The primary purpose of this site is to provide a brief summary of hints that should be useful for the interpretation of a mass spectrum. For known compounds, mass spectra can be used much like fingerprints. A match is extremely strong evidence that the compounds are identical. For unknowns, results from a mass spectrum often provide significant information that can help elucidate the structure of an organic compound. Analysis of a mass spectrum can provide a formula and considerable information about structure. As fragment ions are produced, the challenge is to put the pieces of a puzzle together to form the whole. Coupled with more pieces of the puzzle provided by infrared and nuclear magnetic resonance spectroscopy, it is often possible to determine the structures of very complex molecules.

The mass spectrometer is an invaluable tool for the detection and analysis of minute quantities of organic (and some inorganic) compounds. The technical aspects of the instrument can be simplified according to function into six components.

Sample injection. The sample is introduced into the ionization chamber commonly by one of three methods. The sample must be relatively pure and in the vapor phase when it enters the mass spectrometer. For volatile samples, direct injection works but for solids or liquids of low volatility, a heated inlet is usually used. Mixtures can be separated on a gas or high pressure liquid chromatograph. If the chromatograph is interfaced with a mass spectrometer, mass spectra can be obtained "on the fly".

Ionization. Commonly a beam of 70 volt electrons is used to ionize the ample and produce radical cations. As this is much more than ample energy to ionize compounds and produce molecular ions, the process also results in fragmentation to additional smaller cations.

Acceleration. Positively charged ions are accelerated towards a negative potential and through a slit into the mass separator.

Mass Separator. The heart of the mass spectrometer separates positive ions according to mass/charge values. Different types of mass separators include magnetic sector (positively charged particles with the same energy and charge but different mass follow paths of different radii when they enter a magnetic field and therefore are separated according to mass), quadrapole and time of flight.

Detector. Some type of device is used (commonly an electron multiplier) to detect the positive ions after they have been separated according to mass.

Data Output. Today almost all information from the detector is routed into a computer and can be outputed digitally or graphically and compared to a library of mass spectra for quick identification.

Interpretation of Mass Spectra. Ions formed simply by loss of an electron that live long enough to make it through the mass separator produce a peak at an m/e value corresponding to the molecular ion or parent peak (designated by "P" in this site). This value provides the very important and useful molecular mass of the compound. A few molecular ions fragment so quickly upon ionization that they are not detected but for most compounds at least weak molecular ions can be observed. As mass spectrometers separate isotopes, it is necessary to calculate molecular masses using the masses of the most common isotopes rather that the averages that appear in the periodic table. The molecular ion or parent peak is defined as the peak arising from the ion made up of the most abundant isotopes of its elements. Thus the highest molecular mass peak in a spectrum may be from a isotopic molecular ion and not strictly definable as the molecular ion.

Verification of Molecular ion. To be sure that a suspected peak is attributable to a molecualr ion and not a fragment several tests can be applied.

1. Nitrogen rule. Even numbered parent peaks for compounds containing C, H, O, N, F, Cl, Br, I, S, or P indicate either the absence of nitrogens or an even number of nitrogens. Odd numbered parent peaks indicate the presence of an odd number of nitrogens. If the number of nitrogens is known from other information available, this rule can be used as a test for the authenticity of the molecular ion.

2. Loss of fragments of molecular mass 3 - 14 are extremely rare and fragments at P - 3 to P - 14 should lead to suspicion of the molecular ion. For a justification of this guideline, consider what fragments could be lost that have masses in this range.

Molecular Formula. As the mass spectrometer separates positively charged species according to their mass to charge ratios, isotopes are separated and detected as distinct species. This fact often allows immediate recognition of the presence of certain elements such as bromine and chlorine. As bromine has two essentially equally abundant isotopes (79 and 81), the parent peak region of mass spectra of compounds that contain one bromine have two peaks of the same intensity separated by two mass unit. For chlorine (75.5% chlorine-35 and 24.5% chlorine-37), the (P + 2)/P ration is about 1:3.

The isotopic abundances of carbon-12 and carbon-13 are 98.9% and 1.1%. If several carbons are present (e.g., 6 in benzene) the probability of having a carbon-13 can be large enough to make the intensity of the P = 1 peak easily observable (6 x 1.1 = 6.6% of the intensity of P). Therefore by dividing the (P + 1)/P percentage by 1.1 (or # of carbons = (P + 1)/(0.011P), one obtains an estimate of the number of carbons present. Care must be exercised if heteroatoms are also present as some heteroatoms (e.g., nitrogen) have isotopes that contribute significantly to the P + 1 peak. For hydrocarbons, once the number of carbons has been determined the number of hydrogens is the molecular mass less 12 times the number of carbons. The web site WebElements and the other sites below contain isotopic abundances of all of the elements:

If the intensities of the P, P + 1 and P + 2 peaks can all be measured, it is possible to determine the formula of many compounds. Tabulations of the three values exist that give the corresponding formula when a match is achieved. The values can also be used to estimate the formulas
(CcHhN(0 or 1)Oo) of compounds that contain only the elements C, H, N (0 or 1 only), and/or O. The following equations provide approximate subscripts (one of the approximations involves neglect of the deuterium contribution to the P + 1 peak):

Let 100(P + 1)/P = P' and 100(P + 2)/P = P"

# of C = c = P'/1.1 (If presence of one nitrogen is suspected, round off to lower whole number.)

# of N = n = (P' - 1.1c)/0.37

#of O = o = (P" - 0.0062c2 + 0.0062c)/0.204

# of H = h = P - 12c - 16o - 14n

Degree of hydrogen deficiency. Once the formula is known, it is possible to calculate the hydrogen deficiency of the molecule. For instance, for a saturated hydrocarbon without rings, the formula is CcH2c + 2. The difference between the number of hydrogens in the formula and 2c + 2 divided by two is the hydrogen deficiency or a sum of the number of bonds and rings. The hydrogen deficiency in molecules containing C, H, N, O, Cl, Br, or I for the molecule CcHhNnOoXx (where X represents any halogen and x represents the total number of halogens) can be calculated from the equation:

degree of hydrogen deficiency = U = (2c + 2 - h + n -x)/2

Fragmentation. The ionizing electrons have considerably more energy than is necessary to accomplish simple ionization. The excess energy imparted to the molecules often causes simple and complex fragmentations of the molecules. This creates manyy new ions that have the potential of being detected by the instrument. Simple fragmentations involve cleavage of one bond and complex fragmentations are multicentered reactions (e.g. McLafferty rearrangements, retro Diels-Alder reactions). Either of the two fragments formed in a fragmentation may carry a positive charge and be detected. There is a reasonable correlation between peak intensity and the cation stability guidelines learned in the typical organic chemistry class (e.g., benzylic, allylic,and tertiary cations are more stable than secondary; even less stable are primary and cations on sp2 and sp hybridized carbons).

At least two pieces of information are obtained from fragment peaks: the molecular mass of the fragment and by subtracting this value from the mass of the molecular ion, the molecular mass of the fragment lost. It is sometimes possible to determine whether the fragmentation is simple or complex from the following:

For even numbered molecular ions (no nitrogens or an even number of nitrogens), simple cleavage gives odd numbered fragments and complex cleavage gives even numbered fragments. The situation reverses for odd numbered molecular ions.

The tables below contain compilations of some common fragments and fragments lost. Hopefully the tables will be of some use for the identification of fragments lost and fragments. Once the nature of these pieces have been determined, it is often possible to assemble the pieces into a picture of the complete molecule.

Correlation Tables

Ion  Fragment Lost  Possible Inference 
P-1 H 
P-15 CH3
P-16 NH2 amide
P-17 OH
P-18 H2O alcohol
P-19 fluoro compound
P-26 C2H2  aromatic
P-28 CO 

aromatic, ethyl ether, ethyl ester, n-propyl ketones, McLafferty 

P-29 CHO 
P-30 CH2=NH2 primary amine
P-31 OCH3  methyl ester
P-32 CH3OH    methyl ester
P-35, 37 Cl chloro compound
P-43 C3H7 
methyl ketone
P-45 CO2   carboxylic acid
P-46 NO2  nitro aromatic
P-57 C4H9 butyl
P-60 CH3CO2 acetate
P-79,81 Br  bromo cmpd.

Fragment   Possible Group Possible Inference 
29  CHO+, C2H5+
30 CH2=NH2+ primary amine
31 CH2=OH+ primary alcohol
41 C3H5+ allyl group
43 C3H7 
propyl group 
acyl group
50 C4H2 aromatic
51 C4H3+ phenyl group
57 C4H9 
butyl group 
ethyl ketone, propionate ester 
58 CH2=C(OH)CH3+  methyl ketone (McL. Rear.)
59 CO2CH3+ 
methyl ester  
primary amide (McL. Rear.) 
60 CH2=C(OH)OH carboxylic acid (McL. Rear.) 
71 C5H11+ 
pentyl group 
propyl ketone, butyrate ester  
74 CH2=C(OH)OCH3+ methyl ester (McL. Rear.)
76 C6H4 mono or disubstituted benzene
77 C6H5+ phenyl
85, 99 CcH2c+1 benzyl group
91 C7H7 alkyl group
105 C6H5CO benzoyl group

For compilations of thousands of mass spectra of compounds, see the NIST and the NIMC sites at:

For more information on mass spectra see:

For links to many chemistry directories, interesting chemistry sites and search engines, see:

This site was prepared on 7/23/97 by Steve Murov, and will probably be revised hopefully to contain interactive problems. Please e-mail comments to 

site uploaded 6/9/99, partially updated 12/17/13hit counter started 07/27/12 

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