Show and edit mass spectral libraries

The latest OpenChrom Community Edition 1.1.0 “Diels” contains a lot of improvements to visualize and edit mass spectral libraries. Several formats among others like *.msl, *.msp and *.jdx are supported now. Please select the “Mass Spectrum / Library” perspective.


The perspective can be selected also via the  perspective switcher (Menu > Window > Perspective Switcher), e.g. to select the “Chromatogram Overlay”. In this case, please select the “Mass Spectrum / Library” perspective.


The second upper left tab is the “Mass Spectrum Library Explorer (MSD)“. Please explore your file system. All libraries are marked with a red icon. A double click on the library opens the library editor. On selection of each entry, its mass spectrum is displayed in visual as well as in list representation. If synonyms are stored, these will be displayed too.


The “x” button deletes entries from the library. The “+” button lets you create a new library entry. A default entry with the name “Add a name” is created then. The search filter is automatically set to the “Add a name” search term.


The name, retention time and other values can be edited directly. Please disable to the autofocus functionality, otherwise each click on an entry would cause a new update which disables to edit the selected cell. Please go to the preferences (Menu > Window > Preferences) and disable “Show the perspective dialog” and “Change perspectives and view automatically“.


Then rename the entry e.g. to “New Entry” and clear the search term.


Then e.g. set the retention time to “1.78” minutes.


The mass spectrum can be edited too. Select the “Mass Spectrum Edit List” view.


Synonyms can be added too.


It’s also possible to merge other libraries into the current one. Please press the button on top right to activate the merge library buttons. Please select another library by using the “Select Library” button. After the library has been selected, merge it via the “Merge Library” button.


All entries are displayed in the list now. If the library contains more than 10,000 entries, please use the search term to display entries.


It’s possible to calculate SMILES formulas for each entry. This could fail for some entries due to wrong IUPAC names and missing CAS numbers.


The results are displayed in the SMILES column.


Use “Save” to save the modifications or “Save As…” to export the library into a different format.


1 Comment

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s