superstochiometric binding of a heterooligomeric protein complex along the nanos-mRNA might explain the unusually stable, Smaug-dependent translational repression. Cross-linking in combination with mass spectrometry is a versatile tool that can be used to analyse protein-protein networks or protein structures in solution. Bioinformatic analysis of the complex samples presents the bottleneck of this technique and might be overcome by specialized software tools. Two software tools, presented in this thesis, StavroX and MeroX, can be used to automatically analyse cross-linking/MS datasets with high efficiency and low false discovery rates.