analyzing small molecules by ei and gc-msmsf.chem.indiana.edu/docs/gc-ms-intro-jul2014.pdf · 182...
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![Page 1: Analyzing Small Molecules by EI and GC-MSmsf.chem.indiana.edu/docs/GC-MS-intro-jul2014.pdf · 182 198 272 303 N H O O H O O Cocaine (mainlib) 3,4-Pyridinedimethanol, 5-hydroxy-6-methyl-10](https://reader033.vdocuments.net/reader033/viewer/2022041817/5e5be8c3bdfa8845dc14ee40/html5/thumbnails/1.jpg)
Analyzing Small Molecules by EI
and GC-MS
July 2014
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Samples Appropriate for GC-MS
• Volatile and semi-volatile organic compounds
– Rule of thumb, <250 u will likely work by GC-MS
– Highly polar or ionic compounds may not be sufficiently volatile for GC-MS
– PNP ligand @ 429 u has been analyzed by GC-MS
• Mixtures of semi-volatiles
– Crude reaction mixtures
– Stable isotope labeled samples
• Solvent should be in volatile matrix
– Please remove TBAF, NaCl, urea, or other involatiles if at all possible
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Gas Chromatography Basics
• Vapor-phase molecules separate by their interactions
with the inner wall of the column and the He stream
• Oven temperature is raised to weaken interaction with
stationary phase
• Temperature profile can be altered to improve
resolution of similar compounds or reduce analysis
time
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Basic GC Diagram
Image source: http://www.cubic.uni-koeln.de/research/horstmann/gas_chromatography2.jpg
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Agilent 6890/5973 GC-MS
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GC-MS Injection• A 100-position autosampler feeds one of two
split/splitless injectors
• Normal methods use “split mode” for
concentrated samples
– Usually aim for <50 ng on column
– 1 uL injection, 50:1 split is default on most methods
• 1 mg/mL solution gives 20 ng on column at 50:1
• Splitless mode is available for dilute samples
• Injector kept very hot (280 °C) to ensure instant
vaporization of sample
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Split Injection Mode Diagram
Image source: http://www.sge.com/uploads/yB/sx/yBsxaFxQS4C3FWzlvBJ6Uw/split_injection_2.gif
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Default 6890 Settings
• Default column on front injector is an Rxi-5Sil MS
– 95% dimethylsiloxane, 5% phenylsiloxane
• Very non-polar stationary phase from Restek
– 0.25 mm i.d., 30 m long, 0.25 μm film thickness
• Temperatures can range from -40-350 °C
– <30° is available with liquid CO2 tank
– Up to 20 °C per minute ramp possible
• Default gradients
– A “slow” gradient from 40-300 °C over 30 minutes
– A “fast” gradient from 70-280 °C in 18 minutes
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Other Column Chemistries
• There are entire catalogs full of GC columns with
different chemistries
– Any user-supplied column MUST be compatible with GC-
MS (bonded phase, no particles, limited bleed, etc)
• MSF has the following columns available
– DB-1 (100% dimethylsiloxane)
– DB-17 (50% phenyl, 50% dimethyl siloxane)
– DB-VRX (special dimethylsiloxane for volatile compounds)
– DB-WAX (polyethylene glycol)
• Column change takes about 4 hours
– Schedule this DAYS in advance with Dr. Karty
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Detection of Compounds
• As compound come off the end of the column,
they need to be detected in some way
• A 5973 inert mass spectrometer is coupled to
the outlet of the 6890 GC
– Provides both retention time AND electron
ionization mass spectrometric information
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Electron Ionization (EI)
• Gas phase molecules are irradiated by beam of electrons
• Interaction between molecule and beam results in electron ejection
– M + e- � M+• + 2e-
• EI is a very energetic process
– Molecules often fragment right after ionization
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EI Diagram
Image from http://www.noble.org/Plantbio/MS/iontech.ei.html
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EI Mass Spectrum
Figure from Mass Spectrometry Principles and Applications
E. De Hoffmann, J. Charette, V. Strooband, eds., ©1996
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More EI Mass Spectra
(mainlib) Coca ine10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310
0
50
100
15 27
42
5159 68
77
82
94105
122140 152 166
182
198 272
303
N
HO
O
H OO
Cocaine
(mainlib) 3,4-Pyrid inedimethanol, 5-hydroxy-6-methyl-10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180
0
50
100
27 31
3953
6781
94106
122
136
151
169
HO
OH
OH
NVitamin B6
(mainlib) Androst-4-ene-3,17-dione10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300
0
50
100
18 2941 55 67
79
86
91 97
109
124
131
148
162173 187
201
216 229
244
258 271
286
O
O Androstenedione
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EI Advantages
• Simplest source design of all
• EI mass spectrometers even go to other planets!
• Robust ionization mechanism
– Even noble gases are ionized by EI
• Fragmentation patterns can be used to identify molecules
– NIST ’11 library has over 240,000 spectra
– Structures of novel compounds can be deduced
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EI Disadvantages
• Fragmentation makes intact molecular ion difficult to observe
• Samples must be in the gas phase
• Databases are very limited– NIST’11 only has 213,000 unique compounds
• Interpreting EI spectra is an art– Suggest reading “Interpreting Mass Spectra” by
McLafferty and Turecek as a reference
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04
81
21
62
02
4
01
23
4
pentane
DCM
hexane
pentanal
heptane
Re
ten
tion
Tim
e (m
in)
butanal
hexanal
octane
heptanal
2-pentylfuran
octanal
2-octenal
nonanal
2-nonenal
Octanoic acid
2-decenal
2-undecenal2,4-decenedial
3-methyl-2-
heptanone
Empty vial
Oleic acid heated to 150 C
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40 50 60 70 80 90 100 110 120 130 1400
5000
10000
15000
20000
25000
30000
35000
40000
45000
50000
55000
60000
65000
70000
75000
80000
85000
90000
95000
100000
m/z-->
Abundance
Scan 5576 (17.680 min): BRON-OLEIC3.D57
98
41
7082
114
124109
65 7751 9387 142
Mass Spectrum from 17.68 minutes
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10 20 30 40 50 60 70 80 90 100 110 120 130 1400
2000
4000
6000
8000
m/z-->
Abundance
Scan 5576 (17.680 min): BRON-OLEIC3.D57
9841
70 82
114
12451 91 142
10 20 30 40 50 60 70 80 90 100 110 120 130 1400
2000
4000
6000
8000
m/z-->
Abundance
#19126: Nonanal57
41
987029 82
114 1245113 91 14263 131107
Mass Spectrum from 17.68 minutes
Nonanal Library Mass Spectrum
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A Word About Quantification
• GC-MS is a quantitative technique
• Use only 1 m/z when quantifying a compound
• Intensity is proportional to concentration
– I α [X]
– α is unique to each compound
– The more two compounds differ chemically, the more careful one must be when comparing their intensities
• Ideally a calibration curve is constructed using multiple solutions of pure analyte at varying concentrations
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Let MSF Staff Know
• If peaks look broad or non-Gaussian
– Implies time to change liner or septum
• If the same unexplainable mass is seen in
multiple injections
– 207, 281, 355, 429 are septum bleed
– 185 is tributylamine (from TBA-BF4 or TBAF)
• Any time an error shows up on the computer
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Training Times
• Angie and I usually train groups of 2 or 3
• Training takes about 1 hour
• Read through online training manual prior to
your session to speed the process
• Email [email protected] or
[email protected] to make an appointment