Welcome to the RockerBox project page


A major problem in the analysis of mass spectrometry-based proteomics data is the vast growth of data volume, caused by improvements in sequencing speed of mass spectrometers.
This growth affects analysis times and storage requirements so severely that many analysis tools are no longer able to cope with the increased file sizes.

RockerBox, addresses size problems for search results obtained from the widely used Mascot search engine by filtering the files, without altering their informative content.
Filtering is done based on manual parameters or automatically based on a number of FDR calculation methods.

Moreover, RockerBox allows for a fast evaluation of large result files by means of a number of commonly accepted metrics which can often be viewed through charts.


(this page was previously hosted on




  • Filter .dat files, output a fully functional filtered .dat file, a .csv file or .mgf file
  • Cool charts, X-Y plot for numerical values on PSMs
  • Transforms the .dat file into a .dat.db file
    • Database in a single file
    • Quick access times
    • Handle large .dat files (tested up to 1 million spectra)
  • Note:The output is written to a folder next to the input .dat file




RockerBox requires Java version 8 or newer.




RockerBox has been packaged in several ways:

  • Windows executable [wpfilebase tag=file id=101 /]
  • Java executable .jar file (for other operating systems) [wpfilebase tag=file id=98 /]



van den Toorn HW1, Muñoz J, Mohammed S, Raijmakers R, Heck AJ, van Breukelen B. RockerBox: analysis and filtering of massive proteomics search results. J Proteome Res. 2011 Mar 4;10(3):1420-4. PMID: 21184612. [PubMed] [Read by QxMD]