GCMS fragment identification

[LabProARW]

I'm trying to understand EI fragmentation, in this case a Phorate molecule. I have run the spectrum at STune with a molecular ion at 260. Makes sense great. I thought the next step to understanding the fragmentation pattern would be to look at each bond and find the one with the lowest bond dissociation energy. Should be the Phosphorus - Sulfur bond. The NIST spectrum fragment with the most abundance is at 75 amu, - but breaking Phorate into 2 pieces at the weakest bond results in one fragment of 107 amu and the other fragment is 153 amu. What am I doing wrong in my reasoning? I am trying to use this type of information to help identify unknowns of other molecules. In my current example there is no Chlorine to help and it is not a straight chain alkane.

All help appreciated!

[bcd_GCLCMSMS]

EI is a "hard" ionization technique that extensively fragments organic molecules. The initial fragments you predicted may continue on to be fragmented further. In addition, the relative intensity and identity of which fragments will best maintain the positive charge also need to be considered. I personally find it difficult to predict an EI spectra a priori.

There are extensive empirically derived tables of common EI fragments and large libraries EI spectra available. Working from these tables and reference spectra should enable you to predict many of the ions, but likely not the relative intensities. The spectra of similar compounds containing the same functional groups is the best way to predict fragmentation.

[Cchandresh]

EI is working not only for the weakest bond. we are providing the 70Ev which will break entire molecule not only from weakest bond.
Base peak is the peak where you will have maximum ions which is considered as 100% and against that rest of the fragments are considered.
Now in EI mode there is a fixed pattern at 70EV and it will not change too much. this is the main reason we have library in EI mode only.
Generally when we are applying 70EV on any molecule it will break compound at all bonds and the maximum ions which will reach to detector will make highest intensity and we are considering that as an base peak.
i think in the case of EI mode you not need to focus on weakest bond in the molecule instead of that you need to focus on the same fragmentation pattern.