MassFinder Options - configuration

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MassFinder 4: Manual

The configuration tab sheet of the options dialog controls basic settings for visisualising, searching and reporting chromatographic and mass spectral data.


Generel settings

default visible mass range

The default visible mass range edit boxes control the visible mass range of the main views's mass spectra.

Please note that MassFinder always uses the entire mass spectrum for similarity searches and all other mass spectral operations. Thus, this setting only determines which mass range is visible by default. You may shift, stretch or zoom the visible mass range whenever you want.

Adjust the default visible mass range to the m/z range typically required for your compounds of interest. Do not use too wide mass ranges if not actually needed. MassFinder default mass range is 35 - 240 which covers most volatile compounds up to sesquiterpene hydrocarbons.

Please note that MassFinder will display '+' sign on the left or right side of the m/z axis to indicate that some signals with lower of higher mass, respectively, are not displayed.

automatic zoom

The automatic zoom check box instructs MassFinder to automatically adjust the intensity axis of the total ion chromatogram (the chromatographic profile) after having zoomed into a part of your GC/MS run. The most intense peak will always exactly fit into the profile panel. This mode is the default mode. It makes navigating very convenient.

If deactivated, MassFinder keeps the intensity axis constant while zooming. The advantage of this mode is that equally intense peaks look equally large no matter which peak is the largest peak in the currently visible range. Experienced spectroscopists sometimes prefer this mode in order to more easily keep track of the relative amounts of peaks.

localisation settings

inverse jump order

This check box inverses the function of the '<' and '>' keys. This is necessary due to different international keyboard layouts and a consequently differently felt intuitive function of the keys.

  • English keyboard users please deactivate this check box.
  • German keyboard users please activate this check box.

export with decimal comma

This check box instructs MassFinder to export all floating point values with decimal commas instead of decimal points. This is necessary due to different localised versions of Microsoft Excel and similar software systems.

  • English users please deactivate this check box.
  • German users please activate this check box.

Search algorithm

use ignore noise mode

This option controls how MassFinder's similarity search algorithm reacts to high-molecular noise. If activated, MassFinder tries to ignore irrelevant peaks with low abundance in the higher m/z range.

We recommend to activate this option if your mass spectra exhibit a lot of high-molecular noise, e.g. due to columb bleeding or inappropriate cut-off level. We recommend to deactivate the option if your spectra show no extra signals at high m/z values. By default, this option is deactivated.

Hot-key: You may toggle this option on/off by pressing the key 'r' while being in the main view.

use library match mode

This option controls how MassFinder's similarity search algorithm compares mass spectra with each other. If activated, MassFinder will only compare the library entry's signals with the target spectrum and ignores all signals that exclusively occur in the target spectrum. This is advantageous if the target spectrum is not pure. However, the rate of misidentifications increases due to possibly ignored target signals.

If you use this option while the two-dimensional algorithm is activated (i.e. retention indices are taken into account), the rate of misidentifications is fairly low. If the two-dimensional algorithm is also deactivated, the rate of misidentifications rises drastically; but some of these misidentifications might be useful: For example, in many cases terpene alcohols and their acetate esters have many signals in common. Watch the results carefully and decide which library hits are relevant or interesting.

If deactivated, MassFinder will compare all signals with each other, both those of the library entry and those of the target spectrum. This is the default mode.

Hot-key: You may toggle this option on/off by pressing the key 'l' while being in the main view.

use two-dimensional algorithm

This options controls whether MassFinder takes retention indices into accout or not. By default this option is activated. Using retention indices in addition to mass spectral similarity drastically increases the hit quality of library matches.

However, using this method requires to properly set-up the retention table and to keep it up-to-date.

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