Mass Spectrometry Discussion Examples | How to Estimate Molecular Weight and Interpret Fragmentation

What Is Mass Spectrometry?

Mass spectrometry is an analytical method in which a sample is ionized and the resulting ions are separated and detected based on m/z.
m/z is the value obtained by dividing mass by the number of charges.
Many organic compounds are often detected as singly charged ions, so the m/z value is treated as being close to the molecular weight or the mass of a fragment.

In mass spectrometry, ions originating from the molecule itself, ions formed by addition of a proton or sodium ion to the molecule, and fragment ions produced by molecular decomposition are observed.
By interpreting these peaks, information about the molecular weight and structure of the compound can be obtained.

Main Items to Include in the Results

In mass spectrometry results, organize the sample name, ionization method, measurement mode, measured m/z range, major peaks, molecular ion or pseudomolecular ion, base peak, fragment peaks, isotope peaks, estimated molecular weight, candidate structures, and other information.
Because the ions that are readily observed differ depending on the measurement method, it is important to clearly state the ionization method.

Main Items to Include in the Results

• Sample name
• Analyte
• Ionization method
• Positive-ion mode / negative-ion mode
• Measured m/z range
• Resolution
• Presence or absence of mass calibration
• Molecular-ion peak
• Pseudomolecular-ion peak
• Base peak
• Major fragment peaks
• Isotope peaks
• Adduct ions
• Multiply charged ions
• Estimated molecular weight
• Candidate compounds
• Peak assignments
• Comparison with literature values and theoretical values
• Sources of error and points for improvement

Reference Experimental Values and Analysis Examples for Mass Spectrometry (MS)

Here, reference experimental values are organized for reading molecular-ion peaks, base peaks, fragment peaks, and isotope peaks obtained by mass spectrometry and for discussing clues to molecular weight and structure.

In mass spectrometry, molecules are ionized and separated and detected according to their mass-to-charge ratio (m/z).
Molecular weight can be estimated from the molecular-ion peak, while the way bonds break and partial structures within the molecule can be considered from fragment peaks.
In addition, compounds containing chlorine, bromine, and similar elements show characteristic isotope-peak ratios.

Reference Experimental Conditions

Main Peaks Observed in a Mass Spectrum

Example Mass Spectrum of Toluene

The molecular weight of toluene, C7H8, is 92.
In EI-MS, in addition to the molecular-ion peak, a strong peak at m/z 91 corresponding to a benzyl cation or tropylium ion is observed.

In toluene, m/z 92 is the molecular-ion peak and m/z 91 is the base peak.
For a compound with a molecular weight of 92, if m/z 91 is extremely strong, a compound having a benzyl group or aromatic methyl group becomes a candidate.

Example of Molecular-Weight Estimation

If a molecular-ion peak is observed at m/z 92 in a mass spectrum, the molecular weight is considered to be approximately 92 if it is a singly charged positive ion.

Molecular-ion peak m/z 92 → Molecular weight approximately 92

Calculating the molecular weight from the molecular formula C7H8 of toluene gives:

12.01 × 7 + 1.008 × 8 = 84.07 + 8.064 = 92.13

This agrees well with the measured molecular-ion peak at m/z 92.

Example Mass Spectrum of Acetone

The molecular weight of acetone, C3H6O, is 58.
Carbonyl compounds show characteristic fragments such as acylium ions.

In acetone, the peak at m/z 43 is very strong and indicates formation of a fragment containing a carbonyl group.

Example Mass Spectrum of Methyl Benzoate

The molecular weight of methyl benzoate, C8H8O2, is 136.
In aromatic esters, molecular-ion peaks and aromatic-derived fragments are observed.

From the molecular-ion peak at m/z 136 and the strong peak at m/z 105, the presence of an aromatic ester or benzoyl structure can be considered.

Example of Interpreting the Difference Between the Molecular Ion and Fragments

The difference between the molecular-ion peak and fragment peaks provides a clue to the part of the structure that was lost.

However, fragments may be formed not only by simple bond cleavage but also through rearrangement.
It is important not to make a definitive judgment based only on the mass difference but to consider representative fragments and the structure of the compound together.

Isotope Peaks of Compounds Containing Chlorine

Chlorine mainly consists of 35Cl and 37Cl, and because of their natural abundance, compounds containing one chlorine atom show M and M+2 peaks in an intensity ratio of approximately 3:1.

A reference spectrum of chlorobenzene, C6H5Cl, is shown below.

Because m/z 112 and 114 appear in a ratio of approximately 3:1, the sample is considered highly likely to contain one chlorine atom.

Isotope Peaks of Compounds Containing Bromine

Because 79Br and 81Br occur in nearly a 1:1 ratio, compounds containing one bromine atom show M and M+2 peaks with almost the same intensity.

The intensity ratio of M and M+2 is an important clue for determining the presence or absence of halogen elements.

M+1 Peak and Approximate Carbon Count

Because carbon contains a small amount of 13C, the M+1 peak becomes larger as the number of carbon atoms in a compound increases.
As a rough guide, an M+1 peak of approximately 1.1% per carbon atom appears.

The M+1 peak can be used to estimate the number of carbon atoms, but because isotopes of other elements such as nitrogen, sulfur, and silicon also have an effect, it should be treated only as a guide.

Example Mass Spectrum of Unknown Sample X

A reference example of EI-MS measurement of unknown sample X is shown below.

In unknown sample X, the molecular-ion peak is at m/z 136 and a strong peak is observed at m/z 105.
Because this agrees well with the reference spectrum of methyl benzoate, unknown sample X is considered highly likely to be methyl benzoate.

Comparison of Unknown Sample X With Candidate Compounds

Considering the molecular weight, base peak, major fragments, and presence or absence of isotope peaks together, unknown sample X can be judged to be closest to methyl benzoate.

How the Molecular Ion Appears Depending on the Ionization Method

The EI method provides many fragments, but the molecular-ion peak may become weak.
Soft ionization methods may make peaks related to molecular weight easier to observe.

Depending on the measurement method, a peak may be observed not as “the molecule itself” but as a protonated or sodium-adduct ion.
Therefore, when determining molecular weight from m/z, the type of ion must be confirmed.

Example of Determining Molecular Weight From Adduct Ions

In ESI-MS and similar methods, ions may be observed as [M+H]+ or [M+Na]+ rather than as molecular ions.

Even for compounds with the same molecular weight of 136, the observed m/z changes depending on the ionization method and the type of adduct ion.

Points to Note About Peak Intensity and Quantitation

The relative intensity in a mass spectrum is greatly affected by how readily an ion is generated and by its stability.
Therefore, peak intensity does not necessarily directly represent the amount ratio within the molecule.

Peak intensity in a mass spectrum is useful as a clue for structural analysis, but component amounts cannot usually be compared simply from the ordinary spectrum alone.

Example of How to Write the Results

In the mass spectrum of toluene, a molecular-ion peak was observed at m/z 92, indicating that the molecular weight was approximately 92.
In addition, a base peak was observed at m/z 91.
This corresponds to C7H7+ and is considered to have been observed as a strong peak because it is stabilized as a benzyl cation or tropylium ion.

In acetone, a molecular-ion peak was observed at m/z 58 and a base peak at m/z 43.
m/z 43 is considered to correspond to the acylium ion CH3CO+ and is a fragment characteristic of carbonyl compounds.

In chlorobenzene, a pair of molecular-ion peaks was observed at m/z 112 and 114 in an intensity ratio of approximately 3:1.
Because this originates from the natural abundance of 35Cl and 37Cl, it is an important clue indicating that the sample contains one chlorine atom.

Points for Connecting the Results to the Discussion

In a discussion of mass spectrometry, it is important to interpret not only the molecular-ion peak but also fragment peaks and isotope peaks in combination.

• Can the molecular weight be estimated from the molecular-ion peak?
• Can it be explained that the base peak is not the most abundant component but the ion detected with the greatest intensity?
• Can the lost partial structure be considered from the difference between the molecular ion and fragments?
• Can the meanings of representative fragments such as m/z 91, 43, 105, and 77 be explained in relation to structure?
• Can it be explained that compounds containing Cl show M and M+2 at approximately 3:1, while those containing Br show approximately 1:1?
• Can the number of carbon atoms be roughly estimated from the M+1 peak?
• Can it be explained that observed peaks change depending on the ionization method, such as EI, CI, and ESI?
• Can molecular weight be determined while considering adduct ions such as [M+H]+ and [M+Na]+?
• Is care taken not to interpret peak intensity directly as component amount?

Example Discussion

In this experiment, molecular-weight and fragment information were investigated by mass spectrometry.
In toluene, a molecular-ion peak was observed at m/z 92, confirming a molecular weight of 92.
In addition, a base peak was observed at m/z 91, suggesting that one hydrogen atom was lost from the molecular ion and a stable C7H7+ ion was formed.

In acetone, a molecular-ion peak was observed at m/z 58 and a strong peak at m/z 43.
m/z 43 corresponds to CH3CO+ and is an acylium ion readily formed from carbonyl compounds.
The difference between the molecular ion and m/z 43 is 15, so loss of a CH3 group can be considered.

In unknown sample X, a molecular-ion peak was observed at m/z 136, a base peak at m/z 105, and a peak originating from an aromatic ring at m/z 77.
m/z 105 is considered to correspond to the benzoyl cation C6H5CO+.
In addition, the difference from m/z 136 to m/z 105 is 31, which can be considered to correspond to loss of an OCH3 group.
Because these results agree well with the spectrum of methyl benzoate, unknown sample X is considered highly likely to be methyl benzoate.

Regarding isotope peaks, m/z 112 and 114 were observed in chlorobenzene in an approximately 3:1 ratio.
Because this originates from the natural abundance of 35Cl and 37Cl, it is characteristic of compounds containing one chlorine atom.
On the other hand, compounds containing bromine show M and M+2 in approximately a 1:1 ratio, so Cl and Br can be distinguished from the isotope-peak ratio.

In mass spectrometry, a high peak intensity does not mean that the corresponding partial structure is present in a greater amount.
A strong peak indicates that the ion is readily generated or stable.
Therefore, structure must be estimated comprehensively from molecular weight, fragments, isotope peaks, and differences in ionization method.

Summary

In mass spectrometry, molecular weight can be estimated from the molecular-ion peak, while partial structures can be discussed from fragment peaks.
In addition, isotope peaks such as M+1 and M+2 provide clues for judging the number of carbon atoms and the presence or absence of halogen elements.

This reference example dealt with mass spectra of toluene, acetone, methyl benzoate, chlorobenzene, and unknown sample X.
In a report, it is useful to discuss m/z, relative intensity, molecular ions, base peaks, fragments, isotope patterns, and differences caused by ionization methods in relation to one another.

How to Read a Mass Spectrum

A mass spectrum is a graph with m/z on the horizontal axis and ion intensity on the vertical axis.
In many cases, the strongest peak is set to 100%, and the other peaks are expressed as relative intensities.
The position of a peak indicates the m/z of the ion, while the intensity of a peak indicates how strongly that ion was detected.

When reading a mass spectrum, first check whether there is a peak on the high-m/z side that indicates molecular weight.
Next, check the strongest base peak, major fragment peaks, and isotope peaks.
By relating these to the structure of a candidate compound, the sample can be identified and its structure estimated.

Basics of Molecular-Weight Estimation

When estimating molecular weight by mass spectrometry, attention is paid to the molecular-ion peak or pseudomolecular-ion peak.
In ionization methods such as EI, a molecular ion formed when the molecule loses an electron may be observed.
On the other hand, in ESI, MALDI, and similar methods, pseudomolecular ions such as protonated ions and sodium-adduct ions are often observed.

For example, when [M+H]+ is observed in positive-ion mode, the molecular weight is estimated by subtracting the mass of one hydrogen from the observed m/z.
When [M+Na]+ is observed, the mass of sodium is subtracted.
It is important to understand the measurement mode and the type of adduct ion.

What Is a Molecular-Ion Peak?

A molecular-ion peak is a peak corresponding to a molecule that has been ionized, for example by losing an electron.
A molecular ion may be represented as M+ or M+·.
If the ion is singly charged, the m/z of the molecular-ion peak corresponds to the molecular weight.

The molecular-ion peak is extremely important for molecular-weight estimation.
However, if the molecular ion is unstable, it may immediately fragment and the molecular-ion peak may become weak.
Particularly in EI, a clear molecular-ion peak may not be observed for some compounds.

What Is a Pseudomolecular Ion?

A pseudomolecular ion is not an ion of the molecule itself, but an ion formed by addition of a proton, sodium ion, potassium ion, ammonium ion, or similar species to the molecule, or by loss of a proton from the molecule.
Pseudomolecular ions are often observed in soft ionization methods such as ESI and MALDI.

Representative ions in positive-ion mode include [M+H]+, [M+Na]+, and [M+K]+.
In negative-ion mode, [M-H]- is commonly observed.
If pseudomolecular ions are not correctly understood, the molecular weight may be estimated incorrectly.

Positive-Ion Mode and Negative-Ion Mode

Mass spectrometry has positive-ion mode and negative-ion mode.
In positive-ion mode, molecules are detected as positively charged ions by receiving a proton or by addition of a metal ion.
Amines, basic compounds, and compounds that readily accept protons may be easier to detect in positive-ion mode.

In negative-ion mode, molecules are detected as anions after losing a proton.
Compounds containing carboxylic acids, phenols, phosphate groups, sulfate groups, and similar functional groups may be easier to detect in negative-ion mode.
The appropriate mode is considered according to the functional groups of the sample.

Discussion of the Base Peak

The base peak is the peak with the greatest intensity in a mass spectrum.
Usually, this peak is set to 100%, and the intensities of the other peaks are expressed relatively.
The base peak often represents the most readily generated stable ion.

The base peak is not necessarily the molecular-ion peak.
If the molecular ion is unstable and fragments readily, a stable fragment ion becomes the base peak.
The m/z of the base peak is important for considering partial structures and sites that readily undergo fragmentation.

What Is Fragmentation?

Fragmentation is a phenomenon in which an ionized molecule separates into smaller ions through bond cleavage.
Ions produced by fragmentation are observed as fragment peaks in the mass spectrum.
Fragmentation readily occurs particularly in EI, often producing many peaks useful for structural analysis.

Fragment peaks reflect which bonds in the molecule are readily cleaved and which partial structures readily form stable ions.
Even when details of the structure cannot be determined from the molecular-ion peak alone, analysis of fragment peaks can be used to judge the validity of candidate structures.

Basics of Fragment Analysis

In fragment analysis, the part lost from the molecular ion or pseudomolecular ion 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 a small neutral molecule.
However, it is dangerous to make a definitive assignment based only on mass difference.

In fragment analysis, it is necessary to confirm whether the resulting ion is stable, whether the candidate structure contains the relevant partial structure, and whether the assignment is consistent with other peaks.
Stable cations, resonance-stabilized ions, ions containing aromatic rings, and ions containing heteroatoms may appear as strong peaks.

How to Interpret Representative Fragments

In mass spectrometry, characteristic fragments may be observed depending on the structure of the compound.
Alkyl chains may produce fragments corresponding to carbon number, alcohols may undergo dehydration, esters and ketones may undergo cleavage around the carbonyl group, and aromatic compounds may show stable fragments containing the aromatic ring.

However, representative fragments are only a guide.
Actual peak assignments are judged together with the ionization method, candidate structure, molecular-ion peak, isotope peaks, library spectra, and other analytical results.

Discussion of Isotope Peaks

Isotope peaks are peaks originating from molecules or fragments containing naturally occurring isotopes.
Because carbon contains 13C, an M+1 peak may appear one mass unit above the molecular-ion peak.
The greater the number of carbon atoms in the molecule, the larger the M+1 peak tends to become relatively.

Compounds containing chlorine or bromine show M and M+2 peaks in characteristic ratios.
The isotope-peak pattern is an important clue for estimating elemental composition.
If a candidate compound contains a particular element, it is necessary to confirm whether the measured isotope pattern is consistent with it.

How to Interpret Compounds Containing Chlorine and Bromine

Compounds containing chlorine or bromine may show very clear isotope patterns.
Compounds containing one chlorine atom show M and M+2 peaks in a characteristic ratio.
Compounds containing one bromine atom may show M and M+2 peaks with nearly equal intensity.

If these isotope patterns are observed, they provide evidence for considering candidate structures containing halogens.
Conversely, if a candidate compound contains chlorine or bromine but isotope peaks are not observed, the candidate structure or peak assignment must be reconsidered.

Discussion of High-Resolution Mass Spectrometry

High-resolution mass spectrometry can estimate elemental composition by measuring precise m/z values.
Even compounds having the same nominal mass have slightly different exact masses depending on their elemental composition.
Therefore, in high-resolution MS, it is possible to evaluate how closely a candidate molecular formula agrees with the measured exact mass.

When discussing exact mass, mass error may be expressed in ppm.
The smaller the mass error, the more valid the candidate molecular formula becomes.
However, because exact mass alone cannot readily distinguish structural isomers, information from fragments, NMR, and other methods is also required.

Characteristics of the EI Method

EI is electron ionization, a method in which high-energy electrons collide with molecules to ionize them.
Because a large amount of energy is imparted to the molecules, many fragment ions are readily generated in addition to the molecular ion.
Therefore, EI spectra contain abundant structural information and are also commonly used for library searches.

On the other hand, the molecular-ion peak may become weak.
When molecular weight is required, the presence or absence of the molecular-ion peak must be checked carefully.
In EI, the fragmentation pattern plays an important role in compound identification.

Characteristics of the ESI Method

ESI is electrospray ionization, a method that can ionize molecules in solution relatively gently.
It is suitable for analysis of biomolecules, polar compounds, heat-sensitive compounds, and high-molecular-weight compounds.
In ESI, pseudomolecular ions such as [M+H]+, [M-H]-, and [M+Na]+ are often observed.

Multiply charged ions may be observed in ESI.
Particularly for large molecules such as proteins and peptides, ions with multiple charges are detected, and peaks appear at m/z values smaller than the actual molecular weight.
If multiply charged ions are not understood, the molecular weight may be seriously misinterpreted.

Characteristics of the MALDI Method

MALDI is matrix-assisted laser desorption/ionization.
The sample is mixed with a matrix and ionized by laser irradiation.
It is used for analysis of relatively large molecules such as proteins, peptides, and polymers.

MALDI often detects mainly singly charged ions, making the masses of high-molecular-weight components relatively easy to read.
However, matrix-derived peaks may appear in the low-m/z region, requiring care in small-molecule analysis.

Discussion of Multiply Charged Ions

Multiply charged ions are ions carrying two, three, or more charges.
In ESI, large molecules such as proteins and peptides may receive multiple protons and be observed as multiply charged ions.
For multiply charged ions, m/z is the molecular weight divided by the number of charges, so peaks appear at m/z values smaller than the actual molecular weight.

In spectra containing multiply charged ions, molecular weight is calculated from the spacing between adjacent peaks and the charge number.
It is important to consider the charge number because simply treating m/z as molecular weight leads to an error.

Discussion of Adduct Ions

In mass spectrometry, ions other than protons may be added to molecules and detected.
Representative examples include sodium-adduct ions [M+Na]+, potassium-adduct ions [M+K]+, and ammonium-adduct ions [M+NH4]+.
Adduct ions are particularly common in ESI and MALDI.

If an adduct ion is mistaken for a molecular ion, the molecular weight will be overestimated.
For example, if [M+Na]+ is mistaken for [M+H]+, the estimated molecular weight will be greatly shifted.
If several adduct ions are observed simultaneously, the mass differences among them can be used to confirm the peak assignments.

Discussion When the Molecular-Ion Peak Is Not Visible

If the molecular-ion peak is not visible, possible causes include an unstable molecular ion that fragments readily, an ionization method that is too energetic, an inappropriate measured m/z range, low concentration, or large background.
Particularly in EI, the molecular ion may become weak.

Even if the molecular-ion peak is not visible, molecular weight may sometimes be estimated from fragment peaks, pseudomolecular ions, isotope peaks, library searches, or measurements using another ionization method.
However, because the evidence for molecular weight becomes weaker, it is important not to write too definitively.

Discussion When There Are Too Many Peaks

If there are too many peaks in a mass spectrum, possible causes include extensive fragmentation, the sample being a mixture, contamination by impurities or solvent, background signals, or simultaneous detection of multiple components.
In GC-MS or LC-MS, insufficient chromatographic separation may cause spectra from multiple components to overlap.

When many peaks are present, the major peaks are organized first and compared with blanks and standard substances.
It is not necessary to force an assignment for every peak.
Priority is given to molecular ions, pseudomolecular ions, major fragments, and isotope peaks related to the target component.

Discussion of Background Peaks

In mass spectrometry, background peaks originating from substances other than the sample may be observed.
Possible causes include solvents, plasticizers, silicones, column bleed, matrix, salts, insufficiently cleaned equipment, air, and moisture.
Care is required not to mistake these for peaks from the target component.

To confirm the effect of background, a blank measurement is performed.
If the same peak also appears in the blank, that peak may not originate from the sample.
In trace analysis, the contribution of background becomes relatively large, making this particularly important.

Discussion of Library Searches

In EI-MS and GC-MS, the obtained mass spectrum can be compared with spectra registered in a library to search for candidate compounds.
Library searches are convenient, but identification cannot be confirmed from the search result alone.
This is because different compounds with similar fragmentation patterns may appear as candidates.

When discussing library-search results, the match score, molecular-ion peak, major fragments, isotope peaks, retention time, and comparison with standard substances are checked.
If a standard substance is measured and both retention time and mass spectrum agree, the reliability of identification becomes higher.

Causes of Errors in Molecular-Weight Estimation

Causes of errors in molecular-weight estimation include observing an adduct ion rather than a molecular ion, mistaking a fragment peak for the molecular ion, failing to consider multiply charged ions, mistaking an isotope peak for the main peak, insufficient mass calibration, and mistaking background peaks for sample-derived peaks.

When estimating molecular weight, it is important to confirm what type of ion each observed peak represents.
In particular, adduct ions and multiply charged ions must be considered in ESI, fragmentation in EI, and matrix peaks in MALDI.

When Mass Spectrometry Can Be Considered to Have Given Good Results

Mass spectrometry can be considered to have given good results when a molecular ion or pseudomolecular ion corresponding to the molecular weight can be clearly confirmed, the major fragment peaks can be explained from the candidate structure, and the isotope-peak pattern agrees with the elemental composition.
Reliability becomes even higher when the effects of blanks and impurities are small and the measured peaks are consistent with literature values or standard substances.

In high-resolution MS, it is also important for the measured exact mass to be close to the theoretical mass.
However, because it may be difficult to distinguish structural isomers by mass spectrometry alone, combining the result with NMR, IR, chromatography, and other methods makes the identification more reliable.

Example Discussion When the Experiment Did Not Go Well

When mass spectrometry does not go well, the causes can be considered from results such as no visible molecular-ion peak, multiple pseudomolecular ions that are difficult to distinguish, too many fragments, large background, low library-match scores, or isotope patterns that do not agree with the candidate structure.
Organizing possible causes according to ionization method, sample concentration, sample purity, matrix, background, and measured m/z range makes the discussion easier.

How to Write Points for Improvement

In a discussion of mass spectrometry, including not only sources of error but also points for improvement makes the report easier to organize.
Improvements can be divided into sample preparation, ionization conditions, measurement conditions, and analysis methods.

Improvements to Sample Preparation

• Purify the sample sufficiently
• Reduce the effects of solvents and salts
• Adjust to an appropriate concentration
• Remove insoluble material
• Perform a blank measurement
• Use equipment and solvents with little contamination

Improvements to Ionization and Measurement Conditions

• Select an ionization method appropriate for the compound
• Compare positive-ion mode and negative-ion mode
• Set an appropriate measured m/z range
• If the molecular ion is weak, consider a soft ionization method
• Perform mass calibration
• Confirm the exact mass using high-resolution MS

Improvements to Analysis

• Distinguish molecular ions from pseudomolecular ions
• Check adduct ions
• Consider the possibility of multiply charged ions
• Relate major fragments to the structural formula
• Check isotope peaks
• Do not accept library-search results uncritically
• Combine the results with other analytical methods such as NMR and IR

Difference Between a Superficial Discussion and a Good Discussion

In a discussion of mass spectrometry, simply writing that “the molecular weight was determined” or that “fragments appeared” results in a superficial discussion.
A good discussion relates molecular ions, pseudomolecular ions, adduct ions, fragmentation, and isotope peaks.

Examples of Expressions That Can Be Used in Reports

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

• In mass spectrometry, sample molecules are ionized and detected as peaks at each m/z value.
• The molecular-ion peak provides important evidence for estimating the molecular weight of a compound.
• In ESI, pseudomolecular ions rather than molecular ions are often observed.
• In positive-ion mode, [M+H]+ and [M+Na]+ may be observed, while in negative-ion mode, [M-H]- may be observed.
• The base peak is the peak with the greatest intensity in a mass spectrum.
• Fragment peaks are considered to originate from ions produced by cleavage of specific bonds in the molecule.
• The isotope-peak pattern is useful for estimating elemental composition.
• If the molecular-ion peak is weak, the structure may readily undergo fragmentation.
• Library-search results are useful, but identification cannot be confirmed from the search result alone.
• Because it is difficult to distinguish structural isomers by mass spectrometry alone, the results must be combined with NMR, IR, and other analyses.

Points to Check When Discussing Mass Spectrometry

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

• Is the ionization method clearly stated?
• Has it been confirmed whether the measurement was performed in positive-ion mode or negative-ion mode?
• Has the molecular-ion peak or pseudomolecular-ion peak been checked?
• Has the possibility of adduct ions been considered?
• Has the possibility of multiply charged ions been considered?
• Has the base peak been checked?
• Have the 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?
• Have background peaks been excluded?
• Are library-search results evaluated with supporting evidence?
• Are the results judged together with other analytical results such as NMR and IR?

Summary

Mass spectrometry is an analytical method used to obtain information about molecular weight and structure by ionizing sample molecules and detecting them based on m/z.
Molecular-ion peaks and pseudomolecular-ion peaks provide important evidence for molecular-weight estimation, while fragment peaks provide clues for discussing partial structures and the ease of bond cleavage within the molecule.

The peaks observed vary greatly depending on the ionization method.
EI produces many fragments, while in ESI and MALDI, pseudomolecular ions and adduct ions become important.
In addition, failure to correctly interpret multiply charged ions and isotope peaks may lead to incorrect estimation of molecular weight.

In a report, rather than simply writing that “the molecular weight was determined,” organize and discuss which peaks were used as evidence and the molecular ions, pseudomolecular ions, adduct ions, fragments, and isotope peaks.
Mass spectrometry is an extremely powerful analytical method, but determining structure requires judgment in combination with other analytical results such as NMR, IR, and chromatography.