GCMS - June 28 2011

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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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0

500

1000

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3500

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4500

m/z

A b

u n

d a n c e

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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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4500

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

GCMS - June 28 2011

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