Name: decoding molecular ions in mass spectra
Uploaded: 2025-12-12T12:31:50.000Z
Duration: 1 min 24 s
Channel: JoVE

Given a known molecular ion mass, the unknown compound can be identified.
The empirical formula is determined from the molecular ion mass and the isotope peak intensities.
This spectrum has a molecular ion peak at m/z 16.
The nitrogen rule states that a molecular ion with even mass contains even or zero nitrogen atoms. Since the molecular ion peak is at 16, it contains no nitrogen.
The number of carbon atoms is deduced by comparing the M+1 intensity to the expected M+1 contribution per carbon atom.
The isotope peak intensities and patterns are also compared to the natural abundances of the isotopes of other likely atoms.
Since this compound contains one carbon and no nitrogen, the empirical formula is CH4.
However, larger compounds need further examination for other atoms, the degree of unsaturation, and fragmentation patterns.
The degree-of-unsaturation formula indicates the presence of multiple bonds or rings, and signature fragments at characteristic m/z values like 15 suggest certain structural features.

spectre de masse : interprétation

Mass Spectrum: Interpretation

Un compos&#233; inconnu peut &#234;tre &#233;tabli en identifiant le pic des ions mol&#233;culaires dans le spectre de masse. Le pic des ions mol&#233;culaires est souvent faible ou absent en raison de la pr&#233;dominance de la fragmentation dans les faisceaux d'&#233;lectrons de haute &#233;nergie. Dans de tels cas, un faisceau d&#8217;&#233;lectrons de faible &#233;nergie peut &#234;tre utilis&#233; pour balayer le spectre afin d&#8217;am&#233;liorer l&#8217;intensit&#233; du pic des ions mol&#233;culaires. De plus, les spectres d'ionisation chimique, d'ionisation de champ et d'ionisation par d&#233;sorption sont utilis&#233;s pour obtenir un pic d'ions mol&#233;culaires relativement intense.
Pour d&#233;terminer la formule empirique &#224; partir de la masse des ions mol&#233;culaires, un spectrom&#232;tre de masse &#224; haute r&#233;solution comme un spectrom&#232;tre de masse &#224; double focalisation, un spectrom&#232;tre de masse &#224; temps de vol, un spectrom&#232;tre de masse orbitrap ou un spectrom&#232;tre de masse &#224; r&#233;sonance cyclotron ionique &#224; transformation de Fourier est n&#233;cessaire. 
La comparaison des intensit&#233;s des pics isotopiques (M+1 et M+2), qui r&#233;sultent de l&#8217;abondance naturelle d&#8217;isotopes de masse plus &#233;lev&#233;e, avec le pic des ions mol&#233;culaires (M^+) donne une bonne id&#233;e de la formule empirique d&#8217;un compos&#233; inconnu.
Le nombre d'atomes de carbone pr&#233;sents dans le compos&#233; inconnu peut &#234;tre d&#233;duit en comparant le rapport d'intensit&#233; maximale M+1 &#224; M^+ &#224; la contribution M+1 attendue par atome de carbone.
La r&#232;gle de l'azote, selon laquelle une mol&#233;cule ayant un poids mol&#233;culaire pair contient z&#233;ro ou un nombre pair d'atomes d'azote, pr&#233;dit le nombre d'atomes d'azote pr&#233;sents dans le compos&#233; inconnu.
De plus, le degr&#233; d'insaturation pr&#233;dit &#224; partir de la formule
14589_PT_Figure_1.svg
indique la pr&#233;sence de plusieurs liaisons ou cycles dans le compos&#233; inconnu. Enfin, l'&#233;tude des mod&#232;les de fragmentation des compos&#233;s, bas&#233;e sur une s&#233;rie de lignes directrices, permet d'identifier des fragments de signature &#224; des valeurs m/z caract&#233;ristiques, sugg&#233;rant la pr&#233;sence de certaines caract&#233;ristiques structurelles.

Spectre de masse : interprétation

Given a known molecular ion mass, the unknown compound can be identified.
The empirical formula is determined from the molecular ion mass and the isotope ...

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Principles of Mass Spectrometry

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decoding molecular ions in mass spectra

Mass spectra help scientists identify an unknown compound by finding the molecular ion peak. The molecular ion peak shows the mass of the intact molecule, but it is often weak or missing because high-energy electron beams cause strong fragmentation. When that happens, a soft-energy electron beam can be used to scan the spectrum and improve the molecular ion signal.

Other ionization methods can also give a stronger molecular ion peak. Chemical ionization, field ionization, and desorption ionization spectra are used for this purpose. Once the molecular ion mass is known, a high-resolution mass spectrometer is needed to determine the empirical formula. Instruments such as a double-focusing mass spectrometer, a time-of-flight mass spectrometer, an orbitrap mass spectrometer, and a Fourier transform ion cyclotron resonance mass spectrometer can provide the needed accuracy.

Isotope peaks also help narrow down the formula of an unknown compound. The M+1 and M+2 peaks come from naturally occurring heavier isotopes, and their intensities are compared with the molecular ion peak. The M+1 to M+ ratio can also give an estimate of how many carbon atoms are present. The nitrogen rule helps predict nitrogen content, since a molecule with an even molecular weight contains zero or an even number of nitrogen atoms.

After the formula is estimated, the degree of unsaturation can show whether the compound has rings or multiple bonds. Fragmentation patterns then give more clues by revealing characteristic m/z values. These signature fragments can point to specific structural features and support the final identification of the unknown compound.

Decoding Molecular Ions in Mass Spectra

mass spectrometry: overview

Mass Spectrometry and Molecular Identity

Mass spectrometry helps identify a compound by measuring its molecular mass and molecular formula. It does this by turning the analyte molecule into ions and then comparing ion abundance with mass-to-charge ratio. One common ionization method is electron ionization, or EI. In EI, high-energy electron beams strike analyte molecules in the gas phase. The beam removes an electron and leaves a molecular ion behind. A molecular ion is a radical cation, so it has a positive charge and an unpaired...

mass spectrometry: isotope effect

Isotope Peaks in Mass Spectra

Isotope peaks in mass spectra show how natural isotope mixtures change the signal of a molecule. Most elements occur as a mix of isotopes, which are atoms of the same element with different numbers of neutrons. Because isotopes have different masses, the same fragment can appear at more than one position in a spectrum. The mass of a molecule depends on which isotopes are present in its atoms. The size of each isotope peak also depends on how common those isotopes are in nature. Carbon is a...

mass spectrometry: molecular fragmentation overview

mass-spectrometry-molecular-fragmentation-overview

Mass Spectrometry Fragmentation Patterns

Mass spectrometry fragmentation patterns show how a molecular ion breaks apart after ionization. When a molecule loses an electron inside the mass spectrometer, its structure becomes unstable. The ion then fragments at bonds that often produce the most stable pieces. One common pattern is cleavage of a single bond in the molecular ion. This break forms a radical and a cation. The bond can split in more than one way, but the favored path is the one that gives the more stable carbocation rather...

mass spectrometers

How Mass Spectrometers Sort Ions

A mass spectrometer sorts charged ions by their mass-to-charge ratio and records their relative abundance. It turns vaporized analyte molecules into ions, separates them, and then measures the signal from each type of ion. The process begins in the ionization chamber. The analyte is in the gas phase inside a vacuum, and it is struck by high-energy electrons. The electrons have about 70 eV of energy, which is enough to remove an electron from the analyte and form a molecular ion. After...

mass spectrum

Reading Peaks in a Mass Spectrum

A mass spectrum shows the charged fragments in an analyte as peaks plotted by mass-to-charge ratio, or m/z. The x-axis gives the mass of each charged fragment divided by the number of charges it carries. The y-axis shows the relative abundance of each charged species based on the signal intensity recorded at the detector. The tallest peak is called the base peak. It is assigned an abundance of 100%, and the other peaks are scaled against it. The peak from the molecular ion is called the parent...

mass spectrum: interpretation

Mass spectra help scientists identify an unknown compound by finding the molecular ion peak. The molecular ion peak shows the mass of the intact molecule, but it is often weak or missing because high-energy electron beams cause strong fragmentation. When that happens, a soft-energy electron beam can be used to scan the spectrum and improve the molecular ion signal. Other ionization methods can also give a stronger molecular ion peak. Chemical ionization, field ionization, and desorption...

mass analyzers: overview

Mass Analyzers and Ion Separation

Mass analyzers separate ions by their mass-to-charge ratio, or m/z, in a mass spectrometer. After a sample is vaporized in the ionization chamber, it is hit with a high-energy electron beam. This creates a radical cation and also produces neutral molecules, radicals, and cations. Negatively charged accelerator plates then push the cations into the mass analyzer, where they are sent on to the detector. Several mass analyzer designs are commonly used. These include magnetic sector,...

mass analyzers: common types

Quadrupole, TOF, and Ion Trap Analyzers

Quadrupole, time-of-flight, and ion trap mass analyzers each separate ions in a different way. They are common tools in mass spectrometry and help sort ions by their mass-to-charge ratio, or m/z. A quadrupole mass analyzer uses four cylindrical metal rods arranged in a diamond shape. The rods carry a direct current, or DC, voltage and a radio-frequency AC voltage. Ion motion depends on the field strength, so only ions with a certain m/z resonate and reach the detector at that setting. This...

high-resolution mass spectrometry (hrms)

Mass Accuracy in HRMS Analysis

High-resolution mass spectrometry separates ions by very small differences in mass. This matters because atomic masses are not always exact whole numbers, even though they are often rounded for simple calculations. Atomic mass is usually estimated by adding the masses of protons and neutrons. In reality, the proton and neutron do not have exactly the same mass. That creates small differences when atomic masses are compared to the simplest hydrogen atom. Helium, for example, is made of 2...

mass spectrometry: complex analysis

Hyphenated Mass Spectrometry Methods

Mass spectrometry can be paired with separation methods to study complex mixtures. This combination is called a hyphenated method. It helps when a pure mass spectrum is too hard to read because a mixture causes too much fragmentation and too many overlapping signals. GC-MS is one common hyphenated method. GC stands for gas chromatography, which separates volatile, thermally stable compounds in narrow capillary columns before they enter the mass spectrometer. This approach is widely used in...

tandem mass spectrometry

MS/MS Scan Modes and Fragment Ions

Tandem mass spectrometry uses two or more mass analyzers in series to improve selectivity and lower chemical noise during analyte detection. A set of analyzers separated by an interaction cell lets the instrument break ions apart and study the fragment ions that form. Fragmentation happens in the interaction cell and can be caused in several ways. Collision-induced dissociation, or CID, uses inert gases such as nitrogen, argon, or helium. Other methods include surface-induced dissociation...

gas chromatography&ndash;mass spectrometry (gc&ndash;ms)

How GC-MS Separates and Identifies Compounds

Gas chromatography-mass spectrometry (GC-MS) separates compounds in a mixture and then identifies them. A gas chromatograph first splits the mixture into its parts. A mass spectrometer then analyzes each part on its own to determine molecular masses and molecular structures. The gas chromatograph uses a long, narrow capillary column. The inner wall of the column has a polysiloxane coating. This coating serves as the stationary phase. It has a high boiling point, low viscosity, and low polarity.

inductively coupled plasma&#8211;mass spectrometry (icp&#8211;ms): overview

inductively-coupled-plasmamass-spectrometry-icpms-overview

ICP-MS Sample Ionization and Detection

ICP-MS uses an inductively coupled plasma torch to turn samples into ions for mass analysis. Solid samples are first dissolved and volatilized before they enter the hot argon plasma. Solution samples are nebulized, which means they are converted into a fine spray, and then passed through the same plasma. Inside the plasma, the analytes break apart. Their atoms become positively charged ions, along with some molecular species. These positive ions are sent to the mass spectrometer, where they...

inductively coupled plasma-mass spectrometry (icp-ms): interferences

inductively-coupled-plasma-mass-spectrometry-icp-ms-interferences

ICP-MS Signal Interference Sources and Fixes

Inductively coupled plasma-mass spectrometry (ICP-MS) is a sensitive method for elemental analysis, but its spectra can be affected by interferences. These interferences can make the mass signal less accurate, even when the instrument is working well. Spectroscopic interferences happen when ions in the plasma have the same mass-to-charge ratio, or m/z, as the analyte ion. This group includes isobaric interferences, polyatomic ion interferences, and refractory oxide ion interferences. Isobaric...

key terms and concepts

Learn how molecular ion peaks, isotope ratios, the nitrogen rule, and fragmentation patterns help identify unknown compounds in mass spectrometry.

Decoding Molecular Ions in Mass Spectra | JoVE K12

analytical chemistry

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Decoding Molecular Ions in Mass Spectra

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