MassFinder 3: Features to visualize, interpret and present GC/MS spectra

User interface

MassFinder's main window always displays the gas chromatogram vertically and you may zoom into or stretch the visible area. Peaks can be marked with arrows, with yellow indicating manual identification, red for unknown peaks and blue for automatically assigned peaks.
Three consecutive scans are shown (left column) to facilitate detection of co-eluting peaks, overloading effects or to study substracted spectra and ion traces. You may stretch or shift the mass axis of the spectra with the mouse.
Three library entries are shown (right column) in order of hit quality. By selecting another scan of the GC/MS, the library is automatically searched and the best hits are displayed without further user interaction required.
The user has full control with a minimum of interaction. For navigating the chromatogram, identifying signals and labelling peaks a mouse click is all that is needed.

MassFinder main window

MassFinder's unique two-dimensional search algorithm finds matching library entries not only by their mass spectral similarity but also by comparing their retention indices (which are normalised and system-independent retention times).
For details about this important feature, please read more about retention indices.

Just click on the "flash" icon and MassFinder will auto-assign all relevant peaks defined by your settings (like threshold, peak width). MassFinder applies a smart algorithm, assigning the most probable identifications first and the less probable last (instead of simply processing the peaks in order of elution time). No library entries are assigned more than once and of course you can combine the auto-report with manual identifications, both before and after auto-processing the chromatogram.
View, print and export the report-table with all manual and automatic assignments, including automatic integrals, hit quality and a column for your personal comments.

Another of MassFinder's unique features is the capability of "reverse search". Just select any library entry and click with the right mouse button on its spectrum and MassFinder will search whether this library entry occurs anywhere in the GC/MS run. It has never been easier to search for compounds of interest like substances to isolate or contaminants to be aware of.
If MassFinder can not find the desired substance, it navigates to the retention index (time) the library compound is to be expected, so you may have a look yourself for traces or co-eluting peaks.

labelled gas chromatogram

mass spectrum

MassFinder is particular suited to create and maintain your own mass spectral libraries. Adding, modifying and exporting library entries is highly convenient and using your own libraries efficiently is extremely easy and straight-forward.
only one key stroke ("+") to add a new library entry
only one key stroke ("*") to update an existing library entry
easily update the stored mass spectrum of an existing library entry
conveniently sort and filter library entries by name fragments, base peak, molecular weight, ...
comfortably check quality of entries
export table of library entries

Print both mass spectra and laballed gas chromatograms in publication-ready quality.
Distribute chromatograms over several pages and select whether to include filename, method and acquisition date.
Print collections of all identified peaks or series of library entries for easy documentation!