In full scan gcms, virtually all fragments ions are generated with each scan of the magnet or quadrupoles (50-600 amu) and recorded. In the full scan methods, no data are lost but extensive computer storage are required. Complete mass spectra for the identification of compounds can be generated from full scan analysis. In the full scan mode, several hundred ions per scan (~3 seconds) resulting in <0.0075 seconds of dwell time per mass. By comparison SIM acquisition records at (~10 ions/ second) resulting in a longer dwell time (~0.01 second/ion) and an order of magnitude better sensitivity and signal to noise ratio. Thus SIM is preferred over full scan data acquisition for quantitively biomarker analysis, even though the same kind of mass chromatograms can be displayed from full scan gcms analysis.
In the full scan GCMS mode, the machine scan over range m/z 60-600 in every three seconds (i.e. over 180 ions/second). About 1 nmol of each compound is required for a reliable spectrum comparable to that required for a discernible peak by flame ionization detection in gas chromatography (GC)
The advantages of different mode of GCMS analysis:
Selected ion monitoring (SIM/GCMS) mode or Multiple ion detection mode (MID/GCMS) or selected ion recording (SIR/GCMS);
In the selected ion monitoring (SIM/GCMS) mode or Multiple ion detection mode (MID/GCMS) or selected ion recording (SIR/GCMS) the machine scan only selected ions (e.g. m/z 217, m/z 191, m/z 253, etc) using a dwell time of 100 milli seconds/ion. Depending on the instrument ~1 pmol is required for a reliable response when only two or three selected ions are monitored. In the result, chromatograms of selected ions can be used as fingerprints for the selected compound type (e.g. steranes, hopanes, monoaromatic steroids)
The advantage of this SIM/GCMS mode is the longer dwell time per ion results in better sensitivity compared with the full scan GC MS mode. In this mode the scientist need to know the retention time and fragmentation characteristics of the molecule to be studied. In order to get the unknown data sometimes full spectral data are used and need hard work.
Full scan GCMS data acquisition mode;
In the full scan GCMS mode, the machine scan over range m/z 60-600 in every three seconds (i.e. over 180 ions/second). About 1 nmol of each compound is required for a reliable spectrum comparable to that required for a discernible peak by flame ionization detection in gas chromatography (GC). Full scan GCMS method provide both the mass spectra for the structural elucidation and chromatograms of all ions. The scientist can compare the mass spectra and ion chromatogram of identification of each specific compounds. The advantages of this Full scan GCMS mode allow tentative structural elucidation. Unlike Selected ion monitoring (SIM/GCMS), no data are discarded. It use more computer disk space and has lower sensitivity or signal to noise ratio due to shorter dwell time than SIM mode.
Parent mode GCMS/MS:
In the parent ion mode of a triple quadrupole or other tendem instrument, the third quadrupole (Q3) monitors daughter ions (e.g. m/z 217) and the first quadrupole (Q1) scans for all possible precursors (parent) ions. Both Q1 and Q2 are normally operated in SIM mode for higher sensitivity. Selected precursors that are allowed to pass through Q1 undergo collision -activated decomposition (CAD) when they collide with neutral target gas in the second quadrupole (Q2). In the Parent mode GCMS/MS provides imporived sensitivity and signal to noise ratio with other modes of analysis. But it is more expensive than most of the instrument.
Parent mode metastable reaction monitoring MRM/GCMS;
Monitor a selected daughter ion (e.g. m/z 217) formed from molecular ions that decompose in the first field free region of a double focusing mass spectrometer. This is a commonly used form of GCMS/MS. MRM/ GCMS offers advantages in sensitivity and signal to noise ratio that are similar to parent mode. GCMS/MS using a tandem instrument. It uses a double focusing magnetic instrument which may be more readily available than a tandem instrument.