Storing data from several GC-Tof's in one BinBase database

With BinBase 3.4 we introduce a new couple of possibilities. One of them is the possibility to store the data from different LECO GC-Tofs, which are using different acquisition methods, in one database.

This feature was needed, since a lot of people wanted to measure there data locally, But used slightly different data aquistion methods.

 For example as long as you use the same column in all machine, the flow rate can be different between the measured machines. The retention index correction will automatically shift the peaks to the right position.

It is possible to compare massspecs from different GC-Tof's if they have a different range. For example our database is build on spectra which contains fragments from 85-500 masses, which we recommend and which is the BinBase default setting for derivatized compounds. Now we became some samples which spectra had a range of 85-750 masses.

So we introduce a new configuration in BinBase to automatically remove the unused masses from the spectra, to be able to calculate similarity scores. You do need to be careful to compare data, if the unique mass is below the minimum defined fragement, since the annotation will fail in this case.

Configuration of Massspec fragment ranges

The configuration is done in the binbase.xml file which can be found in the config directory on the application server.

         <!--  similarity settings, basically needed for the similarity algorythm -->
        <similarity>
                <!-- defines the different ranges for the different columns -->
                <range>
                        <!-- all massspec in the binbase column, this is only interressant if you have more than the default column, or your massspecs have different masses than the registered standards -->
                        <column name="rtx5" beginFragment="85" endFragment="500" />
                        <column name="mdn35" beginFragment="85" endFragment="500" />
                        <column name="volatile" beginFragment="1" endFragment="1000" />
                        <column name="test" beginFragment="1" endFragment="1000" />

                </range>
        </similarity>

Please don't forget that a spectra can't have more than a fragment range of 0-1000 in the current BinBase version. This is a limitations because of memory and speed issues.