MS/MS
 
 
 
 

Fragmentation in the Drift Tube

The usual mode of operation for a Time-of-Flight mass spectrometer is to take a packet of ions in the ion optics and pass this packet unhindered and unmodified to the detector. Looking at Fig. 1 this would mean the ion gate is open and there is no gas in the collision cell. This way we will get a mass spectrum showing the masses of the intact ions.
 

In order to get structural information about the (molecular) ions just measured, we have to break them up and measure the weights of the fragments. This is done by filling the collision cell with a gas, preferably Helium. The ions will then collide with the Helium atoms, these collisions exiting internal vibrations. When the amplitude of the vibrations becomes too high the ions will start breaking apart, usually tearing up the weakest bonds first. These weakest bonds are in most cases the links between subgroups of the molecules.

Lets first look at the experimental results of fragmenting molecules in the drift tube, and then attempt to put this into mathematical formulas. Fig. 2 shows three mass spectra of water clusters:


Two things are immediately apparent from Fig. 2:

Fig. 3 shows the (H2O)67H+ and the (H2O)68H+ cluster and mingled in between the isotopes of the (H2O)67H+ cluster the first fragment of the (H2O)68H+ cluster, i.e. a (H2O)68H+ cluster having lost one water molecule. Very well it can be seen where the isotopes of the first fragment are and how different fragments will add up to the resulting spectrum which is the black trace.

Stepping some 17 or 18 mass units to lower mass, we can see in Fig. 4 around mass 1190 the first fragment of the (H2O)67H+ cluster and the second fragment of the (H2O)68H+ cluster. A little bit further to the left we then find the second fragment of the (H2O)67H+ cluster and the third fragment of the (H2O)68H+ cluster. Fig. 2 shows how this series continues over many fragment losses.

Thus the most important piece of information we gather from the figures above is that if a molecule looses some part of its constituents, it will not appear exactly at the mass of its residual mass but at a mass somewhat higher. Actually this shift towards higher mass is proportional to the mass of the fragment that has been lost in the drift tube, this factor of proportionality being a calibration constant specific to each instrument.

Looking again to Fig. 1 this fragment shift can easily be understood. Just divide the path of an ion between the extractor and the detector into two segments:

The idea of separating the path into these two segments is that the point of separation is a time focus point, i.e. a point in space which all ions of the same mass simultaneously pass, irrespective of their initial kinetic or potential energy. This time focus point is called Wiley-McLaren focus, and the time an ions needs on any one of the segments is only a function of its mass and not of its initial or final energy. (Note that an ion loosing some mass on its flight also looses some energy, which would very much complicate our calculation if we did not split up the path in the above way.)

Now all you have to do is compare two paths of two particles:


Since the first segment is only a part of the complete path, this means that if the particle had a higher mass on this segment, the mass or time shift incurred on this segment must be multiplied ratio of the first time segment divided by the complete time-of-flight, thus

m + dm = m + mf*Sf/S

where

  m   :   is the final mass of the particle
  dm :   is the apparent mass shift of the residual particle after fragmentation
  mf  :   is the mass of the fragment lost in the collision cell
  Sf/S :  is the ratio of the length of the first segment to the total length of the flight path
 
 

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