This ontology knowledge-base was designed to capture empirical proteomic knowledge into a form that is easy to understand, while incorporating the ability to record m/z ratios identified within the literature. It records the value found within the whole sample spectra and links it to the protein that was identified and validated.


The UniProt ID is used to identify which protein the M/Z value is associated with - this includes any potential modifications to the protein.  The structure of the ontology can be viewed here, and the references for the ontology can be viewed here.Additionally, the user can submit protein biomarkers into the ontology.  If submitting, please use the submission form to add new proteins and follow the instructions.  To query a single m/z, please use the New Query link.  To query multiple m/zs at the same time, please use the Batch Query.

Thank you!
Sincerely,
Jonathan L. Lustgarten

****UPDATE 05/05/2009****

More of the literature has been added! Please see Query the Knowledge-Base for more details

We have also begun to implement a filtering resource such that a person can submit their dataset and filter the m/zs based on user preference.
It is similar to the approach used in: Lustgarten, et al. Knowledge Based Variable Selection for Learning Rules from Proteomic Data. Presented at the AMIA STB 2009.