GCMS Ionization Modes for the QP2010Plus: EI, CI and NCI

GCMS Ionization Modes

EI: Electron Ionization CI (or PCI): Positive ion Chemical Ionization NCI: Negative ion Chemical Ionization

All 3 ionization mode use the same filaments. No additional (secondary) rotary pump is required to perform CI or NCI.
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QP2010 Plus Models

EI: + Ion Detection

Just uses filament for ionization Positive ion detection

EI and PCI: + Ion Detection

Needs extra reagent gas plumbing, electronics, ion box and reagent gas

EI, CI and NCI: + and Ion Detection

Needs third ion box and extra power supplies and boards to change polarity of lens, quadrupole and conversion dynode voltages.
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EI Ion Box open to vacuum

For the molecules to dissociate electrons and form ions they must stay isolated from other species or they will give away energy to other species and not form ions.
The space in the ion chamber must be at low pressure to keep the molecules isolated. The EI on box and repeller plate have large openings so that the ion chamber is at low pressure
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EI Mass Spectrum of Benzophenone

The EI mass spectrum for Benzophenone below shows the distribution of ions created by dissociation of electrons. Benzophenone molecules that absorb more energy from the filament electrons fragment more, like m/z 51 and 77. Benzophenone molecules that fragment less produce the base peak ion at m/z 105 The benzophenone molecular ion is m/z 182, it dissociated only one electron and did not fragment.

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Chemical Ionization CI & NCI

Ion Box must be pressurized with reagent gas with high vacuum on its outside. CI (PCI) box needs higher pressure; holes in it are smaller than NCI box.
Filament holes are very small
PCI has 2 holes; NCI has 4 holes

Ion exit hole is small Repeller electrode spacer seals ion box. Spacer has no hole for DI probe if not used.
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Ion Box and Spacer EI, CI & NCI

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Chemical Ionization Reagent Gases

3 possible types of reagent gas

Methane (CH4)
cheapest, most common, cleanest

Isobutane (C4H10)
softer ionization for more fragile molecules expensive, hard to come by, purity not so good

Ammonia (NH3)
softer ionization than methane, better results for some compounds, destructive to rotary pump oil and rotary pump

2 Reagent Gas Ports on back of MS

Can select from 2 types of reagent gas when perform autotune.
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Chemical Ionization CI & NCI

Definition of Chemical Ionization:
Some part of the reagent gas molecule must end up as part of the ion that is detected.

Positive Ion Chemical Ionization

Called CI (or PCI) Addition of proton or + ion from reagent gas

Negative Chemical Ionization

Called NCI Addition of electron from filament Jokingly referred to as Not Chemical Ionization.
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CI Positive Ion Chemical Ionization CI adds positively charged ions of the reagent gas to the sample molecules with much less or no fragmentation, compared to EI.
The ion chamber must be pressurized with the reagent gas. (To reduce fragmentation and create abundant reagent gas ions.) Filament electrons ionize the reagent gas producing + charged reagent gas ions. Sample molecules to be ionized must be able to capture a proton or + charged reagent gas ion. A molecular adduct ion is created when the + ion is created with no fragmentation. This identifies the molecular ion; the main reason for chemical ionization.
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CI with Methane Reagent Gas

Methane, CH4, produces these ions:

CH5+ (17 amu)
Adds a proton (+1 amu) to the sample molecule

C2H5+ (29 amu)

Combines with sample molecule

C3H5+ (41 amu)

Combines with sample molecule

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2007 SHIMADZU

Benzophenone EI vs. CI Spectra

EI
M = 182

CI
M+1=183 M+29=211

M+41+223
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NCI Negative Chemical Ionization NCI adds negatively charged electrons from the filament to the sample molecules with less fragmentation than EI.
The ion chamber must be pressurized with the reagent gas to reduce fragmentation.
Reagent gas pressure does not need to be as high as for CI.

Filament electrons lose energy to the buffer gas. Sample molecules form negative ions by capturing low energy filament electrons. Sample molecules to be ionized must be able to capture an electron. The same types of molecules that are detected by an ECD are also detected by NCI. NCI is ECD with Quadrupoles.
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Hexachlorobenzene EI vs. NCI

The mass of an electron is negligible compared to 1 amu. The ion is the same mass whether it loses (EI) or captures (NCI) an electron.
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NCI Ion Box Sub modes

You need to break vacuum to change between the EI, CI or NCI ion box. Without changing the ion box you can use the NCI ion box to run:
SEI, SCI and NCI (all 3 ionization modes)
SCI is CI using the NCI ion box SEI is EI using the NCI ion box

The software will run autotune for each or all of the 3 modes NCI, SCI and SEI. The ionization mode is changed in the method file. Reagent gas in the tune file.
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Sensitivities of Ionization Modes

Most sensitive to least sensitive:

NCI (- ion, capture electron)
Extremely sensitive; like ECD

EI (+ ion, lose electron) SEI (+ ion, lose electron) CI (+ ion, add reagent gas ion) SCI (+ ion, add reagent gas ion)
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Endosulfan Mass Spectra

(x100,000) 1.0 75 69 109 89 61 91 0.0 50 (x1,000) 2.5 111 135 161 105 50 (x1,000,000) 2.5 242 100 150 407 277 373 405 279 243 375 411 307 343 325 207 271 369 197 229 253 269 435 383 401 200 250 300 350 400 450 100 207 241 170 193 159 229 263 162 199 216 252 150 200 250

EI
339 337 350 407 429 463 479 400 450 500

126

307 300

CI

0.0

497 500

NCI

0.0 50

101 100

234 130 148 169 150 198 200 250

270

300 300

336 350

372

406 431 400 450

481 500

Chromatogram of Organochlorine Pesticide Mix, EI Mode

(x10,000,000) 1.25 TIC

1.00

0.75

0.50

0.25

7.5

10.0

12.5

15.0

17.5

20.0

Chromatogram of Organochlorine Pesticide Mix, CI Mode

Chromatogram of Organochlorine Pesticide Mix, NCI Mode

Endosulfan EI and SEI Mass Spectra

(x100,000) 1.5 1.0 0.5 0.0 50 (x10,000) 1.0 241 243 229 269 339 170 193 272 201 230 279 305 180 261 337 165 182 323 360 223 254 288 200 250 300 350 204 207 195 265 100 195 75 85 109 69 99 121 50 61 55 91 126 170 193 159 241 237 243 229 231 263 267 272 252 250

EI

162 169 199 216 181 147 150 200

339 337 307 323 343 300 350

407 429 463 400 450

500

SEI

0.5

57 78 75 53 64 61 50 100

119 136

0.0

150

391 418 400

449 472 499 450 500

Endosulfan CI and SCI Mass Spectra

(x1,000) 3.0 2.0 243 245 239 250 277 275 307 281 309 325 343 291 323 345 293 313 329 349 300 350 373 371 407 409

CI

1.0 0.0

111 135 107 100 (x100)

207 161 150 197 200

377 413 435 383 401 421 400 450

477 497 500

7.5 5.0 2.5 0.0

277 109 107 117 103 135 115 131 207 209 161 165 152 100 150 187 201 200 243 275 373 281 371 245 307 327 289 309 235 265 287 313 249 333 353 250 300 350

407

SCI
409

413 431 447 400 450

495 500

BHC isomer chromatograms, EI, CI, and NCI

EI

CI

NCI

BHC isomer chromatograms, EI and SEI

EI

SEI