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CBiRC Student Seminar
Basics of Mass Spectroscopy
Michael NolanJune 28, 2011
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Overview
Using MS/how it works
Types of MS instruments
Interpreting spectra + example
GC notes
MS Resources
Stump the Chump: Mystery Compound
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How does MS work?
Source:ElectronIonization
Mass Selector:Quadropole Detector
GC/LC/Inject
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MS Data
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MS Data
Molecular Ion (M+·)
Ionized compound
[M+1] and [M-1] often observed
Mass-to-charge ratio (m/z) X axis: MW of fragment divided by charge
Assume z=1, though z=2 can also be observed
Abundance• Y Axis: output signal proportional to # of fragments
Base peak
Peak with highest abundance
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Types of MS
Mass Selector
Magnetic selector
− Common
Quadrupole− Common
− Expensive, great spectra
Ion Trap
− Can be done w/ LC− Cheap
Time of Flight (TOF)
− Multiple inputs
Ionizer
Direct Electron Impact (EI)
− Common/MW<500
Chemical Ionization (CI)
− Easier to get M+· as [M+1]+
Electrospray (ESI)
− Good for high MW
Matrix-Assisted Laser
Desorption Ionization
(MALDI)
− Coupled with TOF
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When to use MS
Different Molecular weights (MW)
Different functional groups
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When not to use MS
Similar MW and similar groups
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How does MS work?
Fragmentation
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How does MS work?
Rearrangement
McLafferty (top) and water/ethylene elimination(bottom)
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Spectra!
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What's this?
m/z
A b
u n
d a n c e
98
83
69
5755
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Interpreting SpectraExample: MW=98
Before starting: Determine system chemistry
Elemental analysis if needed (Likely C6)
Do you have C,H,O,N,X present? (CHO)
Do you know the anticipated empirical formulas?
Step 1: Molecular formula
Step 2: Calculate unsaturation number
Hydrocarbons:
O, N, X:
UN= ( H saturated − H molecule )2
UN=[ (2a+2 )−(b−d+e ) ]
2
C a H
bO
cN
d X
e
H saturated
:C n H
n+2
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Interpreting spectra
Step 3: Determine if your biggest m/z is M+·
Alcohols (amines) rarely show M+·
Aldehydes have weak M+·
Conjugated molecules have strong M+·
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Interpreting structures
Step 4: Look for fragments in your spectra
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MS Spectrum
m/z
A b
u n
d a n c e
# 1 2 3 4 5
M/Z (i) 98 83 69 57 55
i-(i+1) 15 14 12 2
i-(i+2) 29 26 14
i-(i+3) 41 28
H: 1 CH
2:14
CH3: 15 OH: 17 H
2O: 18
C2H
2: 26
C2H
4: 28
CO: 28 C
2
H5
: 29 CHO: 29 COO: 44 COOH: 45
1
2
34
5
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MS Spectrum of a Hexenal (likely cis-2-hexenal)
m/z
A b
u n
d a n c e
Interpreting spectra
Step 5: Based on the above, propose and rationalizemolecules
Account for both fragments observed andpossible/likely rearrangements
Lose CH3
Lose CHO/Et
Lose CH2
Lose C2H
2
Lose CO
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Common fragmentations
Fragmentation rules
Fragments most able to hold a charge have moreabundance
You (typically) can't cut a double or triple bond
Below m/z=50 is fragment range, above is lossrange
α- and β-cleavage
Common for N, O containing molecules
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Other useful rules
Naturally occurring isotopes
13C: 1.1%
37Cl 1:3 with 35Cl
81
Br 1:1 with79
Br These are great for determining molecular formulas
Rearrangement rules
Cycles may form if doing so brings stability
Alkyl benzenes often show tropylium ion
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Notes on GC
Determine separation characteristics for your GC, and propose ranges of possible molecules
This helps to eliminate possible moleculeswhen interpreting MS
Peak convolution: raster MS peaks for overlap
Alkenals2.5-6 min
Pyrans6-8 min
Diols8-12 min
Triols13-21 min
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GC - Impurities
Use subtraction tool in your data interpreter toeliminate noise from:
Persistent air: 18 (H2O), 28 (N
2), 32 (O
2), 40 (Ar), 44
(CO2) Column additives (visible at higher temps)
Bake your GC column to remove “sticky”compounds
Wash GC injection syringe to eliminate “sampleecho”
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Simulating MS
Chemdraw (Windows/Mac)
Fragment tool: Draw a line through the bond(s) you
want to cut, that's it
BKChem (Linux/Cross Platform)
Draw fragments manually
Contributors needed for BKChem
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Using MS Libraries
MS Libraries are helpful, but not reliable
[M-18] alcohol loss, [M-29] aldehyde loss missed
Statistics may miss a critical m/z but meet others
Rule of thumb for libraries
A good match is 90+% accurate
NIST: common molecules get multiple matches Most often: Library gives you a lot of structures
similar to your structure
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MS Resources
Structure Determination of Organic Compounds – 4th edition
NIST Libraries
–
http://www.nist.gov/srd/nist1a.cfm – http://webbook.nist.gov/chemistry/
CHEM 572 @ ISU
– MS, IR, NMR course
CBiRC Intranet
– Message board in SLC section
– https://webspace.eng.iastate.edu/cbirc/
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Further resources
Student seminars on CBiRC Intranet
– SLC page > Student Seminar Discussion
This seminar is also onhttp://www.laboratorymike.com/openscience
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A b u n d a n c e
S c a n 5 4 7 3 (5 3 . 9 5 5 m in ): K O - 4 . D \ d a ta .m s
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1 6 0 1 8 0 2 0 0 2 2 0 2 4 0 2 6 0 2 8 0 3 0 0 3 2 0 3 4 0 3 6 0 3 8 0 4 0 0 4 2 0 4 4 0 4 6 00
2 0 0 0 0
4 0 0 0 0
6 0 0 0 0
8 0 0 0 0
1 0 0 0 0 0
1 2 0 0 0 0
1 4 0 0 0 0
1 6 0 0 0 0
1 8 0 0 0 0
2 0 0 0 0 0
2 2 0 0 0 0
2 4 0 0 0 0
2 6 0 0 0 0
2 8 0 0 0 0
3 0 0 0 0 0
3 2 0 0 0 0
3 4 0 0 0 0
3 6 0 0 0 0
m / z -->
( ) \
1 5 0 .1
1 9 2 . 2
4 4 4 .5
2 4 8 .22 2 0 .2 3 8 8 .4
2 7 6 .3 3 0 4 .3 3 4 6 . 3 4 7 2 .54 1 6 .4
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5 0 1 0 0 1 5 0 2 0 0 2 5 0 3 0 0 3 5 0 4 0 0 4 5 0 5 0 0
0
2 0 0 0 0
4 0 0 0 0
6 0 0 0 0
8 0 0 0 0
1 0 0 0 0 0
1 2 0 0 0 0
1 4 0 0 0 0
1 6 0 0 0 0
1 8 0 0 0 0
2 0 0 0 0 0
2 2 0 0 0 0
2 4 0 0 0 0
2 6 0 0 0 0
m / z -->
A b u n d a n c e
S c a n 5 3 2 6 (5 2 .7 2 3 m in ): K O - 4 .D \ d a ta .m s
1 2 3 .1
5 7 .2 4 7 3 .5
1 9 2 .2 4 3 0 .4 5 0 9 .62 4 8 .2 3 8 8 .43 1 8 .32 8 1 .19 1 .1 1 5 9 .2 3 5 5 .1
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1 4 0 1 6 0 1 8 0 2 0 0 2 2 0 2 4 0 2 6 0 2 8 0 3 0 0 3 2 0 3 4 0 3 6 0 3 8 0 4 0 0 4 2 0 4 4 0
0
2 0 0 0
4 0 0 0
6 0 0 0
8 0 0 0
1 0 0 0 0
1 2 0 0 0
1 4 0 0 0
1 6 0 0 0
1 8 0 0 0
2 0 0 0 0
m / z -- >
A b u n d a n c e
S c a n 5 3 2 6 (5 2 . 7 2 3 m in ): K O - 4 . D \ d a ta .m s
1 5 0 .2
1 9 2 .2
4 3 0 .4
2 4 8 . 23 8 8 .42 2 0 . 2
3 1 8 .32 8 1 .13 4 6 .4
4 5 6 .5