Empirical Proteomics Ontology - Knowledge Base (EPO-KB)

Single M/Z Query

Running the EPO-KB New Query Function

During mass spectrometry analysis, a researcher may be interested in the following question: "are there any pre-existing validated proteins in the literature already associated with a certain m/z value?" The answer to this question can save the research both a-lot of time and money, and here is how to find the answer using the EPO Knowledge Base!

  1. Click on the New Query link.

    The New Query link is used to enter a single m/z value. Multiple m/z values can also be entered at one time by clicking on the Batch Query link. The output for this query is a little bit different. The steps to using the Batch Query function are found in the "Batch Query Tutorial."

  2. Paste your m/z value into the M/Z value window (the m/z value 13,750 will be used for this example).

    Other optional parameters can be specified to fine tune the search for the given m/z value. The Percent Width specifies the range of the window around the given m/z value to search for. For example, if the Percent Width is .5% and the given m/z value is 13750, the range will be 13750 +/- .005 * 13750 = (13681, 13,819) or a range from 13,681 to 13,819 M/Z.

    Query Front End

  3. Click the Query button and wait for the results!

    Query Results

 

Understanding the EPO-KB output

The output of the EPO knowledge base is fairly simple to follow but below are some definitions that might help clear up some ambiguities. The valuable part about the output is that the information can possibly save a researcher a significant amount of time and money. The time speed up is two fold:

      1. The researcher can search through the litterature stored in the knowledge base for pre-identified validated biomarkers and their protein counterparts.

      2. The proposed list of biomarkers gives candidate proteins associated with that m/z which would require a much quicker procedure using an affinity chromatography experiment to discover if the identified peak is one of the listed proteins. This however might still require the full sequencing if the protein is not listed in the knowledge base.

Since it is costly to perform sequencing, the ability to have possible proteins without having to sequence the peak provides a cheaper alternative since sequencing is more expensive than affinity chromatography, which would have to be performed regardless of which method you utilize to acquire the list of possible proteins.

An overview of the EPO-KB output

  1. The score: In general, the closer the user inputted m/z value is to the m/z value for the pre-identified biomarker protein, the smaller the score. In actuality, the scoring function is a little more complex.

  2. The protein biomarker(s): The name of the protein(s) found during the search. If its desired to increase or decrease the number of biomarker proteins outputted, change the percent width metric on the following screen.

  3. The protein individual: This section contains the basic information pertaining to the protein biomarker. For example, the beginning and ending position along the amino acid chain for the protein is given along with a link to the UniProt ID for the protein.

  4. Corresponding Mass to Charge: This section contains the link to the paper in the literature associated with the validated protein biomarker. Additionally, the experimental protocol parameters are provided (i.e. biofluid type, platform, substrate used).

  5. Re-query: After the first query, the user can start a new query, by selecting the "Start a New Query" link or refine the current results by changing the query parameters and clicking on the query button.