Organic Mass Spectrometry Interpretation of Mass Spectra.

Organic Mass Spectrometry

Interpretation of Mass Spectra

Basic Interpretation

Most mass spectra are not trivial to decipher due to:– – interferences – complexities of fragmentation– (exception: some elemental analysis cases)

Instead, MS Interpretation is problem solving, ‘playing chess’, or ‘cracking a code’

Basic Interpretation

Use all available information in a logical and organized manner

Our focus: EI spectra of “small” organic molecules– but interpretation techniques are applicable to spectra

obtained with other ionization techniques (homework, examples…)

References on MS Interpretation

McLafferty & Turecek, Interpretation of Mass Spectra, 4th Ed., 1993.– Best book on the subject– We will follow it closely

Smith & Busch,Understanding Mass Spectra, 1999.– Alternative to McLafferty, somewhat easier to read

References on MS Interpretation

Lee, A beginner’s Guide to Mass Spectral Interpretation, 1998.– More basic, easy to read. Useful introduction before

tackling McLafferty. Sorrell, Interpreting Spectra of Organic

Molecules, 1988.– Older and more general.

MS Interpretation: First Steps

You have a sample to be analyzed. How do you proceed?

Three steps:1. Run the spectra you get against a database (if

available)

2. Obtain a high resolution spectrum if possibleThis will help constrain the elemental compositions

3. Follow the standard interpretation procedure (SIP) and make sure that your identification is self-consistent

Standard Interpretation Procedure

Ask questions in a logical order– Big picture questions first

E.g. which elements are present

– Avoid “blind alleys”– More detailed questions later

E.g. molecular substructures

Put it all together at the end Postulate a molecule that is consistent with all

previous information


(1) Study all available information (spectroscopic, chemical, sample history). Give explicit directions for obtaining spectrum (better yet, do it yourself).

– Verify the m/z assignments. Use calibrants if needed.

(2) Using isotopic abundances (where possible) deduce the elemental composition of each peak in the spectrum; calculate rings plus double bonds.


(3) Test molecular ion identity; must be the highest mass peak in spectrum, odd-electron ion, and give logical neutral losses. Check with CI or other soft ionization.

(4) Mark ‘important’ ions: odd-electron and those of highest abundance, highest mass, and/or highest in a group of peaks.


(5) Study general appearance of the spectrum: molecular stability, labile bonds, etc.

(6) Postulate and rank possible sub-structural assignments for:a) Important low-mass ion series

b) Important primary neutral fragments from M+. indicated by high-mass ions (loss of largest alkyl favored) plus those secondary fragmentations indicated by MS/MS spectra.

c) Important characteristic ions.


(7) Postulate molecular structures; test against a reference spectrum, against spectra of similar compounds, or against spectra predicted from mechanisms of ion decompositions

Remember to follow SIP step-by-step in order.

Library Databases

Databases are critical for even the most grizzled MS veterans

EI databases– NIST’s Chemistry WebBook @

http://webbook.nist.gov/chemistry 6000 molecules, but free and on the web

NIST off-line, Wiley, Palisades • Hundreds of thousands of molecules, $2k-$8k

Reproducibility of Spectra


Be aware that database (and other) spectra have limited signal-to-noise and reproducibility

McLafferty examples:– +/- for each peak 10% relative to itself– +/- 0.2 absolute (base peak = 100)

Library spectra depend on instrument used, how long ago, etc.


Be aware that background/leak/contaminant peaks may be present that are not related to the molecule of interest.

Take a “background” spectrum just before your analysis

Make sure m/z values are correct!

High Resolution Information

Elemental Composition

Reminder: use high resolution spectra (if at all possible) and always attempt to identify the peaks of every fragment.

Even with unit resolution, the presence of isotopes of known natural abundances provides a useful & simple method.

Isotopic Abundances

Note that the isotope of lowest mass is the most abundant for all of these elements.– “A”, “A+1”, and “A+2” elements

A + 2 Elements: Cl, Br, O, S, and Si

Especially prominent in the spectrum Look for these first!

A + 2 Elements

Linear superposition of isotopic patterns

If there is more than one atom in the molecule of one of the A+2 elements, the result is even more striking

Structural Isomers vs. MS

A + 2 Elements Oxygen isotopes

– The A+2 abundance of O is low (0.2%)– Need high abundance accuracy– Other isotopic patterns can interfere (C), thus estimate

number of oxygen after A+1 and other A+2 elements Absence of A+2 elements

– Often they are not there. Value of negative info– If [(X+2)]/[X] < 3%, the peak X cannot contain the most

abundant isotope of Si, S, Cl, or Br

A + 1 Elements

2H/1H is so small that it is considered “A” Increasing number of C atoms linearly increases

the probability that one of them is a 13C (see table 2.2)– A way to deduce the number of carbon atoms– 1.1% of 13C changes ~2% with source

• Don’t worry about N for now (next class)– “Nitrogen Rule” will come to our rescue

Unknown 2.4

Check for A+2 elements • Isotopic composition of 43 and 58? • Loss between 58 and 43? • Identity of the molecule?

Note about Unknown 2.4

Note the many small peaks below the major ones, due to neutral losses of H and H2

If you don’t see those, the molecule likely has no H Also note that those peaks are less important in

determining the structure– Start with the higher m/z (overall and in each group of

peaks)

Unknown 2.5

Is 0.2% at m/z 80 due to an oxygen atom? Elemental formula of base peak? Identity of the molecule?

Unknown 2.6

A Elements: H, F, P, and I

After the number of A+1 and A+2 elements have been assigned, A elements should provide the balance of the mass

Use number of atoms consistent with rules of bonding (no CH6 please!)

Note that only H can be used until we need to add 19 (F)

Example 1:

Example 2:

Unknown 2.7

Unknown 2.8

Rings + Double Bonds Because of the valences, the total number of rings and

double bonds in a molecule of the formula CxHyNzOn will be:

Calculate: C4H10 , C6H6 , C5H5N , C7H5O For ions, the value may end in 0.5 (‘even electron ion’) More general case AyBnCzDx, where A = H, F, Cl, Br,

I; B = O, S; C = N, P; and D = C, Si Does not count double bonds to elements in higher

valence states

Organic Mass Spectrometry Interpretation of Mass Spectra.

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