Import and preprocess spectrum data (BioNumerics 7)


In this video, I will show how we can import and preprocess spectrum data files using a database with levels. As you can see in the Database design panel, the necessary levels are already created. My dataset consists of spectra from several species, for each species, several isolates
have been analyzed, and for each isolate, there are multiple technical replicates. Before I can start importing spectrum data in my database, I need to create a spectrum type experiment. I press the button ‘Create new experiment
type’ and I select ‘Spectrum type’ from the list. I enter a name for the spectrum type and press ‘Next’. In the second and last window, I can specify which template to use as default. I select the last option and press ‘Finish’. The new spectrum type now appears in the Experiments panel. Next, I will import several spectra from text files. These files contain a list of mass-intensity points. Most important manufacturers allow for export in this format. As I will be importing raw spectra data, I
will import the data in the level Raw spectra. I need to make sure this level is active. I press the ‘Import’ button in the toolbar and under ‘Spectrum data’, I select the option ‘Import spectrum data’. In the next window, I browse for my files. I press ‘Next’ to go to the next step where the import template can be defined. There is one import template included by default. This template will create a new entry for
each spectrum with an automatically generated key. As I wish to include several pieces of information available in the file name, I will define my own import template. The only source of information that is available is the file name. As this is unique per spectrum, I can use
the file name as a Key. I select the row, click on the ‘Edit destination’ button and select ‘Raw spectra key’. The entire file name will now be used as Key in the lowest level. Next, I will create all the links to the higher
levels. I make sure the ‘Advanced options’ is
checked to visualize some additional options. I will add a new rule choosing the file ‘Name’ as data source and the ‘Species key’ as data destination. The Species is the first part of my file name before the underscore, so my parsing string will be [Data]_* The term ‘Data’ represents the piece of information I am interested in; an asterisk is used as wildcard and will match anything. I will add a second rule, again with file ‘Name’ as data source, but now with the ‘Isolate key’ as destination. In my file name, the part that identifies
my isolate can be found in the start of the file name, before the hyphen. Therefore, my parsing string will be [Data]-* After finalizing all rules, I can verify that all information is parsed correctly by pressing the ‘Preview’ button. This will give you an overview of all the
information that will be included in the import of the spectrum data. I close the preview and I can go to the final step. When importing information into a Key, this will automatically be used to create any links to information already in the database. Finally I need to specify a name for my new template. I make sure my new template is selected and my ‘MALDI’ experiment type, and I press ‘Next’ to go to the next step. An overview is given of the actions that will be performed during the import. As my database is empty, no entries will be updated, only created. As my spectrum files originate from 8 different isolates, and three different strains, and each isolate has been analyzed in tenfold, these numbers are indeed what I expect and I can continue to the next window. In the last step I can press ‘Finish’
to finalize the import of the spectra. Once the spectra have been imported, the Spectrum preprocessing window will open. To execute an action in the workflow I can simply click on it. If I click on the last action the entire preprocessing workflow will be executed at once. I will leave the default ratio and press ‘Next’. Once the calculation is finished I can save the results to the database by selecting ‘File>Save spectrum data’. The Spectrum preprocessing window can now be closed. If I would want to make changes to the preprocessing later, I can open this window again with the entries selected in the database by pressing ‘Analysis>Spectrum types>Open preprocessing window’. This ends this video, please tune in to our other videos where more functionality is explained.

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