MassFinder Options - retention indices

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MassFinder 4: Manual

The retention indices tab sheet of the options dialog allows to create, edit, delete and check alkane patterns and retention tables. This tab sheet is fundamental for MassFinder's unique two-dimensional search algorithm taking into account the retenton indices of library entries and target scans.


Alkane pattern retention tables

You may store as many retention tables as you need. In most cases it is enough, though, to store one retention table per method you use. Different methods usually have different temperature programs. You need to update your retention tables regularly in order to keep them up-to-date. Always watch the retention indices of constituents you know very well in order to note deviations early.

If you open and save all acquired data files with MassFinder, you do not need to store old retention tables, because the valid retention indices are stored in the *.mfg files of your GC/MS runs forever. We strongly recommend to do so! If you do, you simply can update the alkane pattern whenever necessary and overwrite the exisiting retention table. Thus, we do not recommend to keep a history of retention tables. Try to keep the retention table list in MassFinder as short as possible, i.e. one retention table per method.

Image:Button-Add.png The button add creates a new, empty retention table.

Image:Button-Delete.png The button delete removes the currently selected retention table. You cannot remove the last remaining retention table. One retention table is always present. However, you may rename the retention table and overwrite its content.

Image:Tutorial-ButtonEditName.png The button edit name allows to rename the currently selected retention table. Enter a short description for the retention table, e.g. corresponding with your method name. If you use multiple stationary phase, we suggest to include an abbreviation of your stationary phase in the name of the retention table. Many customers include a reference to the date of the alkane pattern. Please note that this name will be shown in the open dialog selection box. You may edit this name anytime without problems. Example: "DB1-081012" for an alkane pattern measured on 12th October 2008 on a DB1 column with your default temperature program. After updating the retention table, simply rename the table to reflect the new date.

Image:Tutorial-ButtonEdit.png If you want to modify the current retention table manually, you need to deactivate the write-protection by pressing down the edit button. You can then click into the table and enter new retention times. Please note that MassFinder writes cells in black if they are part of a proper retention table, while MassFinder writes all cells in grey if they are outside the proper range. A range is called proper if it does not have any gaps and all times are in increasing order of retention. When finished, click save to save the modified values. You may use the abort button to cancel the edit and restore the previous values.

While editing the retention table, you may select to which retention index field the current retention table belongs. Each MassFinder library entry offers two RI fields called RI1 and RI2, which can be used for different stationary phases. Make sure to select the appropriate retention index field when creating a new retention table. You may read more about this issue in the section Library tools.

Retention table operations

Accept times of marked peaks. The button accept times of marked peaks allows you to transfer the retention times of the marked peaks of the current GC/MS run into the currently selected retention table. This is the easiest and fastest way to update the retention table. To do so, open the new alkane pattern data file, mark all relevant alkane peaks, then use this function to update the retention table. It does not matter whether the alkane peaks are marked as unknown or identified. You may use the auto-report feature to mark the peaks.

Reconstruct table. The button reconstruct table from current GC/MS transfers the retention times from the appropriate scans into the currently selected retention table. This feature enables you to open any old *.mfg data file and reconstruct the retention table of that file. MassFinder will copy the retention times of the all scans with RI 100, 200, 300, and so on into the table. This is useful, if you have at least one file with correct retention index information but other old data files measured with the same method only in your native data file format. However, we recommend to open all acquired data files with MassFinder and the correct retention table and save them as *.mfg files so they contain proper retention indices.

Recaclulate GC/MS. The button recalculate current GC/MS converts the retention times of the current GC/MS into retention indices using the current retention table. This is useful after having updated the retention table to apply the new table to the opened alkane pattern GC/Ms run. After recalculation all peaks of the alkane pattern should have retention indices equal to multiples of 100. This enables you to easily check that the new retention table is correct.

See also

The other tab sheets of the options dialog:

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