Guidelines for experimental design and data analysis of proteomic mass spectrometry-based experiments

Abstract

The end of the 1990s saw a surge in the use of mass spectrometric applications in proteomics research. A huge amount of data was being generated. But proportionally little of the acquired data was being validated biologically. As the years went by it became evident that many false positives were being presented as bona fide results. In 2004, Molecular and Cellular Proteomics (MCP) generated guidelines for proteomics data (Carr et al. 2004). The editorial that accompanies the guidelines published in MCP in 2004 discusses the background to the criteria for publishable MS data. Those guidelines were largely adopted by Proteomics and J. Proteome Res. in subsequent years (see author proteomics data guidelines of respective journals). In 2006, the guidelines were made official and in 2009, MCP had a meeting in Paris to revise and update the guidelines, rendering the criteria for publication more applicable and broadened to include quantitative data (Bradshaw et al. 2006; Chalkley et al. 2009). It is essential, that journals, such as Amino Acids, publishing mass spectrometric proteomics data also adhere to these guidelines. We hope that other journals who publish mass spectrometry proteomics data will follow suit.