To generate the annotated spectra, we used the following workflow: to parse just the msms scan results and the peak list files we used a modified in house max quant parser (https://github.com/compomics/colims/tree/master/colims-distributed/). We then combined the separate results and extracted the relevant msms ids. Subsequently, all relevant data were presented as a PDF composed out of jfreechart (http://www.jfree.org/) charts.