Workshop Skills

1. Overview of Utility of GCMS to

Environmental sampling
2. Extraction of organics
3. Sample Transport
4. Protocol for remote access (PC-Anywhere)
a) Remote access
b) Running Instrument
c) Analyzing Data
d) Transferring Data
5. Future of Data Base – portals
6. Future of Data Base – Overview of Utility of
GIS mapping for the pesticide data

Peng et al: 2004:

Acceptable Samples tricholoromethane:MeOH
1. GC-MS input requirements Concentrated by evaporation,
Dried with Na2SO4, concentrated again.
AND
2 USDA, EPA (TSCA), CDC restrictions Ayadi et al:, 2002
Solid phase extracted with Chloroform
3. Stability of the sample

1. Extract (Dichloromethane) 1. Extract (n-hexane)

2. Dry (sodium sulfate) 2. Dry (sodium sulfate)
3. Reduce 3. Reduce
4. Convert solvent (cyclohexane) 4. Convert solvent (hexane)

Pesticides Petroleum Contamination

Sedimentation Terrestrial Markers
USEPA # For
1664 Extact and Weighing of Total Petroleum
3510 Solvent Extracton of non-aromatic Volatile organics
3570
8015 GC determination
8270c GCMS determination

PDF files of methods are on GLIC website

1
 Example Application

Lower Njoro

2000000

1800000 Mass Spectra of Individual

1600000
Chromatographic peaks
1400000 M+.

1200000
Abundance

1000000
Lower Njoro River
800000

600000 25000000

400000

200000
228 16/18 Total
11.03-11.15 Ion Chromatogram (TIC)
12.53-12.58
0
0 100 200 300
20000000
400 500 600 700 800
M/z 7.56-7.59
13.99-14.06

15000000
Intensity

15.06-15.11

10000000

Identification
Indicates that these 5000000

Are n-alkanes
UCM
0

5 7 9 11 13 15 17 19
Tim e (m inutes)

2
 Interpreting n-Alkane results

Source Discrimination
carbons name b.p. oC Source of n-alkane
1 methane -162
2 ethane -88.6 1. Ranges of #C Differ
3 propane -42.1
4 butane -0.5
2. Center of Range is Characteristic
5 pentane 36
6 hexane 68.7 Gasoline
7 heptane 98.5 Range
8 octane 125.6 Organics
9 nonane 150.8 (GRO)
10 decane 174.1
11 undecane 195.9 Diesel
12 n-dodecane 216.3 Range
13 tridecane 235.4 Organics Kerosine
14 tetradecane 253.5 (DRO)
15 pentadecane 270.6
16 hexadecane 286.8 Algae
17 heptadecane 302
18 octadecane 316.3
19 nonadecane 329.9
20 eicosane 343
21 heneicosane 356.5
22 n-docosane 368.6
23 n-tricosane 380
24 n-tetracosane 391.3 Terrestrial
25 n-pentacosane 401.9 Plant
26 n-hexacosane 412.2 Leaf
27 n-heptacosane 442 Waxes
28 octacosane 431.6
29 n-nonacosane 440.8 center of distribution
30 n-triacontane 449.7
31 n-hentriacontane 458 center of distribution
32 dotriacontane 450.87
33 n-triacontane 464.89
34 n-tetratriacontane 478.92
35 n-pentratriacontane 492.95

3
http://www.whoi.edu/science/MCG/dept/education/MOG_course_djr_tie/MORG2005%20Terrestrial%20OC%203-29-05.pdf

What do you notice? Max peak at C31

Intensity Codd > Ceven

http://www.whoi.edu/science/MCG/dept/education/MOG_course_djr_tie/MORG2005%20Terrestrial%20OC%203-29-05.pdf

C31

C29

C33

C27

What do you notice? Max peak at C31 Intensity Codd > Ceven

4
 Source Discrimination
carbons name b.p. oC Source of n-alkane
1
2
methane
ethane
-162
-88.6
1. Ranges of #C Differ
3 propane -42.1 2. Center of Range is Characteristic
4 butane -0.5
5 pentane 36 3. Even/Odd preference varies
6 hexane 68.7 Gasoline
7 heptane 98.5 Range
8 octane 125.6 Organics
9 nonane 150.8 (GRO)
10 decane 174.1
11 undecane 195.9 Diesel Carbon preference index: CPI
12 n-dodecane 216.3 Range
13 tridecane 235.4 Organics Kerosine
14 tetradecane 253.5 (DRO)
2∑ odd C21 to C35
15 pentadecane 270.6 CPI =
16
17
hexadecane
heptadecane
286.8
302
Algae
(∑ even C 20 ) (∑ even C
to C34 + 22 to C36 )
18 octadecane 316.3
19 nonadecane 329.9
20 eicosane 343
21 heneicosane 356.5
22 n-docosane 368.6
23 n-tricosane 380
24 n-tetracosane 391.3 Terrestrial
25 n-pentacosane 401.9 Plant
CPI Source of n-alkane
26 n-hexacosane 412.2 Leaf 1 Petroleum Algae
27 n-heptacosane 442 Waxes
28 octacosane 431.6 2
29 n-nonacosane 440.8 center of distribution 3 Terrestrial
30 n-triacontane 449.7
31 n-hentriacontane 458 center of distribution 4 Plants
32 dotriacontane 450.87 5 3.69-5.12
33 n-triacontane 464.89
34 n-tetratriacontane 478.92 6
35 n-pentratriacontane 492.95

Original Article describing odd vs even C preference

5
 Why the difference in even/odd? ???Related to solubilities???
12

10

C21
8

6
-log (Solubility)

C8 C12
c15
4

2 C20 C26
C18
Increasing solubility
0
0 50 100 150 200 250 300 350 400 450 500

-2 algae Terrestrial plants

C9
-4
molar mass (g/mole)

6
 Excellent reference article,
Included in workshop materials

Petroleum
1. n-alkanes, ESPECIALLY C16
2. Aromatic hydrocarbons
3. Naphthenic materials

Unresolved complex mixture

Petroleum: peaks on the UCM

4. Presence of pristance
Brodskii et al, 2001 and phytane

7
 GC South China Sea sediment extract,

UCM

Single Ion Chromatogram

m/z 85 = (CH2)5CH3
SIMS advantage Terrestrial Source
Greater time on a single mass
Better Signal/Noise ratios

What do you see? Unresolved Complex Mixture (UCM) at >C33

C29, C31, C33 odd abundance, centered at 31
C15 to c21, no carbon preference

Peng, Ping’an; Chiling Yu, Guodong Jia, Jianfang Hu, Jianzhong Song, and Gan Zhang; 2004

N-Alkane Interpretation can be supported

Petroleum Terrestrial
Pristane lignin derived phenols
Phytane

8
10,000 ya to 1.8 mya C17 C18
Pristane, plant source

Phytane, oceanic source

Branched; decay more

slowly than n-alkanes

5.3 to 23 mya
(C18) of corresponding
Similar mass

33 to 54 mya

What Features do we observe?

Large Phytane peak

(Oceanic source)

UCM

Low CPI

Late eluting UCM peak

Three observations are consistent with oil

9
What is the source here? Peat coal which shows predominately terrestrial plant
input

N-Alkane Interpretation can be supported

Petroleum Terrestrial
Pristane lignin derived phenols
Phytane

10
 Softwood lignin

Pyrolysis and/or products

oxidation

http://www.whoi.edu/science/MCG/dept/education/MOG_course_djr_tie/MORG2005%20Terrestrial%20OC%203-29-05.pdf

Non-woody angiosperms and gymnosperms

Woody
Non-woody angiosperms

Lignin-phenols measured by GC-MS will allow determination of The terrestrial source

of sedimentary Organic carbon: Hedges and Ertel, 1982; Goni and Hedges, 1992
Bianchi 1997; Clifford 1995; McKinney 1995 References refer to GC-MS methods

11
 Summary of n-alkane Source Attribution

Petroleum
Terrestrial Materials 1. n-alkanes, ESPECIALLY C16
1. n-alkanes (C22-C33) 1. CPI ~1
1. CPI, terrestrial 3-5 2. Sit on UCM hump
2. Predominance higher chains 2. Aromatic hydrocarbons
3. Max ~31 C 3. Naphthenic materials
2. Other characteristic markers 4. Other characteristic markers
1. (lignin derived phenols) 1. Pristane
2. Phytane

Algae
1. n-alkanes (C15-C19)
1. CPI,>1 for non-silaceous planktonic origin
2. Ratio n-C29/n-C17 measure of plankton to terrestrial

Contribution
Sum CPI=1 n-alkanes plankton+petroleum
Sum CPI = 10 n-alkanes terrestrial plants
UCM petroleum
Paul V. Doskey, Spatial Variations and Chronologies of Aliphatic Hydrocarbons
In Lake Michigan sediments, EST, 2001, 35, 2, 247.

What is the pattern? UCM= unresolved complex mixture

Algae, Terrestrial higher plants;
1< CPI < 2 CPI 3.69-5.12

C14 to C22 C23 to C35

UCM14-22 =algae
No UCM23-35 = no petroleum

E. Lipiatou, R. E. Hecky, S. J. Eisenreich, L. Lockhart, D. Muir, and P. Wilkinson, Recent Ecosystem

Changes in Lake Victoria Reflected in Sedimentary Natural and Antrhopogenic Organic Compounds,
1996

12
 Use in Sedimentation (Erosional) Studies
Increased microbial activity
Suggested – related to agricultural runoff

Aquatic microbial
E. Lipiatou, R. E. Hecky, S. J. Eisenreich, L. Lockhart, D. Muir, and P. Wilkinson, Recent Ecosystem Changes in Lake
Victoria Reflected in Sedimentary Natural and Anthropogenic Organic Compounds, 1996

Terrestrial, C29

Paul V. Doskey, Spatial Variations and Chronologies of Aliphatic Hydrocarbons in Lake Michigan Sediments, Env. Sci. Tech.,
35, 2, 2001, 247

13
Range 16 to 26 Interpreting the Lower Njoro Data
CPI = 1 Lower Njoro River
Petroleum
25000000

C18
16/18 C20
11.03-11.15
C22
12.53-12.58

20000000

7.56-7.59
More
C16
C24
13.99-14.06 N-alkanes

15000000
Intensity

C26
15.06-15.11

10000000

5000000

UCM
0

5 7 9 11 13 15 17 19
Tim e (m inutes)

(CH2)4CH3
NIST C16 Lower Njoro 7.57 min. Peak
Mass
1200000 Abundance Rel Abundance Mass Abundance Rel. Abundance
71 603 1.000 69.93 1104487 1.000
72 33 0.055 71.15 570393 0.516
73
1000000 1 0.002 72.11 306988 0.278
73.15 16466 0.015

800000
Abundance

0.0525
600000

400000

200000

0
64 65 66 67 68 69 70 71 72
m/z
With “good” data can use the variations in 13C for additional environmental
inferences

14
 A biological example of this process Stable Isotopes of Carbon
% Abundance Mass
12
6 C 98.89 12.0000
13 1.11 13.00335
6 C

Reaction of CO2 with

Rubisco depends upon gas
phase velocity carrying the
molecule to the reaction site

Will the resulting

Sugars contain the
Same relative abundance
Of 12C and 13C?

http://www.msu.edu/~smithe44/calvin_cycle_process.htm

3RT
MM 12 CO = 12 + 16 + 16 = 44
urms mole =
2
M

MM 13CO = 13 + 16 + 16 = 45 δ 13 C
2
PeeDeeB 0
Air -8
3RT
C4 -10 to -15
u44 M 44 M 45 45
= = = = 10113
. Marine -21 to -22
u45 3RT M 44 44 12C Plankton
M 45
C3 -20 to -30
Expect biofractionation of isotopes to result in greater 12-C

=
[ 13
]
Ci ⎡ [ 13
Csample ] ⎤
Where PDB = Pee Dee
Belemite A South
[ C]
Ri 12 ⎢ ⎥
[ ]
Carolina, U.S.
i
⎢ 12
Csample ⎥ Iimestone, CaCO3
δ 13 C = ⎢ − 1⎥ 1000
⎡ Rsample ⎤
⎢
⎢
[ 13
C PDB ] ⎥
⎥
δ C= ⎢
13

⎣ Rs tan dard
− 1⎥ 1000
⎦
⎢
⎣
[ 12
C PBD ] ⎥
⎦

15
 Who moves to Rubisco faster?

Table 7a-1: Average composition of the

O2 atmosphere up to an altitude of 25 km.
Chemical Percent
Gas Name
Formula Volume
Nitrogen N2 78.08%
Oxygen O2 20.95%
*Water H2O 0 to 4%
Argon Ar 0.93%
*Carbon
CO2 0.0360%
Dioxide
Neon Ne 0.0018%
Helium He 0.0005%
*Methane CH4 0.00017%
Hydrogen H2 0.00005%
*Nitrous
N2O 0.00003%
Oxide
*Ozone O3 0.000004%

* variable gases

http://www.msu.edu/~smithe44/calvin_cycle_process.htm http://www.physicalgeography.net/fundamentals/7a.html

Using Gas Phase Reactions to 3RT

Understand Climate Change urms mole =
MM O2 = 16 + 16 = 32 M
MM CO2 = 12 + 16 + 16 = 44

3RT
u32 M 32 M 44 44
= = = = 117
.
u44 3RT M 32 32
M 44

O2 can swamp Rubisco reaction by

1. Concentration
2. Gas phase velocity in arriving at the reaction center

16
 4C chain: oxaloacetate 4C chain: Malate
OH O
CO2
O O
HO
+e + H+ OH
HO
OH Calvin
O
cycle
O
Arrival
Rate of gas
CO2 Independent
HO O
Of gas
Phase
Velocity
O CH3
No
ADP ATP Mass
effect in
favor of
3C chain: phosphoenolpyruvate 3C chain: pyruvate 12C
Outer Cell Inner Cell
4C Chain Plants maize, sorghum, sugarcane, millet, fonio, tef, papyrus

12C
C4
C3

2.5 million
Years

www.fsl.orst.edu/~bond/fs561/lectures/isotope%20lecture%202005.ppt

17
 N-Alkane ratios CPI C4 plant derived; based on 12C/13C

-20 to -30 δ 13 C

Land PeeDeeB 0 13C

Ocean
Organic Matter isotopes
Air -8
C4 -10 to -15
Marine -21 to -22
Plankton 12C

C3 -20 to -30

18
 Another Way to Quantify Isotopic Discrimination

δ 13C Air − δ 13C Plant

∆ =
fractionation
1 + δ 13C Plant

δ 13 C ∆ fractionation

Pee DeeB 0 0
Air -8
C4 -10 to -15 2 to 7
Marine -21 to -22
Plankton
C3 -20 to -30 12 to 22

19
Workshop Skills
1. Overview of Utility of GCMS to
Environmental sampling
2. Extraction of organics
3.Protocol for remote access (PC-
Anywhere)
4.Downloading data via PC-Anywhere
5.Downloading NIST standard data
6.Data manipulation via GLIC tools

A 14,000-year oxygen isotope record from diatom silica in two Alpine lakes on Mt
Kenya
Barker, P. A. et al, Science, 2001; 292 (5525) 2307-2310
Monitors oxygen isotopes and relates that to soil erosion and forests

Late Quaternary primary tephras in Sacred Lake sediments, northeast Mt. Kenya,
Kenya
Olago, D. O., et al. Journal of African Earth sciences 2000, 30(4), 957-969

Late Quaternary glacial-interglacial cycle of climatic and environmental change on

Mount Kenya, Kenya. Ogago, D. O., et al., J. of African Earth Sciences, 1999,
29(3) 593-618. - measures C4 (grassland) and C3 (trees and shrubs) plant debris

δ 13 C analyses of individual lignin phenols in Quaternary lake sediments: a

novel proxy for deciphering past terrestrial vegetation changes, Huang, Yongsong
et al Geology, 1999, 27(5), 471-474. - sediments of Sacred Lake, Mt. Kenya
measures lignin phenols

Glacial-interglacial env. Changes inferred from molecular and compound-specific

δ 13 C analyses of sediments from Sacred Lake, Mt Kenya, Huang, Yongsong,
et al. Geochimica et Cosmochimica Acta, 1999, 63(9), 1383-1404. measures
algal biomarkers – 5 unstd. Hydrocarbons

20
 Glacial/interglacial variations in carbon cycling revealed by molecular and isotope
stratigraphy of Lake Nkunga, Mt. Kenya, East Africa. Ficken, K. J. et al, Organic
Geochemistry 1998, 29(5-7), 1701-1719 - lipid content of n-alkanes, npalkanols,
n-alkanoic acids

Impact of lower atmospheric carbon dioxide on tropical mountain ecosystems.,

Street-Perrot, F. Alayne et al, Science, 1997, 278(5342), 1422-1426. Measures
carbon isotope values from lakes on Mt. Kenya and Mt. Elgon.

Mass spectrometry in the biosynthetic and structural investigation of lignins,

Reale, Samantha et al, Mass Spectrometry Reviews 2004, 23(2) 87-126.

Lignin – discusses measurements by MS-electrospray ionization (ESI-MS) and

matrix assisted laser desorption/ionization (MALDI)-MS on lignin analysis

Determination of 13C natural abundance of amino acid enantiomers in soil:

methodological considerations and first result. Glaser, Bruno, et al, Rapid
Communications I Mass Spectrometry 2002 16(9) 891-898

Application of GC-C/IRMS – methods discussed

Alkaline CuO Oxidation with a Microwave Digestion System: Lignin Analyses

of Geochemical Samples, Goni, Miguel A., Analytical Chemistry, 2000, 72(14)
3116-3121 - discusses digestion

Incorporation of 13C-labeled coniferyl alcohol into developing Ginkgo biloba

L. lignin revealed by analytical pyrolysis and CuO oxidation in combination
with isotope ratio monitoring-gas chromatography-mass spectrometry.
Eglinton, T. I., et all., Holzforschung 2000 54(1), 39-54

Analytical pyrolysis of humic substances and dissolved organic matter in

aquatic systems: structure and origin, Water Research 1999, 33(11) 2489-
2498 - Pyrolysis –GC-MS method

21
 From the web page of Huang at the Geology dept of Brown University

Organic compound remnants in lake sediments – tool for paleoclimate researh

Lipids are resistant to degradation and preserved in sediments.

(Yongsong Huang; Lockheart M., Collister, J. W., and Eglinton G.1995 Molecular
And isotopic biogeochemistry of the Miocene Clarkia Formation: Hydrocarbons
And Alcohols. Organic Geochemistry 23; 785-801)

Monitor C3 vs C4 plants by measuring carbon isotopic compositions

(e.g. leaf wax n-alkyl lipids or lignin phenols

Huang, Y., Street-Perrott F. A., Perrott F. A., P. Metzger, and Eglinton G. 1999a
Glacial- interglacial environmental changes inferred from the molecular and compound specific d13C
analyses of sediments from Sacred Lake, Mt. Kenya. Geochim. Cosmochim. Acta 63: 1383-1404

Huang Y., Freeman K. H., Eglinton T. I., Street-Perrott F. A. 1999b d13C analyses of individual lignin
phenols in the lacustrine environment: a novel proxy for deciphering the past terrestrial vegetation
changes. Geology 27, 471-474.

Huang Y., Street-Perrott F. A., Metcalfe S. E., Brenner M., Moreland M. and Freeman K. H. 2001
Climate change as the dominant control on glacial-interglacial variations in C3 and C4 plant abundance.
Science 293 1647-1`651.

Street-Perrott F. A., Huang Y., Perrott A., Eglinton, G., Baker, P., Khelifa L. Harkness, D. D. and Olago D.,
1997, The impact of lower atmospheric CO2 on tropical mountain ecosystems. Science 278, 1422-1426.

22