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GC/MS-Full Scan vs GC/MS-SIM

February 15th, 2008

GC-MS-Full-Scan-vs-GC-MS-SIMIf you’ve had your laboratory run low-level polyaromatic hydrocarbons (PAHs) or other low level analyses, chances are you have heard of Gas Chromatography/Mass Spectroscopy- Selective Ion Monitoring (GC/MS-SIM). Over the years clients have asked us “What’s the difference between GC/MS-Full Scan and GC/MS-SIM?” To address this question we must start with the basics. (For our example we will be talking about a standard quadrupole mass spectrometer using electron ionization.)

GC/MS is an instrumental analytical technique comprised of a gas chromatograph and a mass spectrometer. In general, the GC is used to separate complex chemical mixtures into individual components. Once separated, the chemicals can be identified and quantified by the mass spectrometer.

Before analysis can occur a sample must be prepared, usually by extracting the analytes of interest into a liquid solvent phase. This extract is then injected into the GC where it is swept onto a separation column by an inert carrier gas such as hydrogen or helium. The analytes in the mixture are carried through the column by the carrier gas where they are separated from one another by their interaction between the coating (stationary phase) on the inside wall of the column and the carrier gas. Each analyte interacts with the stationary phase at different rates. Those that react very little move through the column quickly and will exit into the mass spectrometer before those analytes having longer interaction and retention times.

When the individual analytes exit the GC column they enter the ionization area (ion source) of the MS. Here they are bombarded with electrons which form ionized fragments of the analyte. These ionized fragments are then accelerated into the quadrapole via a series of lenses and separated based on their mass to charge ratio. This separation is accomplished by applying alternating RF frequency and DC voltage to diagonally opposite ends of the quadrapole, which in turn allows a specific mass fragment to pass through the quadrapole filter. From here the fragments enter the mass detector (electron multiplier) and are recorded. The MS computer graphs a mass spectrum scan showing the abundance of each ionized mass fragment.

A GC/MS system in Full Scan mode will monitor a range of masses know as mass to charge ratio (abbreviated m/z). A typical mass scan range will cover from 35-500 m/z four times per second and will detect compound fragments within that range over a set time period. Laboratories have extensive computer libraries containing mass-spectra of many different compounds to compare to the unknown analyte spectrum. The Full Scan mode is quite useful when identifying unknown compounds in a sample and providing confirmation of results from GC using other types of detectors.

Operation of a GC/MS in SIM mode allows for detection of specific analytes with increased sensitivity relative to full scan mode. In SIM mode the MS gathers data for masses of interest rather than looking for all masses over a wide range. Because the instrument is set to look for only masses of interest it can be specific for a particular analyte of interest. Typically two to four ions are monitored per compound and the ratios of those ions will be unique to the analyte of interest. In order to increase sensitivity, the mass scan rate and dwell times (the time spent looking at each mass) are adjusted.

When properly setup and calibrated, GC/MS-SIM can increase sensitivity by a factor of 10 to 100 times that of GC/MS-Full Scan. Because unwanted ions are being filtered, the selectivity is greatly enhanced providing an additional tool to eliminate difficult matrix interferences.

The ability of the mass spectrometer to identify unknowns in the full scan mode and quantitiate know target analytes in the SIM mode, makes it one of the most powerful tools available for trace level quantitative analysis in the lab today.


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16 Responses to “GC/MS-Full Scan vs GC/MS-SIM”

  1. jayesh darji Says:

    Pl provide method of analysis of O-dichlorobenzene & Dimethylcarbamoyl chloride by GC/MS-SIM if, possible.

  2. Dee O'Neill, Columbia Analytical Says:

    We can run dichlorobenzene by EPA Method 624, 524, 8260 or 8270, SIM or full scan. We have never run dimethylcarbamoyl chloride. Let us know if you have any further questions.

  3. jayesh darji Says:


  4. david henderson Says:

    This explanation of SIM vs SCAN is misleading in the reasons why SIM has a better S/N ratio. When using SCAN mode, one can use software to filter out all the unwanted ions. Thus this filtering effect is not the reason for enhanced sensitivity.

    The actual reason relates to the time spent monitoring the ions of interest in the two modes. A SCAN mode spectrum typically requires about 1 second to obtain. If one scans from 50-550 M/z, then the dwell time on one mass is about 2 ms. One is monitoring each ion of interest for only 0.2% of the total scan time and data points are spaced at 1 second intervals.

    In SIM mode, the fact that you spend the entire time monitoring only the ions of interest means you have longer time to accumulate data for those ions and hence get a larger signal. At the same time, the longer monitoring time provided more opportunity for noise to cancel. The S/N improvement should be related to the relative time spent integrating each ion.

    Another problem in fast GC-MS analysis is that peaks are often only a few seconds wide. One needs at least 8 data points to accurately define a gaussian peak. Thus a SIM mode scan can be set up to acquire more data points across a peak and provide a more accurate profile.

  5. Dr. Vivek Dhole Says:

    Generally for the quantification in GC-MS, “SIM mode” is prefered compared to “SCAN mode”. Further do we also need to use standards of known concentrations for quantification? as we use in case of GC for quantification. Kindly explain.

  6. Columbia Analytical Says:

    Yes, certified standards are used to plot calibration curves prior to quantitation.

  7. vani Says:

    After the GCMS SIM mode I see the chromatogramn similar to SCAN mode with peaks? Do i use that peaks correlated a compound to obtain the calibration curve?

  8. Dee O'Neill Says:

    Hello Vani.

    I would suggest you review the EPA’s guide to calibration found at the following location: I think it gives the most comprehensive answer to your question.

  9. ahmad Says:

    I acquired SIM and SCAN data simultaneosly but found peak area of SCAN data higher than peak area of SIM data. However it is said that SIM analysis is more sensitive ( 10 -100 times). Please explain.

  10. Tom Kissinger Says:


    You cannot compare areas when running this as you are not comparing apples to apples. The principle for SIM is that you are scanning fewer ions per second than you are for a full scan, thus you have greater signal to noise ratio (not abundances). Hope this helps!

  11. Linda Says:

    What is the most accurate lab to test for hexavalent chromium 6, manganese, arsenic and some other toxic chemicals.
    Also best lab to test human and animal tissue.
    Thank you

  12. admin Says:

    Hello Linda,

    Of course, we think we’re the best lab to test for your analytes of interest, however, any lab that holds the proper certifications for the tests you want to have done can perform the tests for you. What tests you need to have run depends on the regulatory program to whom you’ll be reporting the results. Different analytical methods have different limits of detection – from high to the low. The cost of the test is usually higher for the lowest levels of detection. As far as matrix type – again you need to see if the laboratory is certified to perform the analyses for that particular matrix. The question of human or animal tissue makes me wonder if you are asking this question for medical reasons. If that is the case you will need to contact your health provider or local health department to provide information on how levels of these analytes affect health.

    Thank you,

    Columbia Analytical Services, Inc.

  13. Cosmas Mutsimhu Says:

    Q1 I acquired GC-MS SIM and Full Scan simultaneosly and Full Scan gave lower LOD than SIM but full scan gave higher MDL than SIM MDLS in EI and PCI.But it said SIM is more sensitive than full scan.

    Q2 Is EI more sensitve than PCI and NCI?

  14. Miguel Says:

    Cual seria la tempoeratura apropiada en la rampla para utilizar el metodo Full Scam????

  15. Veronica Says:

    I want to ask if SIM mode for acquisition (and also for calibration) is enough for confirmation of an analyte in a sample. I used one prominent ion for quantitation and two or three ions for qualification. Thanks

  16. M. Suresh Says:

    Dear All, Please send Dimethylcarbamoyl chloride method of analysis if available with you. I tried in the GC-HS and also injection technique, and observed two split peaks instead of one.

    Kind Regards,

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