Multiple comparisons in mass-spectrometry-based -omics technologies

• We present a review on the statistical tools used to deal with multiple comparisons.
• We discuss the fundamental theoretical concepts and ideas.
• We present application to metabolomics and proteomics.

Survey technologies, such as metabolomics and proteomics, play increasingly important roles in the investigation of complex biological systems. These methods produce data sets that typically provide a huge amount of information using relatively few samples, so that finding differences between two groups, a fairly common question in this context, runs the risk of leading to many false positives. Often, the comparison is made on several thousand experimental variables, and strategies to correct for multiple-testing issues are necessary.We highlight the most important ideas, and assess their applicability in the fields of mass-spectrometry-based proteomics and (especially) metabolomics.