GC-MS Discussion Examples | Molecular-Ion Peaks and Fragment Analysis

What Is GC-MS?

GC-MS is an analytical method that combines GC and MS.
First, components in the sample are separated by GC according to differences in time, and each component is introduced into the MS.
In MS, the introduced components are ionized, and the resulting molecular ions and fragment ions are detected according to their mass-to-charge ratio, or m/z.

With GC alone, components are estimated from retention time, but it may be difficult to distinguish another component with a similar retention time.
GC-MS provides a mass spectrum in addition to retention time, allowing more reliable identification based on information about molecular weight and partial structure.

Main Items to Include in the Results

In GC-MS results, organize the retention time of the chromatogram, peak area, mass spectrum of each peak, molecular-ion peak, base peak, major fragment peaks, isotope peaks, library-search results, and other information.
Because GC and MS conditions affect the identification results, the measurement conditions should also be clearly stated.

Main Items to Include in the Results

• Sample name
• Analyte
• Column used
• Carrier gas
• Column temperature conditions
• Inlet temperature
• Injection volume
• Ionization method
• Measurement mode
• Measured m/z range
• Retention time
• Total ion chromatogram
• Peak area
• Molecular-ion peak
• Base peak
• Major fragment peaks
• Isotope peaks
• Library-search results
• Candidate compounds
• Basis for identification
• Sources of error and points for improvement

Reference Experimental Values and Analysis Examples for GC-MS

Here, the process of identifying components in a mixed sample using retention time, molecular-ion peaks, fragment peaks, and library-search results obtained by GC-MS is organized using reference experimental values.

In GC-MS, a mixture is separated into individual components by gas chromatography (GC), and the mass spectrum of each peak is measured by mass spectrometry (MS).
GC retention time reflects the volatility of each component and its interaction with the column, while molecular-ion peaks and fragment peaks in MS provide clues to molecular weight and structural estimation.

Reference Experimental Conditions

Information Obtained From GC-MS

GC-MS Measurement Results for a Standard Mixture

A reference example is shown for measurement of a standard mixture containing acetone, toluene, ethyl acetate, methyl benzoate, and limonene.

Even limonene and methyl benzoate, which have the same molecular weight of 136, can be distinguished because their retention times and fragment peaks differ.
In GC-MS, it is important to combine retention time and mass spectrum.

Example Calculation of Relative Composition From Peak Area

The relative amount of each component in a mixture can be determined from the peak areas in the GC chromatogram.
Here, the calculation is performed as a simple area percentage without correcting for differences in sensitivity.

The area percentage is calculated using the following equation.

Area percentage (%) = Area of each peak ÷ Total peak area × 100

If the peak area of limonene is 480000 and the total peak area is 1500000,

Area percentage = 480000 ÷ 1500000 × 100 = 32.0%

However, because ionization efficiency and detection sensitivity differ among components, the area percentage cannot be regarded directly as a mass percentage.

MS Fragment Analysis of Acetone

The molecular-ion peak at m/z 58 indicates a molecular weight of 58, while the strong peak at m/z 43 suggests a compound containing a carbonyl group.

MS Fragment Analysis of Toluene

Because m/z 91 appears strongly as the base peak, it provides a clue for considering the presence of a benzyl structure or alkylbenzene.

MS Fragment Analysis of Methyl Benzoate

The difference from m/z 136 to m/z 105 is 31, which can be considered to correspond to loss of an OCH3 group.
The strong peak at m/z 105 provides a clue indicating a compound with an aromatic carbonyl structure.

Example of Distinguishing Components With the Same Molecular Weight

In GC-MS, even components having the same molecular weight can be distinguished from differences in retention time and fragmentation pattern.
Limonene and methyl benzoate both have a molecular weight of 136, but their spectra differ greatly.

Even when the molecular-ion peaks are the same, the components can be judged to be different because the retention times and base peaks differ.

Example GC-MS Measurement of Unknown Sample A

A reference example is shown in which three major peaks were observed when unknown sample A was measured by GC-MS.

Unknown sample A may contain toluene, limonene, and methyl benzoate.
In particular, peaks 2 and 3 both have a molecular ion at m/z 136, but because their retention times and fragments differ, they can be judged to be different components.

Area Percentages of Unknown Sample A

From the area percentages, limonene was detected as the largest peak in unknown sample A.
However, because GC-MS peak area is affected by differences in sensitivity among components, a calibration curve or internal-standard method is necessary to determine accurate concentrations.

Example of Interpreting Library-Search Results

In GC-MS, the measured spectrum can be compared with a database to display candidate compounds.
However, even when a candidate with a high match score is obtained, it is important to confirm the result together with retention time and comparison with a standard substance.

Library-match score is a powerful clue for component identification, but misidentification may occur because of coelution, noise, or isomers with similar spectra.

Spectral Disturbance Caused by Coelution

Coelution refers to two components that are not sufficiently separated and are detected overlapping near the same retention time.
When coelution occurs, the mass spectrum becomes a mixture of multiple components and the library-match score may decrease.

If coelution is suspected, the separation must be improved by changing the column conditions or temperature-program conditions.

Changes in Retention Time and Separation Caused by the Temperature Program

In GC, retention time and peak separation change depending on the oven temperature program.
If the temperature is increased too rapidly, the analysis time becomes shorter, but peaks may overlap more easily.

In GC-MS component identification, it is necessary to check not only the mass spectrum but also whether the components are sufficiently separated in the chromatogram.

Errors When Judging From Retention Time Alone

Retention time is a clue for component identification, but it is risky to identify a component from retention time alone.
Different compounds may show similar retention times.

Even if retention times are close, compounds can be judged to be different if their molecular ions or fragments differ.
Therefore, it is important to examine both retention time and the MS spectrum.

Reference Example of Quantitation by the Internal-Standard Method

For more accurate quantitation, an internal standard is added and the peak-area ratio is used.
Here, a reference example using ethylbenzene as the internal standard is shown.

The internal-standard method can compensate to some extent for variations in injection volume and instrument sensitivity.
It is effective when greater quantitative accuracy than simple area percentage is required.

Example of How to Write the Results

When the standard mixture was measured by GC-MS, peaks were observed at retention times of 2.15, 3.42, 5.80, 9.65, and 12.30 min.
Comparison of the mass spectrum of each peak with the library suggested acetone, ethyl acetate, toluene, limonene, and methyl benzoate.

For toluene, a molecular-ion peak was observed at m/z 92 and a base peak at m/z 91.
m/z 91 corresponds to a benzyl cation or tropylium ion and is a fragment characteristic of alkylbenzenes.
Because these spectral characteristics and the retention time agreed with those of the standard substance, peak 3 was judged to be toluene.

In unknown sample A, a molecular-ion peak at m/z 136 and a base peak at m/z 68 were observed for the peak at a retention time of 9.66 min.
On the other hand, a molecular-ion peak at m/z 136 was also observed for the peak at a retention time of 12.28 min, but the base peak was m/z 105.
Therefore, although the two components have the same molecular weight, they have different fragmentation patterns and are likely to be limonene and methyl benzoate, respectively.

Points for Connecting the Results to the Discussion

In a GC-MS discussion, it is important to interpret retention time, peak area, molecular ions, fragments, and library-match scores together.

• Can the separation of components be confirmed from retention times?
• Can the molecular weight be estimated from the molecular-ion peak?
• Can the base peak and fragment peaks be explained in relation to the structure?
• Can compounds with the same molecular weight be distinguished from differences in retention time and fragments?
• Can the result be judged together with standard substances and retention time rather than being determined solely from the library-match score?
• Can it be explained that peak-area percentage is not necessarily the same as exact mass percentage?
• Can it be discussed that coelution produces mixed spectra and lowers the library-match score?
• Can it be explained that temperature-program and column conditions affect retention time and separation?
• Can it be explained that the internal-standard method can compensate for variation in injection volume and sensitivity?

Example Discussion

In this experiment, GC-MS was used to separate and identify components in a mixed sample.
Multiple peaks were observed in the GC chromatogram, and the mass spectrum at each retention time was analyzed.
Peak 1 showed a retention time of 2.15 min, a molecular ion at m/z 58, and a base peak at m/z 43, which agreed with the spectrum of acetone.
m/z 43 corresponds to CH3CO+ and is a fragment characteristic of carbonyl compounds.

For peak 3, a molecular-ion peak at m/z 92 and a base peak at m/z 91 were observed.
m/z 91 is stabilized as a benzyl cation or tropylium ion and therefore appears strongly in alkylbenzenes such as toluene.
Because the retention time and library-match score also agreed well with toluene, this peak was judged to be toluene.

In unknown sample A, two peaks having a molecular ion at m/z 136 were observed.
One had a base peak at m/z 68 and showed fragments characteristic of limonene.
The other had a base peak at m/z 105, corresponding to a benzoyl cation, and was therefore considered to be methyl benzoate.
These results show that even compounds having the same molecular weight can be distinguished by combining retention time and fragmentation pattern.

When the area percentages were calculated, unknown sample A contained 49.4% limonene, 29.4% methyl benzoate, and 21.2% toluene.
However, GC-MS peak area is affected not only by component concentration but also by ionization efficiency and detection sensitivity.
Therefore, area percentage is only a relative guide, and accurate quantitation requires a calibration curve or internal-standard method.

Possible sources of error include coelution, variation in injection volume, deterioration of the column, inappropriate temperature-program conditions, and misidentification in library searches.
When coelution occurs, the spectrum contains fragments originating from multiple components and the library-match score decreases.
In addition, if the temperature ramp is too fast, the retention time becomes shorter but separation between peaks may become poorer.
Therefore, in GC-MS analysis, it is necessary to examine not only the mass spectrum but also the separation state in the chromatogram.

Summary

In GC-MS, mixtures can be separated by GC and the molecular weight and fragments of each component can be examined by MS.
Combining retention time, molecular-ion peaks, base peaks, fragments, and library-match scores improves the reliability of component identification.

This reference example dealt with component identification, area percentage, distinction between components with the same molecular weight, coelution, and the internal-standard method using a standard mixture and unknown sample A.
In a report, it is useful to discuss retention time, molecular ions, fragment analysis, library searches, peak separation, and precautions for quantitation in relation to one another.

How to Read a Total Ion Chromatogram

In GC-MS, components separated by GC are introduced into the MS over time, and the total intensity of ions detected at each time is recorded.
This graph is called the total ion chromatogram, or TIC.
In a TIC, retention time is plotted on the horizontal axis and total ion intensity on the vertical axis.

Each peak in the TIC represents a component introduced into the MS at a particular time.
Selecting each peak makes it possible to examine the mass spectrum corresponding to that retention time.
Therefore, in GC-MS, components are estimated by combining the peak positions in the TIC with the mass spectrum of each peak.

Discussion of Retention Time

Retention time is important in GC-MS just as it is in GC analysis.
Retention time is the time required for a component to move through the column and reach the detector.
It changes depending on the volatility of the component, interaction with the stationary phase, column temperature, carrier-gas flow rate, and type of column.

If the retention time agrees with that of a standard substance, it becomes one piece of evidence for identification.
However, retention time alone may not be sufficient to distinguish another component.
In GC-MS, the reliability of identification is improved by confirming agreement of the mass spectrum in addition to retention time.

What Is a Mass Spectrum?

A mass spectrum is a graph showing the intensity of ionized molecules and fragment ions at each m/z.
m/z is plotted on the horizontal axis and relative intensity on the vertical axis.
Normally, the strongest peak is set to 100% and the intensities of the other peaks are shown relative to it.

A mass spectrum contains molecular-ion peaks, base peaks, fragment peaks, and isotope peaks.
From this information, molecular weight, the presence of elements, partial structures, and the ease of bond cleavage can be estimated.
Particularly in the EI method, molecules undergo relatively extensive fragmentation, producing many peaks useful for structural analysis.

What Is a Molecular-Ion Peak?

A molecular-ion peak is a peak corresponding to a molecule that has lost an electron and become ionized.
In general, the m/z of the molecular-ion peak corresponds to the molecular weight.
For example, if a compound has a molecular weight of 100 and a charge of +1, the molecular-ion peak appears near m/z 100.

However, the molecular-ion peak does not always appear clearly for every compound.
In the EI method, molecules may undergo extensive fragmentation, so the molecular-ion peak may be small or difficult to observe.
If the molecular-ion peak cannot be seen, library searches, fragment peaks, and results obtained by soft-ionization methods are used as references.

When the Molecular-Ion Peak Is Difficult to Observe

Causes of a molecular-ion peak being difficult to observe include the compound readily decomposing during ionization, instability of the molecular ion, extensive fragmentation, the measured m/z range, insufficient concentration, and effects of background.
In compounds such as alcohols, ethers, esters, and compounds with branched structures, the molecular-ion peak may become weak.

If the molecular-ion peak is not clear, it is important not to assume that the peak at the highest m/z is the molecular ion.
The result should be judged by combining library searches, isotope peaks, consistency of fragments, and comparison with standard substances.

What Is a Base Peak?

The base peak is the peak with the greatest intensity in a mass spectrum.
Normally, this peak is assigned a relative intensity of 100%, and the intensities of the other peaks are expressed relative to it.
The base peak often corresponds to the stable ion produced in the greatest amount and reflects the fragmentation characteristics of the compound.

The base peak is not necessarily the molecular-ion peak.
If a fragment ion more stable than the molecular ion is generated in large amounts, that fragment becomes the base peak.
Therefore, examining the m/z of the base peak makes it possible to consider which partial structure readily remains as a stable ion.

What Is a Fragment Peak?

A fragment peak is a peak corresponding to a smaller ion formed when the molecular ion undergoes bond cleavage.
In the EI method, molecules are ionized by high-energy electrons, so the molecular ion may undergo further decomposition and produce many fragment peaks.

Fragment peaks indicate which bonds in the molecule are readily cleaved and which partial structures readily form stable ions.
Therefore, fragment analysis is important for structural estimation of unknown compounds and for confirming the validity of library-search results.

Concept of Fragment Analysis

In fragment analysis, the portion lost from the molecular-ion peak is considered.
For example, a peak 15 mass units lower than the molecular ion may correspond to loss of a methyl group, a peak 18 lower may correspond to loss of water, and a peak 28 lower may correspond to loss of CO or ethylene.
However, because actual fragments depend on the structure of the compound and the stability of the ions, it is important not to make a definitive assignment from the mass difference alone.

Fragment ions tend to appear strongly when they have structures stable as carbocations, resonance-stabilized structures, or structures containing aromatic rings.
Therefore, the m/z of the peak is compared with the structural formula of the compound to estimate which bond was cleaved.

How to Interpret Representative Fragments

In mass spectra, characteristic fragments may be observed depending on the type of compound.
In alkyl chains, fragment peaks corresponding to the number of carbon atoms are likely to appear, while in aromatic compounds, peaks corresponding to benzyl cations or tropylium ions may be important.
Alcohols may undergo dehydration, while esters and ketones may show cleavage around the carbonyl group.

However, representative fragments are only clues for discussion.
In actual peak assignment, the molecular formula, molecular-ion peak, isotope peaks, and agreement with library spectra are checked.

Discussion of Isotope Peaks

Isotope peaks are peaks originating from molecules or fragments containing naturally occurring isotopes.
For example, because carbon contains a certain proportion of 13C, an M+1 peak may appear one mass unit above the molecular-ion peak.
Compounds containing chlorine or bromine show characteristic M and M+2 peak patterns.

Isotope peaks are useful for estimating elemental composition.
Particularly in compounds containing chlorine or bromine, the intensity ratio of isotope peaks is characteristic and provides an important clue for discussing the presence of halogen elements.

How to Interpret Compounds Containing Chlorine and Bromine

Isotope peaks are extremely important for compounds containing chlorine or bromine.
Chlorine has 35Cl and 37Cl, and the molecular-ion peak and M+2 peak appear in a characteristic ratio.
Bromine has 79Br and 81Br, and M and M+2 may appear with nearly equal intensities.

Such isotope patterns are useful for confirming the validity of library-search results.
If a candidate compound contains chlorine or bromine, the measured spectrum should be checked for the corresponding isotope peaks.

Discussion of Library Searches

In GC-MS, the obtained mass spectrum can be compared with spectra registered in a database to search for candidate compounds.
Library searches are useful for identifying unknown components, but it is risky to treat the search result itself as definitive identification.
This is because another compound having a similar fragmentation pattern may appear as a candidate.

When discussing library-search results, similarity, agreement of the molecular-ion peak, agreement of major fragment peaks, isotope pattern, retention time, and comparison with standard substances are checked.
If possible, a standard substance is measured to confirm whether both retention time and mass spectrum agree.

Discussion of Mass-Spectrum Match Score

In a library search, the degree of agreement between the measured spectrum and the database spectrum may be shown numerically.
The higher the match score, the stronger the candidate compound, but the score changes depending on measurement conditions, background, peak overlap, concentration, and ionization conditions.

Even when the match score is high, caution is required if the molecular-ion peak or major fragments cannot be explained.
Conversely, even if the match score is somewhat low, agreement of retention time and major peaks with a standard substance can provide evidence for identification.
It is important to examine the content of the peaks rather than relying only on the numerical value.

Discussion When Peaks Overlap

If separation by GC is insufficient, multiple components may elute near the same retention time and appear as a single peak in the TIC.
In this case, the mass spectrum at that retention time contains ions originating from multiple components, causing library-search results to become unclear or leading to misidentification.

If peak overlap is suspected, it can be checked by examining an extracted-ion chromatogram, changing the column-temperature conditions, using another column, or adding a standard substance.
Tracking only a specific m/z may make it possible to distinguish overlapping components.

Discussion of Extracted-Ion Chromatograms

An extracted-ion chromatogram, or EIC, is a chromatogram that extracts only a specific m/z and displays its change over time.
In a TIC, signals from multiple components are summed, whereas in an EIC, attention can be focused on a specific ion, making it useful for checking peak overlap and trace components.

By selecting an m/z characteristic of the target component, it is possible to confirm at what retention time that component appears.
However, because a fragment with the same m/z may also be generated from another component, it is important not to confirm identification using only one m/z.

Discussion of the EI Method

The EI method commonly used in GC-MS is electron ionization.
Because molecules are ionized by collision with high-energy electrons, many fragment ions are generated in addition to molecular ions.
Therefore, EI spectra contain abundant structural information and are well suited to library searches.

On the other hand, molecular-ion peaks may become weak in the EI method.
When molecular weight must be confirmed, it is important to check whether the molecular-ion peak is visible.
If the molecular ion is difficult to confirm, a soft-ionization method such as CI may be effective.

Difference From the CI Method

The CI method is chemical ionization.
It is often treated as a gentler ionization method than EI and may make it easier to obtain information about molecular weight.
In CI, the molecule may be observed not as the molecular ion itself but as a protonated ion or an adduct ion originating from the reagent gas.

The EI method provides abundant fragment information and is suitable for library searches.
The CI method may be advantageous for molecular-weight estimation.
Which method is appropriate depends on the purpose of the analysis.

Concept of Qualitative Analysis

In qualitative analysis by GC-MS, components are estimated by comprehensively considering retention time, molecular-ion peaks, fragment peaks, isotope peaks, and library-search results.
Rather than making a definitive judgment from a single piece of evidence, it is important to confirm that multiple pieces of information agree with the candidate compound.

In particular, if a standard substance can be measured, it is checked whether the retention time and mass spectrum agree between the standard substance and the unknown sample.
If no standard substance is available, it is appropriate to describe the result as “tentative identification” based on library-search results and fragment analysis.

Concept of Quantitative Analysis

GC-MS may also be used for quantitation using peak area or the area of a specific ion.
In some cases, the TIC peak area is used, while in others an m/z characteristic of the target component is selected and the area of the extracted-ion peak is used.
For quantitation, a calibration curve is prepared from standard solutions and the peak area of the unknown sample is substituted into the calibration curve.

Because the MS response differs depending on the component and ionization efficiency, a calibration curve using a standard substance is important.
If there are matrix effects or variation in injection volume, the internal-standard method is effective.
Particularly in quantitative analysis, not only library searches for identification but also reproducibility of peak areas and linearity of the calibration curve must be checked.

Relationship Between the Molecular-Ion Peak and Molecular Weight

If a molecular-ion peak is clearly observed, the molecular weight can be estimated from its m/z.
In ordinary GC-MS, ions are often detected as singly charged positive ions, so m/z is close to the molecular weight.
Isotope peaks such as M+1 and M+2 may also appear near the molecular-ion peak.

When considering a molecular-weight candidate, it is necessary to confirm whether the molecular-ion peak is really the molecular ion, whether there is a small peak at a higher m/z, and whether the relationship with the isotope peaks is natural.
If a fragment peak is mistaken for the molecular ion, the molecular weight will be underestimated.

Fragment Analysis and Structural Estimation

In fragment analysis, the structural formula of the candidate compound is used to consider which bonds would have to break to produce the observed m/z ions.
Characteristic cleavage may occur at positions where stable cations can readily form, near heteroatoms, at benzylic positions, and around carbonyl groups.

If fragment peaks can be naturally explained from the structural formula, the validity of the candidate compound increases.
Conversely, if the major peaks cannot be explained from the candidate structure, possibilities such as an incorrect library candidate, overlapping peaks, or contamination by background must be considered.

Discussion of Background Peaks

In GC-MS, peaks originating from background rather than sample components may also be observed.
Possible causes include column bleed, solvent, air, moisture, silicone contamination, sample containers, septa, and insufficient cleaning.
It is important not to mistake these peaks for target components.

To check the effects of background, a blank measurement is performed and compared with the sample measurement.
If the same peak also appears in the blank, it may not originate from the sample.
In trace analysis, the effect of background becomes particularly large.

Discussion of Solvent Peaks

In GC-MS, the sample solvent may be observed as a large peak.
If the solvent peak is too large, it may obscure components eluting nearby or place a load on the MS detector.
Solvent-derived fragments may also become mixed into the spectrum.

The solvent is selected by considering sample solubility, volatility, compatibility with the column, and overlap of retention time with the target component.
If the solvent peak overlaps with the target component, it is necessary to change the solvent or adjust the temperature conditions.

When GC-MS Results Can Be Considered Good

GC-MS results can be considered good when the peak of the target component is clearly separated in the TIC, its retention time agrees with that of a standard substance or the expected value, molecular-ion peaks and characteristic fragment peaks are observed in the mass spectrum, and the results are also consistent with the library search.

In addition, if the isotope-peak pattern agrees with the elemental composition of the candidate compound and the major fragments can be explained from the structural formula, the reliability of identification becomes higher.
Measuring a standard substance and confirming agreement of both retention time and spectrum provides even stronger evidence.

Example Discussion When the Experiment Did Not Go Well

When GC-MS analysis does not go well, possible causes are considered from results such as an invisible molecular-ion peak, low library-match score, overlapping peaks, large background, a large solvent peak, shifted retention time, or fragments that do not agree with the candidate structure.
Organizing the possible causes into GC separation, MS conditions, sample preparation, concentration, contamination, and limitations of library searches makes the discussion easier.

How to Write Points for Improvement

In a GC-MS discussion, including not only sources of error but also points for improvement makes the report easier to organize.
Improvements can be divided into sample preparation, GC separation, MS measurement, and data analysis.

Improvements to Sample Preparation

• Dilute the sample to an appropriate concentration
• Prevent loss of volatile components
• Store the sample in a sealed container
• Remove nonvolatile components and solids
• Perform a blank measurement
• Use solvents and containers with little contamination

Improvements to GC Separation

• Review the column-temperature conditions
• Adjust the temperature ramp rate
• Optimize the carrier-gas flow rate
• Use an appropriate injection volume
• Search for conditions that avoid peak overlap
• Consider a column with another stationary phase

Improvements to MS Measurement

• Set an appropriate measured m/z range
• Check the background
• Check contamination of the ion source
• Consider a soft-ionization method when necessary
• Measure and compare a standard substance

Improvements to Analysis

• Confirm the molecular-ion peak
• Assign the major fragment peaks
• Check isotope peaks
• Do not accept library-search results uncritically
• Judge the result using both retention time and mass spectrum
• Use extracted-ion chromatograms

Difference Between a Superficial Discussion and a Good Discussion

In a GC-MS discussion, simply writing that “it appeared in the library search” or that “there was a molecular ion” results in a superficial discussion.
A good discussion relates retention time, molecular-ion peaks, fragments, isotope peaks, and library-search results.

Examples of Expressions That Can Be Used in Reports

The following expressions can be used when writing the results and discussion of GC-MS.
Adjust the necessary parts according to your own experimental results.

• In GC-MS, combining retention time and mass spectrum improves the reliability of component identification.
• The molecular-ion peak provides important evidence for estimating the molecular weight of a compound.
• In the EI method, molecules readily fragment, so the molecular-ion peak may become weak.
• The base peak is the peak with the greatest intensity in a mass spectrum and often corresponds to a stable fragment ion.
• Fragment peaks are considered to originate from ions produced by cleavage of specific bonds in the molecule.
• The isotope-peak pattern provides clues to the presence of particular elements such as chlorine or bromine.
• Library-search results are useful, but identification cannot be confirmed from the search result alone.
• If peaks overlap, ions originating from multiple components may be mixed in the mass spectrum.
• An extracted-ion chromatogram can be used to track an m/z characteristic of the target component.
• If both retention time and mass spectrum agree with those of a standard substance, the reliability of identification becomes high.

Points to Check When Discussing GC-MS

Checking the following points before writing the report makes the discussion easier to write.

• Have the retention times of peaks in the TIC been checked?
• Has the mass spectrum of each peak been checked?
• Has the molecular-ion peak been searched for?
• Has the possibility of a weak molecular-ion peak been considered?
• Have the base peak and major fragment peaks been organized?
• Has it been checked whether the fragments can be explained from the candidate structure?
• Has the isotope-peak pattern been checked?
• Are library-search results evaluated with supporting evidence?
• Are both retention time and mass spectrum used for judgment?
• Have the effects of peak overlap and background been considered?
• Have comparisons with standard substances and blanks been performed?
• Do the points for improvement correspond to the sources of error?

Summary

GC-MS is an analytical method that combines component separation by GC with mass-spectrum measurement by MS.
GC provides retention time, while MS provides molecular-ion peaks, base peaks, fragment peaks, and isotope peaks.
Combining this information makes it possible to identify components more reliably than with GC alone.

Molecular-ion peaks are important for estimating molecular weight, but in the EI method the molecular ion may become weak.
Fragment peaks provide clues to bond cleavage and stable partial structures in the molecule.
Isotope peaks are useful for discussing the number of carbon atoms and the presence of elements such as chlorine and bromine.

In a report, rather than simply writing that “it matched in the library search,” organize and discuss retention time, molecular-ion peaks, major fragments, isotope patterns, comparison with standard substances, and the effects of peak overlap and background.
In GC-MS, confirming that multiple pieces of evidence do not contradict one another leads to persuasive identification.