Name: using reagent gas in ci mass spectrometry
Uploaded: 2024-12-05T18:32:21.000Z
Duration: 1 min 21 s
Channel: JoVE

Electron impact is the conventional method for ionizing sample molecules in mass spectrometry. However, for some molecules, the high-energy electron beam causes excessive fragmentation of the primary molecular ion.
The absence of a molecular ion peak in such mass spectra makes identifying the sample difficult.
An alternative chemical ionization method is the gas-phase protonation reaction, where first, the relatively stable conjugate acid of the sample molecule is created. This species then fragments into low-molecular-weight components. 
For instance, consider the chemical ionization of di-sec-butyl ether. The ether is mixed with methane gas. A high-energy electron beam then ionizes methane preferentially.
The methane radical cation formed collides with another methane molecule, generating a methanium ion and a methane radical.
The methanium ion is a superacid and source of a gas-phase proton, which protonates the ether. Compared to the molecular ion formed by electron-impact ionization, the protonated ether is stable, giving the M+1 peak in the mass spectrum.

chemical ionization (ci) mass spectrometry

Chemical Ionization (CI) Mass Spectrometry

The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the corresponding conjugate acid. In this process, the sample is mixed with an excess reagent gas, which ensures the electron impact occurs primarily on the reagent gas. The charged species formed from the reagent protonates the analyte molecule, producing a relatively stable protonated analyte (conjugate acid) compared to the molecular ion. This results in an M+1 peak in the mass spectrum. The conjugate acid may then undergo fragmentation that generates additional signals.
For example, the CI of di-sec-butyl ether in methane gas illustrates this process. When the ether is mixed with excess methane gas as a reagent, electron impact occurs on methane rather than the ether. The resulting methane radical cation can react with another methane molecule to generate a methane radical and a methanium ion. The methanium ion is a source of gas-phase protons, which can protonate the ether to form its conjugate acid. The sequential reactions during the chemical ionization of di-sec-butyl ether are depicted in Figure 1.
<img alt="Methane reaction pathway, chemical equations, resulting in m/z=131, diagram, process analysis." src="/files/ftp_upload/12300/12300_PT_Figure_1.svg" style="text-align: center; height: 175px;" data-altupdatedat="1761830439000" data-alt="Figure1" />
Figure 1: Chemical ionization of di-sec-butyl ether methane mixture.
This conjugate acid of the ether (m/z = 131) is relatively more stable than the molecular ion (m/z = 130) of ether formed via the conventional electron impact ionization. In the traditional route, the molecular ion undergoes fragmentation via &#945; cleavage, giving a signal at m/z = 101. Figure 2 illustrates the reactions that occur during electron impact ionization directly on di-sec-butyl ether.
<img alt="Mass spectrometry fragmentation diagram; electron impact, alpha cleavage, m/z 130 and 101." src="/files/ftp_upload/12300/12300_PT_Figure_2.svg" style="text-align: center; height: 175px;" data-altupdatedat="1761830439000" data-alt="Figure2" />
Figure 2: Electron impact ionization of di-sec-butyl ether and fragmentation of the molecular ion.
So, the mass spectra of di-sec-butyl ether ionized via CI feature an M+1 peak at m/z = 131. On the other hand, mass spectra of di-sec-butyl ether ionized via electron impact ionization do not show any peak at the m/z value of its molecular weight. Figures 3a and 3b show the mass spectra of di-sec-butyl ether ionized via the electron impact and chemical ionization methods, respectively.
<img alt="Chromatography analysis graph showing peak results for compound separation and identification." src="/files/ftp_upload/12300/12300_PT_Figure_3.svg" style="text-align: center; height: 225px;" data-altupdatedat="1761830439000" data-alt="Figure3" />
Figure 3: a) No m/z = 130 peak is visible in the mass spectrum obtained via electron impact ionization of di-sec-butyl ether. b) The m/z = 131 peak is clearly visible in the mass spectrum obtained via chemical ionization of di-sec-butyl ether.

The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ...

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Mass Spectrometry Fragmentation Methods

KEY TERMS AND CONCEPTS

using reagent gas in ci mass spectrometry

Chemical ionization mass spectrometry uses a reagent gas to help detect molecules that break apart too quickly in electron impact ionization. It is a milder ionization method that can extend the life of the ionized analyte, which makes molecular identification easier.

In chemical ionization, the sample is mixed with an excess reagent gas. This setup makes the electron impact occur mainly on the reagent gas instead of on the analyte. The charged species formed from the reagent then protonates the analyte molecule and forms a stable conjugate acid.

The protonated analyte is usually more stable than the original molecular ion. As a result, the mass spectrum often shows an M+1 peak. The conjugate acid can still fragment and produce extra signals.

The chemical ionization of di-sec-butyl ether in methane shows this process clearly. Methane acts as the reagent gas, and electron impact first creates a methane radical cation. That species reacts further to form a methanium ion, which donates a gas-phase proton to the ether and forms its conjugate acid.

The protonated di-sec-butyl ether appears at m/z = 131 and is more stable than the molecular ion at m/z = 130. With conventional electron impact ionization, the molecular ion fragments by alpha cleavage and gives a signal at m/z = 101. In the mass spectrum, CI shows the M+1 peak at m/z = 131, while electron impact ionization does not show a peak at the molecular weight of the ether.

Using Reagent Gas in CI Mass Spectrometry

using-reagent-gas-in-ci-mass-spectrometry

mass spectrometry: long-chain alkane fragmentation

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Mass Spectra of Linear Alkane Chains

Mass spectra of linear alkanes show a clear fragmentation pattern. The molecular ion often breaks at a carbon-carbon bond away from the end of the chain. This cleavage forms a stable carbocation and a stable radical, so the middle of the mass-to-charge plot usually has the strongest signals while the ends are weaker. As each bond breaks, a methyl group is lost and the main peaks in the spectrum appear 14 u apart. Smaller peaks near each main signal can also appear. These come from secondary...

mass spectrometry: branched alkane fragmentation

mass-spectrometry-branched-alkane-fragmentation

Branched Alkanes in Mass Spectra

Branched alkanes in mass spectrometry fragment quickly because branching can create stable carbocations. When cleavage happens at a branching point, a secondary or tertiary carbocation may form. That stability helps explain why the molecular ion peak is often very weak or missing compared with a linear alkane. The lesson uses 2-methylbutane, neopentane, and n-pentane to show how this pattern appears in mass spectra. 2-methylbutane and neopentane break apart to form secondary and tertiary...

mass spectrometry: cycloalkane fragmentation

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Cycloalkane Ions and Mass Peaks

Cycloalkane ions in mass spectrometry often give strong peaks because the ring structure helps stabilize the molecular ion. Compared with linear or branched alkanes, this added stability changes how the molecule breaks apart. As a result, cycloalkanes can produce prominent signals in the mass spectrum. Cyclohexane is a clear example. Its molecular ion has an m/z of 84, and this peak is often stronger than the signal from hexane, a linear alkane. The closed ring helps hold the ion together,...

mass spectrometry: alkene fragmentation

Alkene Ion Fragmentation Patterns

Alkene ion fragmentation patterns in mass spectrometry begin when the molecule loses one electron from the unsaturated π bond. This ionization forms a stable molecular ion. The ion can then break apart by three main reaction pathways. The most common pathway is cleavage at the allylic position, which is the carbon next to the double bond. This produces an allylic carbocation that is stabilized by resonance. In terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In internal...

mass spectrometry: cycloalkene fragmentation

mass-spectrometry-cycloalkene-fragmentation

Cycloalkene Side-Chain Cleavage in Mass Spectra

Cycloalkenes can break apart in a mass spectrometer through retro-Diels–Alder fragmentation. In this process, two carbon-carbon bonds in the ring split, and ethene is released. The remaining fragment is a dienyl radical cation that is 28 u less than the molecular ion. This pathway is similar to the fragmentation of cycloalkanes that also releases ethene. The difference is the type of charged fragment that remains. Cycloalkanes form an alkyl species, while cycloalkenes form a dienyl species.

mass spectrometry: alkyne fragmentation

Alkyne Mass Spectra and Key Peaks

Alkyne mass spectra often show strong peaks from two main fragmentation paths. One path breaks the carbon-carbon bond between the alpha and beta carbons of the alkyne bond. This produces a 3-propynyl cation, also called a propargyl cation. In terminal alkynes, this is the only fragmentation path that gives the 3-propynyl cation. The unsubstituted 3-propynyl cation appears at a mass-to-charge ratio of 39. In internal alkynes, the 3-propynyl cation is substituted. For example, 2-pentyne forms a...

mass spectrometry: alcohol fragmentation

Alcohol Fragmentation Patterns in Mass Spectra

Alcohols fragment in mass spectrometry in predictable ways. When an alcohol, written as R-OH, ionizes, it can lose one non-bonded electron from the oxygen atom. That forms a molecular ion, but the molecular ion peak is often weak or may not appear because alcohols break apart quickly. Two main fragmentation routes are important for alcohols: β-cleavage and dehydration. In β-cleavage, the bond at the β-position next to the hydroxyl group breaks. This gives a resonance-stabilized cation and a...

mass spectrometry: aromatic compound fragmentation

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Mass Spectra of Benzene and Toluene

Mass spectra of aromatic compounds show a strong molecular ion peak. In ionization, the molecule becomes a molecular ion, which appears as a prominent peak in the spectrum. Benzene gives a molecular ion at m/z 78, and toluene gives one at m/z 92. Benzene’s molecular ion is especially stable. It does not fragment readily because breaking the aromatic benzene ring requires a large amount of energy. Alkyl-substituted benzenes behave differently in mass spectrometry. Toluene can lose a hydrogen...

mass spectrometry: amine fragmentation

Amines in Mass Spectra: Nitrogen Rule

Amines can be identified in mass spectrometry by their fragmentation patterns and by the nitrogen rule. The molecular ions of amines often break apart through β-cleavage, which cuts a carbon-carbon bond next to the nitrogen. This process forms an alkyl radical and a resonance-stabilized nitrogen-containing cation. The nitrogen rule helps predict the mass of the molecular ion. A compound with one nitrogen atom, or any odd number of nitrogen atoms, gives a molecular ion with an odd molecular...

mass spectrometry: alkyl halide fragmentation

mass-spectrometry-alkyl-halide-fragmentation

Mass Spectra of Alkyl Halides

Mass spectra of alkyl halides show clear isotope patterns from the halogen atom. Chlorine has two common isotopes, 35Cl and 37Cl, in a 3:1 ratio. Bromine has two common isotopes, 79Br and 81Br, in a 1:1 ratio. These isotope ratios create two molecular ion peaks, [M] and [M + 2], with relative heights that match the halide abundance. This pattern is easy to see in examples such as 2-chloropropane and 1-bromopropane. 2-Chloropropane gives peaks in a 3:1 ratio. 1-Bromopropane gives peaks in a 1:1...

mass spectrometry: aldehyde and ketone fragmentation

mass-spectrometry-aldehyde-and-ketone-fragmentation

Carbonyl Fragment Patterns in Mass Spectra

Aliphatic aldehydes and ketones break apart in mass spectrometry through a few key carbonyl fragment patterns. The main pathways are alpha-cleavage, inductive cleavage, and the McLafferty rearrangement. These patterns help chemists read the mass spectrum and spot a carbonyl group. Alpha-cleavage is a common break next to the carbonyl group. The bond beside the carbonyl splits, and this forms an alkyl radical and an acylium cation. The acylium cation is often seen in the spectrum because it is...

mass spectrometry: carboxylic acid, ester, and amide fragmentation

mass-spectrometry-carboxylic-acid-ester-and-amide-fragmentation

Mass Spectra of Carboxylic Compounds

Mass spectra of carboxylic acids, esters, and amides often show two key fragmentation routes: β-cleavage and McLafferty rearrangement. In β-cleavage, the carbon-carbon bond at the β-position next to the carboxylic group breaks. This produces a neutral radical and a cation. Long-chain compounds can also fragment by McLafferty rearrangement if they have a hydrogen on the γ-carbon. The γ-carbon is the third carbon away from the carboxylic group. This rearrangement gives a radical cation and a...

Chemical ionization mass spectrometry uses a reagent gas to help detect molecules that break apart too quickly in electron impact ionization. It is a milder ionization method that can extend the life of the ionized analyte, which makes molecular identification easier. In chemical ionization, the sample is mixed with an excess reagent gas. This setup makes the electron impact occur mainly on the reagent gas instead of on the analyte. The charged species formed from the reagent then protonates...

electrospray ionization (esi) mass spectrometry

electrospray-ionization-esi-mass-spectrometry

How ESI Turns Biomolecules Into Ions

Electrospray ionization, or ESI, is a mass spectrometry method used to detect biomolecules that are too large or nonvolatile for conventional electron impact ionization. These molecules may break down before they can ionize or evaporate. ESI helps prevent rapid fragmentation and lets scientists record a mass signal for the whole biomolecule. ESI uses electrical energy to move ions from the liquid phase into the gas phase. The analyte biomolecule is mixed with an ionic liquid, which is a...

matrix-assisted laser desorption ionization (maldi)

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How MALDI Turns Samples Into Ions

Matrix-assisted laser desorption ionization (MALDI) is a mass spectrometry technique that turns biomolecules into ions for analysis. It is used to identify and characterize proteins, peptides, nucleic acids, and carbohydrates. Because of this, it is common in biological and medical research, as well as pharmacology and biochemistry. In MALDI, the analyte of interest is mixed with a matrix material. The matrix is usually an organic compound, such as a small organic acid or a crystalline...

key terms and concepts

See how chemical ionization uses a reagent gas to protonate analytes, form a stable conjugate acid, and produce an M+1 peak in mass spectra.

Using Reagent Gas in CI Mass Spectrometry | JoVE K12

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Using Reagent Gas in CI Mass Spectrometry

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