Absolute concentrations of proteins that have been experimentally determined in specific tissues or biofluids by proteomics approaches can vary based on the methods used, such as the digestion protocol or even depending on the peptides selected to represent a given protein. This means that while quantification of the individual surrogate peptide concentrations may be accurate, results from many experiments using multiple surrogate peptides need to be integrated to determine an accurate concentration range of the target protein in a specific tissue or sample type.
An international team of researchers from Canada, Netherlands and Germany designed a knowledge base called PeptideTracker for collecting and storing information on protein concentrations in biological tissues derived from different experiments along with the acquisition protocols and conditions used. PeptideTracker has a web interface and is designed to store information on SRM or MRM measurements (selected reaction monitoring and multiple reaction monitoring, respectively). Using the “Wikipedia approach” whereby information is made more accurate over time, the goal of the project is to populate the database with empirical data on surrogate peptides from a large number of samples and from multiple laboratories that will let the protein concentrations converge to their true concentration ranges.
PeptideTracker currently includes information on human, mouse, rat and pig proteins. Scientists are encouraged to submit information on their own synthetic peptides and observed peptide and protein concentrations for inclusion in the knowledge base online. Further details,links and related protocols can be found in the Technical Brief published in PROTEOMICS.