Guidelines to build an entry I

Guidelines I

Guidelines to build a library entry I.

1 Analyze compounds in the DAU, RFD and /or Source CID mode.

First, spectra of a compound have to be acquired. The intention is to get a series of spectra of a range of offset voltages. The scan mode to be used depends on the instrument and scan modes available.

For a Triple Quad mass spectrometer the daughter or product ion scan mode is very useful, because it only gives daughter ions belonging to the selected parent or precursor ion. The RF-only Daughter scan mode [1, 2 ] can be used for additional information. It gives both fragment ions and isotopic ratios.

For an ion trap mass spectrometer several MS/MS stages must be performed to get a range of fragment ions. The number of stages depends on the fragmentation of a compound. When after the first stage only one fragment ion dominates the spectrum, this ion must be selected for the next stage and so on.

The Source CID scan mode of an API source can also be used. In this scan mode it is not possible to select a parent ion. All ions formed during ionization are involved in the fragmentation process. Therefore loop injections or retention time is needed to find the specific ions after background subtraction. A disadvantage of the Source CID mode is the fact, that even adduct ions of fragment ions can be found in the spectra.

Fig. 1 to 3: Single spectra of atrazine at three offset voltages.

2. Make a list of all ions belonging to the compound.

Above three spectra of atrazine at different collision offset voltages are shown.
Make a list of all masses, e.g. by combining the mass lists of the spectra.
Be sure that each ion belongs to the compound.
This is especially important for the RF-only daughter and the Source CID modes.

For GCMS criteria to identify a compound, 3 to 5 specific masses in combination with a retention time are used. So 10 to 20 masses must be far enough to describe a compound. Therefore low abundance masses (<1% in all separated spectra or in the combined spectrum of the offset voltage range) are discarded in spectra with more then 20 masses. In the library spreadsheet file a maximum of 50 masses can be entered for each entry.

3. Calculate isotopic peaks of the highest masses.

Isotopic peaks (A+1, A+2 etc.) of each A-ion [3, Mc Lafferty] can be calculated from the formula of an ion. This formula is often known for the highest masses, but not for the lower fragment ions.
So enter at least the isotopic ratios of the molecular ion(s). Try to determine and enter all fragment ions with Cl, BR and S - atoms. When it is not sure that an ion is an isotopic ion (e.g. the Cl-37 isotope of an fragment ion has the same m/z as another fragment ion. In such a case the measured ratio is not the same as the theoretical value) treat the isotopic ion as a normal fragment ion (at 50 or 100%).
The isotopic ratios are calculated for the molecular ions and fragment ions of which the structure is known to prevent wrong values caused by the normal variations of an ion signal.