Proper Benchmark Data for Mass Spectrometry-Based Proteomics

This is a preliminary version of the full website to go online in January 2013.


The aim is to collect data stemming from only measurements of synthetic peptides as their sequence is known a priori. Such measurements can provide a gold standard for benchmarking algorithms in mass spectrometry-based proteomics. Please see Allmer, J. 2012, Journal of Integrative OMICS for details why current datasets are not suitable for benchmarking.

No data has been submitted, yet.


As there are currently no submissions, no credits can be displayed here. Periodically, with increasing data, new release bundles of the overall data will be created and published with all contributors as co-authors.

How to measure

Currently, we are aiming for a basic simple dataset encompassing as many MS instruments and fragmentation methods as possible.

  1. All measurements must originate from pure directly injected synthetic peptides
  2. It would be great if the following points would be considered during measurement but subsets of the requirements below are also helpful
    1. Measure the synthetic peptide at high concentration (10-50 MS/MS spectra)
    2. Decrease the concentration (e.g.: lower the flow rate) and measure 10-50 MS/MS spectra
    3. Keep decreasing the concentration and measure 10-50 MS/MS spectra
    4. Stop measuring when the signal is disappearing in the noise.


As the official web site has not yet been opened, submissions are via email communication: Data may be transferred via Tranche or via some online drive e.g.: dropbox. All submissions must include a description of the procedure (see short form), the data, annotation of spectra in the dataset with their sequence. The laboratory which was used to make the measurements, the list of contributors involved, and supporting grants should be given in order to give proper credit.