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The CHROMacademy Essential Guide Webcast:
GC-MS Ionization Processes

Thursday 24th April 2014, 8:00am PDT / 11:00am EDT / 16:00 BST / 17:00 CEST

The focus of this month’s Essential Guide webcast is GC-MS ionization processes.  The two main forms of ionization, Electron Ionization (EI) and Chemical Ionization (CI), will be discussed in depth.  The molecular reactions which occur within the ion source to produce ions will be examined along with which form of ionization should be used for particular analytes.  Finally, our speakers Dr. John Langley (Southampton University) and Scott Fletcher (Crawford Scientific) will impart some of their expert knowledge regarding optimization of the GC-MS process and some general interpretation strategies. 

Topics covered include:

  • Why use GC-MS
  • Anatomy of a typical ion source
  • Electron and Chemical Ionization – explanation of key parameters and how they effect your analysis
  • How to improve sensitivity and specificity by manually tuning source parameters
  • Recognizing ionization problems in your chromatographic and mass spectral data
  • Analyte fragmentation and basic interpretation strategies

Who Should Attend:

  • Anyone working with GC-MS who would like to further understand the ionization process
  • Anyone using GC who would like to utilize GC-MS in their laboratory
  • Anyone involved in developing GC and GC-MS methods
 
GC-MS Ionization Processes

 

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The CHROMacademy Essential Guide Tutorial:
GC-MS Ionization Processes

The focus of this month’s Essential Guide webcast is GC-MS ionization processes.  The two main forms of ionization, Electron Ionization (EI) and Chemical Ionization (CI), will be discussed in depth.  The molecular reactions which occur within the ion source to produce ions will be examined along with which form of ionization should be used for particular analytes.  Finally, our speakers Dr. John Langley (Southampton University) and Scott Fletcher (Crawford Scientific) will impart some of their expert knowledge regarding optimization of the GC-MS process and some general interpretation strategies. 

  • Why use GC-MS
  • Anatomy of a typical ion source
  • Electron and Chemical Ionization – explanation of key parameters and how they effect your analysis
  • How to improve sensitivity and specificity by manually tuning source parameters
  • Recognizing ionization problems in your chromatographic and mass spectral data
  • Analyte fragmentation and basic interpretation strategies

 
GC-MS Ionization Processes

 

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GC-MS is a hyphenated technique, which combines the separating power of Gas Chromatography (GC), with the detection power of mass spectrometry.
GC-MS can be used for the following:

  • Identification or characterization of analytes within a sample
  • Increased analytical sensitivity when a compound or element specific detector such as ECD, NPD, FPD or chemiluminesence cannot be used

The mass spectrometric detector can be used to fragment analytes and produce a mass spectrum which can serve as a ‘fingerprint’ of the molecule and which can be identified from one of the many commercial or in-house GC-MS libraries. Furthermore, if the compound is new or cannot be found within a library, then the spectrum itself may be used to propose analyte molecular weight and elemental composition, identify major features, and elucidate the structure of the molecule.

As the mass spectrometer can be used to essentially ‘filter’ the gas-phase column effluent for a specific mass, it is possible to achieve higher detection sensitivity by filtering out background noise and concentrating on the signal of interest only.

Fairly recently, GC has been coupled to triple quadrupole mass spectrometric detectors which allow even greater sensitivity through the use of multiple reaction monitoring type spectral experiments. GC-MS analysis with Time of Flight (ToF) detection is now also possible and ToF instruments give the added advantage of high resolution (and high accuracy) mass measurement which can result in empirical formulae and less ambiguous compound identification as well as high sensitivity.

 
 

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An exploded diagram of an electron ionization (EI) source is shown in Figure 1. Most EI sources have a cylindrical geometry to ensure the proper concentric alignment of the source elements, will typically have low thermal mass, and be slotted in some way to improve the vacuum level within the source. 1-2 

Minor changes to the source are required for chemical ionization (CI) which requires a reagent gas to ionize the analyte molecules, however, most modern mass spectrometers can perform both EI and CI.

 

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Figure 1: GC-MS ion source.
 
 

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In electron ionization (EI) electrons are emitted from a heated filament (usually made of tungsten or rhenium) and are accelerated across the source by using an appropriate potential (5-100 V) to achieve the required electron energy (sufficient to ionize the molecule) (Figure 2). 3

 

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Figure 2: Electron impact ionization.
 
 

The analyte is introduced into the mass spectrometer ion source where it is impacted by the beam of ionizing electrons leading to the formation of an analyte cation radical (Figure 3-4).

 

Figure 3: Electron impact ionization.

 

This process is a relatively harsh form of ionization and as a consequence the parent molecule often breaks apart producing a variety of fragments with a relatively small amount of the precursor ion remaining.  In some circumstances, if the molecule is sufficiently labile, no precursor ion will be observed in the resulting spectrum.  The degree of fragmentation depends on the magnitude of the first ionization potential of the analyte molecule, the energy of the impacting electrons, the ability of the ions to stabilize a charge and its ionization cross-sectional area.

Standard EI uses electron energy of 70 electron volts (eV), which as previously mentioned, creates highly energetic cations which tend to fragment extensively to produce detailed and reproducible spectra which are useful for library searching and spectral interpretation to elucidate analyte structure.  Some energy from the ionizing electron is transferred to the molecule as molecular translational or rotational modes.  The ionization of most molecules is between 6 and 15 eV.  All gas phase molecules which are impacted by an ionizing electron will ionize via the removal of a single electron to form a high energy radical cation.  The abundant characteristic ions which are formed can be used for quantitation. 

 

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Figure 4: Electron ionization fragmentation process.
 
 

A typical MS spectrum is shown in Figure 5, the mass (m) to charge (z) ratio is plotted on the x-axis and ion abundance is normalized to the most intense peak and plotted on the y-axis.  The base peak is the ion with the greatest abundance and all other peaks are reported relative to this peak.  The molecular ion is the parent ion which is produced from fragmentation of the analyte molecule; the intensity of this ion will vary depending on the stability of the radical cation which is formed during the ionization process.

 

Figure 5: Mass spectrum.

 
 

The order of ease with which electrons are lost under electron ionization is:
Lone pairs > π-bonded pair > α-bonded pair
The electron ionization of formic acid is detailed in Figure 6.

 

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Figure 6: Ionization of formic acid under EI conditions to form the radical cation which will be transferred to the mass analyzer using electrostatic fields and subsequently mass filtered and detected.
 
 

Having formed the radical cation from the analyte molecule it must be considered what will happen to this highly energetic species. 4
Most organic compounds will have an ionization energy in the region 6 to 15 eV.  Most of the excess energy imparted by the ionizing electron (55-64 eV), will be internalized and dissipated via vibrational and electronic excitation modes. It should also be stated here that radical species are highly excited states and, therefore, not energetically stable.

In electron ionization, the radical cation formed typically undergoes a single or a series of fragmentations or a re-arrangement reaction, resulting in the elimination of a neutral species in order to achieve a more stable state. The degree of fragmentation or intermolecular re-arrangement will depend upon the analyte molecule (typically on the ionization cross-sectional area and the ability of the molecule to stabilize charge) 5 and the energy of the ionizing electrons
(although this is typically 70 eV as stated above).

While there are many complicated schemes for the possible ionization and fragmentation/rearrangement pathways in electron ionization, for everyday purposes, we need only consider relatively few potential pathways which are demonstrated in Figure 7 and 8.

 
 
 

Figure 7: Typical fragmentation pathways and the resulting spectrum for an excited radical cation molecule ABC formed during electron ionization.

 
 

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Figure 8: Homolytic bond fission within a radical cation.
 

There are many important considerations relating to the scheme above. 6-7

  1. Only charged species are seen in the mass spectrum - neutrals and radical species are not influenced by the electrostatic fields within the instrument and therefore are lost to the vacuum within the instrument – i.e. if it doesn’t carry a charge, it won’t be seen.
  2. All reactions are assumed to be unimolecular - under the high levels of vacuum within the instrument (10-6 Torr, 10-9 Atmospheres) there are no background species to react with radical cations or their fragmentation/re-arrangement products.
  3. The intensity of the fragments gives an indication of the relative stability of each species.
  4. As will be discussed subsequently, re-arrangement reactions are restricted in the time domain and certain reactions will predominate depending upon analyte chemistry.
  5. Each of the fragmentation products formed may undergo further fragmentation.
  6. Loss of a neutral typically results in an even mass fragment - something which is highly indicative in spectral elucidation.
  7. The products formed under 70 eV conditions will be predictable and the resulting spectrum can be used as a ‘fingerprint’ of the molecule which can be used for library searching or used for ab initio spectral interpretation/analyte characterization.
 
 

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Most EI spectra are recorded at 70 eV, primarily because most species which are likely to be investigated using GC-MS will ionize at this energy as the electron de Broglie wavelength (matter wavelength) matches the length of common bonds in organic molecules (circa. 0.14 nm) and at this energy the transfer of energy from the ionizing electron is maximized.

Under these conditions around 1 in every 1000 analyte molecules is ionized (0.1% ionization efficiency). Maximum energy transfer also leads to maximum fragmentation of most common organic compounds. Furthermore, 70 eV represents an ionization energy plateau on which small variations in electron energy will not adversely affect ionization efficiency, therefore, library searching will be a practical reality. 5 
This is demonstrated further in Figure 9.

 

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Figure 9: Effect of ionizing electron energy on ion abundance and degree of ionization for a lactam compound under electron ionization conditions.
 

At higher electron energy, the de Broglie wavelength of the electrons becomes smaller than the bond lengths in typical analytes and, as such, the analyte molecules become ‘transparent’ to the ionizing electrons and ionization efficiency decreases very quickly.

At lower electron energy, the efficiency of ionization also decreases, although some ionization will occur down to around 20 eV. This can be usefully used when attempting to reduce the degree of analyte fragmentation in order to generate a more intense molecular ion (i.e. the intact radical cation of the precursor molecule) within the spectrum, which can be of great use for spectral interpretation. As electron energy reduces, the degree of analyte fragmentation reduces and, thus, the chance of recording an intact molecular ion increases. The efficiency of ionization also decreases dramatically, however, and a reduction in the absolute ion intensity must be balanced against any enhancement in the molecular ion intensity.

The useful ionization energy window for most bench top GC-MS instruments will be around 20-80 eV.

New technology allows the electron ionization energy to be changed on a sliding scale (70-10 eV).  Spectra can be obtained at 10 eV without the need for soft ionization techniques (no source switching, no reagent gas etc.) without a loss of sensitivity (Figure 10).  This is particularly useful for distinction between similar species (i.e. hydrocarbon isomers).

 

Figure 10: Spectra obtained with various electron ionization energies.  Markes, Llantrisant, Wales, UK.

 
 

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The voltages applied to the various ion source components must be ‘tuned’ to achieve target ion abundances for various analyte ion masses. This ensures optimal instrument sensitivity and a predictable response across a range of masses, which allows for subsequent library searching of spectra.
During tuning (sometimes called ‘autotuning’), the relative and absolute abundances of fragments of a known tune compound are established and the mass assignment, resolution, and spectral peak width generated by the mass analyzer are also adjusted and set.
The tuning process involves adjusting a number of mass spectrometer parameters. Some are purely electronic and only affect the way the electronics process the signal. Other parameters affect the voltage settings or current to the ion source components, the mass analyzer, and detector. In general terms, the tuning process will:

  • Set voltages on the ion source elements.
  • Set gain and offset of the mass analyzer for correct spectral peak width (resolution).
  • Set the electron multiplier voltage.
  • Set the mass axis for proper mass assignment.

The importance of tuning cannot be overemphasized and is performed to check the mass spectrometer is working correctly and/or to ensure that spectra (mass assignment and relative abundance of spectral signals) resemble a previously determined standard. The process of tuning will:

  • Check to see that spectrometer contamination or degraded electronic components have not changed assigned m/z positions (calibration of the m/z axis).
  • Ensure repeatable analysis from instrument to instrument (or lab to lab).
  • Check the spectrometer gives expected relative ratios of ion fragment intensities for a target compound.
  • Act as a diagnostic tool to indicate the service/cleaning requirements of the spectrometer
  • Act as a chronicle of system performance.
  • Match fragments from a known calibration compound and adjust m/z axis so it agrees with the expected m/z assignments.

Several compounds might be used to calibrate the mass spectrometer; one of the most common tuning standards is perfluorotributylamine, also known as PFTBA, FC-43 or heptacosafluorotributylamine (heptacosa) (Figure 11-12).

 

Figure 11: PFTBA.  C12F27N, M.Wt. 670.9600.

 

Perfluorotributylamine has several characteristics which make it amenable for use as a tuning standard including:

  • It is a liquid that is volatile at room temperature and under the vacuum conditions inside the spectrometer. The liquid is kept separate from the system by means of a valve. When the instrument requires calibration the valve is opened and the calibration gas is allowed to volatilize into the spectrometer. The calibration gas is ionized in the mass spectrometer ion source and its fragments are mass filtered and detected.
  • It fragments very reproducibly and predictably under EI and CI conditions to yield ions across a wide mass range and with reproducible relative ion intensity.
  • It does not contain protons and, therefore, there are no issues with mass ‘rounding’ (as hydrogen atoms are mass sufficient) and the 13C isotope peak can be easily used to measure relative isotopic abundance.
 

Figure 12: PFTBA EI spectrum (over simplified).

 

Nominal m/z

Rel. Abundance

Nominal m/z

Rel. Abundance

69

100

176

1.5

70

1.1

181

1.8

76

0.7

214

1.2

81

0.6

219

50.7

93

1.3

220

2.3

95

0.6

226

1

100

17.7

264

13.4

101

0.7

265

0.7

112

0.8

314

1.8

113

0.8

326

0.3

114

7.9

352

0.7

119

13

376

0.4

131

47.9

414

3.4

132

1.7

415

0.4

145

1

426

0.6

150

2.8

448

0.2

164

1.4

464

1.5

169

4

502

2.6

Table 1: PFTBA usable masses.

 
 

Tune Results

It is important that the ion source and mass analyzer combination are able to report the correct relative intensity of the fragment peaks as the relative abundance of ion signals is critical in both ab initio spectral interpretation (indicating the relative stability of the ions created) as well as being essential for library searching, where relative intensity is a key search criteria. The relative isotope peak area ratios are also important in analyte characterization where the cluster of isotope peaks (especially around the molecular ion) can be used to postulate an empirical molecular formula.

Typically, during the tune process, each key ion source component will have a ramped voltage applied whilst the abundance of key fragments are monitored for ion abundance. The resulting instrument output is shown in Figure 13.

 

Figure 13: Optimization of the repeller voltage during an EI source tune. Ion abundance of fragment ions across a wide mass range are plotted against applied voltage to yield the optimum ‘average’ value.

 
 

Manual Tuning

Whilst it is useful to apply auto-tune values and parameter targets for ion source tuning, there is no facility to tune on ‘YOUR COMPOUNDS’. This is often overcome by optimizing the tuning parameters of the mass spectrometer using a tune compound which has a mass near to the compounds of interest – e.g. if the compounds are typically in the mass range 100-150 amu (Da) then the 131 peak within the PFTBA spectrum may be selected (in most instruments) as being ‘typical’ of your analyte species, and the tune centered around this mass. Note that autotune will not allow the change in mass – rather the instrument is autotuned first, and then each element manually tuned using the 131 peak to optimize at this mass. Some manufacturers, however, will allow the operator to build specific autotune routines where new alternative ions and tune performance targets may be specified.  There are several strategies for developing manual (user) tune approaches but ultimately it is the experience of the operator in optimizing the MS parameters that will govern whether or not this approach is valid.
These techniques can be very useful tools for quickly optimizing certain parameters.  For example if maximum sensitivity is required at lower mass, the user tune will allow the operator to ramp the amu offset (a detector parameter) to its optimum value by providing a graphical output of the parameters entered by the operator.
To examine each of the tuneable components in turn would take too long, however, a general principle applies to each of the voltages which may be ramped within the spectrometer.  In each case selected ion abundance is measured across the voltage range selected for each source component, the optimum value for the ion or ions of interest may then be selected.

When optimizing lens voltages ensure that the curve produced is smooth in every case.  A noisy or non-sigmoidal curve will indicate that the component is dirty, damaged, or very far from its optimum value.

In every case an optimum (or curve maxima) should be able to be located.  This indicates that the voltage (or current) applied to that particular component is the optimum with respect to the other system voltages at any given time.  Of course all of the system voltages are interactive and the process should be repeated iteratively to optimize each of the system components.

 

Figure 14: Repeller voltage optimization.  Note that 25 V ensures good intensity for all masses, however, the voltage chosen optimizes on the response of the 100 amu (Da) signals.

 
 

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Chemical ionization involves the ionization of a reagent gas, such as methane, at relatively high pressure (~1 mbar) in a simple electron ionization source.  Ionization of the reagent gas produces a plasma (Figure 15) which contains highly reactive ions which will ionize the analyte molecules.

 

Figure 15: Methane reagent gas plasma produced upon ionization.

 
 

Once produced the reagent gas ions collide with the analyte molecules producing ions through gas phase reaction processes such as proton transfer.

 

Figure 16: Proton transfer reactions with ammonia reagent gas.

 
 

Proton transfer will predominantly give [M + H]+ ions, however, acidic analytes may also form [M + H]- ions via protonation of another neutral species.  Electrophilic addition mainly occurs by attachment of reagent gas ions i.e. [M + H]+.  Hydride abstraction is an abundant form of anion abstraction i.e. an aliphatic alcohol will produce [M + H]+ ions.  Charge exchange produces low energy radical ions. 8

 

Figure 17: Positive CI ion formation reactions.

 
 

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Figure 18: Chemical ionization.
 

Chemical ionization is a soft process, because the energy of the reagent ions in general never exceeds 5 eV, and as a consequence the spectra produced by this technique usually show little fragmentation.  Under chemical ionization conditions the spectra obtained will depend strongly upon the nature of the reagent gas used and, because of that, different structural information can be obtained by choosing different gases.  Commonly used reagent gases are methane, iso-butane, ammonia or combinations of these gases (Table 2).

 

Reagent Gas

Reactant Ions

Neutral from Reactant Ions

Analyte Ions

CH4

CH5+

C2H5+

C3H5+

CH4

[M + H]+

[M + C2H5]+

[M + C3H5]+

[M + CH3]+

i-C4H10

t-C4H9+

i-C4H8

[M + H]+

[M + C4H9]+

[M + C3H3]+

[M + C3H5]+

[M + C3H7]+

NH3

NH4+

NH3

[M + H]+

[M + NH4]+

Table 2: Reagent gases used for CI.  Reactant and analyte ions formed.

 
Methane
  • Good for most organic compounds
  • Usually produces [M + H]+, [M + CH3]+ and [M + C3H5]+ adducts
  • Adducts are not always abundant
  • Extensive fragmentation
Iso-butane
  • Usually produces [M + H]+, [M + C4H9]+ adducts and some fragmentation
  • Adducts are relatively more abundant than for methane CI
  • Not as universal as methane
Ammonia
  • Fragmentation virtually absent
  • Polar compounds produce [M + NH4]+ adducts
  • Basic compounds produce [M + H]+ adducts
  • Non-polar and non-basic compounds are not ionized
 
 

The energy of reagent gas rarely exceeds 5 eV making CI a softer ionization technique which gives rise to more intense molecular species and fewer fragments (although this will make library searching more difficult). A typical spectrum from CI is shown in Figure 19.

 

Figure 19: CI spectrum of Aflatoxin B1.

CI positive ion mode is less sensitive as the reagent gas is also detected. 
The ion source is often tuned with an alternative tune compound - i.e. perfluoro-5,8-diemthyl-3,6,9-trioxydodecane.  User tuning/voltage ramping is still possible.

 
 

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Common ion source problems include:

  • Contaminated with sample/contaminant residues
  • Blown filament wire
  • Broken/shorted heater or sensor
  • Backstream of foreline pump oil

GC–MS ionization processes are typically 0.1% efficient. Non-ionized solute molecules will be adsorbed to the surface of the ion source or transported through the vacuum system to reside ultimately in the rough pump oil or will be vented to the atmosphere.
The GC–MS ion source is, therefore, subject to contamination. The degree of this contamination is dependent largely on the concentration and nature of the sample. For example, analysis of samples that consist of a dirty/complex matrix will lead to rapid ion source contamination; here increased frequency of ion source cleaning becomes a necessity.

The system will become increasingly contaminated with each tune performed and each sample analyzed, as neutral species are adsorbed onto the surface of the various electrostatic components. If possible, ‘screen’ unknowns using an FID or TCD detector before injection into the GC–MS. This will indicate if the sample needs a pre-cleaning step (typically solid phase extraction or similar) and will maximize the time between source cleans.  It will also serve to provide an indication for a suitable solvent delay time in order to maximize filament lifetimes.

The GC–MS ion source contains no moving parts, so mechanical wear is minimal.

Broken or shorted filaments will result in the total loss of signal from the instrument. Filament lifetime can be optimized by operating at high levels of vacuum and by switching the filament off during the pressure surge created by the elution of the sample solvent.

Backstreaming of pump oil will cause the spectrum to contain a very high number of prominent ions in the mass spectrum (Figure 20).

 

Figure 20: MS spectra obtained from pump oil (top).  Library search of pump oil (bottom); m/z 39, 41, 43, 55, 57. 
Vacuum Diagnosis with an RGA, Stanford Research Systems, Sunnyvale, CA.

 

Filaments

In addition to the AC power source that heats the filaments, each filament carries a –70 V DC bias voltage. The emission current is typically set between 50 and 300 mA with the current being variable in order to adjust the amount of the electrons being emitted.  Only one filament is operational at any one time.
Broken or shorted heater/sensor will cause a “temperature control fault” message.

Repeller

  • A positive charge on the repeller plate pushes positive fragments and parent ions out of the source via the lenses. 
    The ions only receive a fraction of the repeller energy.
  • The repeller voltage can be varied typically between 0 and + 42.7 V DC.
  • Too low a repeller voltage results in poor sensitivity and poor high mass response
  • Too high a repeller voltage results in poor mass filtering (precursor ions) and poor low mass resolution.
  • The repeller is also used to sense excessive source pressures.

Ion Focus

  • The voltage on the ion focus lens can typically be varied from 0 to –242 V DC and is commonly between –60 and –100 V DC.
  • In general increasing the ion focus voltage improves sensitivity at lower masses
  • Decreasing the ion focus voltage improve sensitivity at higher masses
  • Poor ion focus adjustments result in poor high mass resolution

Increasing the entrance lens offset voltage increases the abundance of ions at low masses without substantially decreasing abundance of high mass ions.


Leaks

Leaks can occur after any routine maintenance (i.e. cleaning, changing the column) and can be evident by the appearance of characteristic ions in the mass spectrum from water and air (Figure 21), loss of vacuum, poor sensitivity etc.
In order to repair the leak it must be located.  If there has been any maintenance performed all fittings should be checked to ensure that they have been properly tightened.  The procedures detailed below can also help to diagnose where the leak is:

  • When the system is running verify if there are peaks at m/z 28 and 32 indicative of nitrogen and oxygen which would indicate a leak to the atmosphere.
  • Cap the transfer line and pump down the system and see if the vacuum holds.  Also again monitor for peaks m/z 28 and 32.  If these peaks are not present then the leak is not from the source onwards.
  • Cap the transfer line at the inlet of the GC system and again monitor pressure.  If the pressure holds then the leak is further back.
  • Check for leaks at other points in the system.  An easy way to do this is to use a dust removal aerosol (this contains chlorodifluoromethane).  While looking at masses between m/z 35 and m/z 75, spray the dust off (chlorodifluoromethane) and look for peaks to appear at m/z 51, 52 and 67. Spray short bursts of this at fittings in the interface oven, around the separator and in the GC allowing time for it to show up on the oscilloscope or monitor.
    Tightening or replacing the fittings or ferrules should fix the leak.
  • Check the user manual to see if there are any other fittings, or seals within the transfer line which may need tightened or replaced.
  • If vespel or vespel blended ferrules are being used these need to be tightened regularly to maintain a proper seal (weekly), therefore, then a quick tighten of these may help.
 
 

Figure 21: Normal air/water background spectrum (top), spectrum obtained with a small leak (middle), spectrum obtained with a large leak (bottom).  m/z 18 = H2O and m/z 28 and 32 = N2 and O2/air.

 
 

Usually if m/z 28 is larger than m/z 18 there is a leak.  Ratio m/z 18 to 32 should be 4:1.
When examining the spectrum generated by the tune, it is good practice to check for the presence of ions resulting from known sources of contamination. Table 3 lists some common contaminating ions.

 

Ions (nominal m/z)

Compound

Possible Source

13, 14, 15, 16

Methane

Chemical ionization gas

18, 28, 32, 44 or 14, 16

H2O, N2, O2, CO2 or N, O

Residual air and water, air leaks

31, 51, 69, 100, 119, 131, 169, 181, 214, 219, 264, 376, 414, 426, 464, 502, 576, 614

PFTBA and related ions

PFTBA (tuning compound)

31

Methanol

Cleaning solvent

43, 58

Acetone

Cleaning solvent

78

Benzene

Cleaning solvent

91, 92

Toluene or xylene

Cleaning solvent

151, 153

Trichloroethane

Cleaning solvent

69

Foreline pump fluid or PFTBA

Foreline pump oil vapor or calibration valve leak

73, 147, 207, 221, 281, 295, 355, 429

Dimethylpolysiloxane

Septum bleed or methyl silicone column coating

77, 94, 115, 141, 168, 170, 262, 354, 446

Diffusion pump fluid

Diffusion pump fluid and related ions

149

Plasticizer (phthalates)

Vacuum seals (o-rings) damaged by high temperatures, use of vinyl or plastic gloves, vial caps

Peaks spaced 14 m/z units apart

Hydrocarbons

Fingerprints, foreline pump oil

Table 3: Ion peaks produced by common contaminants.

 
 

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Electron ionization sources produce ions that can be subsequently used for both quantitative and qualitative purposes.
The field of qualitative spectral analysis or spectral interpretation is well documented. However, as is the remit of the Essential Guide series, we will take this opportunity to present a selection of highly practical tips and tricks from CHROMacademy to get you started with spectral interpretation.
Step 1 - Obtain a representative spectrum
Begin by getting as many data points across each spectral peak as possible (7+ for spectral interpretation).
Quadrupole mass analyzer scanning speed is increased by:

  • Restricting the mass range to only look for the compounds of interest - typically this will be in the range m/z 40–700.
  • The narrower the mass range the faster the scan speed.
  • Restricting the ‘oversampling’ of the mass analyzer - i.e. how many measurements are taken for each mass (or 0.1 m/z unit).  This will typically be 2 to 4 for most quadrupole mass analyzers.

Take an ‘average’ spectrum across the peak at half peak height (which will average all spectra taken from halfway up the peak upslope, across the peak apex, to half way down the downslope (Figure 22).

 

Figure 22: Half height averaged spectrum taken from an EI total ion chromatogram.

 
 

This will avoid the problem of spectral ‘tilting’ which occurs because the analyte concentration is constantly changing across the elution profile (Figure 23).

 

 Figure 23: All of the spectra (634–636) are taken from the total ion current to the left, however, due to the changing concentration profile the relative ration of ions is varying markedly.

 

Tilting causes the relative intensities of spectral signals to vary according to the changes in analyte concentration during acquisition. Tilting phenomena are accentuated when the spectral acquisition/duty cycle  time is ‘long’ in comparison to the peak elution time (i.e. there are a low number of scans across the peak). Spectral ‘averaging’ helps to avoid this problem.

Further, when generating spectra it is important that any ions arising from the ‘background’ signals are removed. This is generally achieved using ‘background subtraction’ data processing techniques; however one must take care not to remove ions from the analyte spectrum.

 

Step 2 - Library Searching
Some of the most useful tools in spectral interpretation are the many reference libraries which exist in digital form and which can be searched (using a variety of proprietary algorithms), primarily to match ‘unknown’ spectra to those within the library.
There are many comprehensive libraries available including those from:

  • Wiley
  • National Institute of Standards and Technology (NIST)

There are also hundreds of application specific libraries available from a host of providers.
Matching an unknown mass spectrum against a library file requires: 9-11

  • The unknown and reference spectra were acquired under identical conditions.
  • A database with sufficient information (for example, the NIST database contains spectra from almost 200,000 different compounds, however, smaller databases which are more application specific may also be very useful).
  • A well-structured library searching algorithm.

Searching a database will result in a list of candidate compounds for the unknown, with a certain level of confidence based on the parameters of the search algorithm. These usually involve the uniqueness and abundance of ions within the unknown spectrum.

 
 

Case one. The spectrum of the unknown molecule IS in the database
Modern matching algorithms implement an objective function that accounts for the “distance” between the unknown and the reference spectra. As expected, the smaller the value of the objective function (closeness), the more likely that both spectra correspond to the same molecule.
Most matching algorithms implement a pre-screen, where only a limited number of peaks (of certain intensity) are considered versus the full database. Once this step is done, a more refined matching procedure with the results of the pre-screen is performed.
In order to rank the “closeness” between two spectra, matching algorithms implement match factors. In general terms, you can find peaks in the unknown sample spectrum that are not reflected in the reference spectrum, as well as the opposite case (peaks in the reference spectra that are not reflected in the unknown sample spectrum). As a consequence, two different match factors are required:

  • Match factor: accounts for peaks in the unknown sample spectrum
  • Reverse match factor: accounts for peaks in the reference spectrum

The overall matching score parameter considers both the match and the reverse match factors. This parameter indicates how closely the sample spectrum matches the library spectrum on a peak by peak comparison of the two spectra.

 
 

Case two. The spectrum of the unknown molecule IS NOT in the database
When there are good reasons to think that the spectrum of the unknown is not in the database, one of the following options should be considered:

  • Similarity search: this mode compares the sample spectrum against the spectra of the database to see which spectra are similar, even if they do not match.
  • Neutral loss search: this mode looks for spectra in the database that exhibit the same neutral losses from the molecular ion.
  • Substructure identification: this mode helps to confirm the existence (or not) of substructures within the unknown molecule which give rise to certain characteristic ions.

Figure 24 shows a typical screen from a NIST library search. As can be seen there are many facilities available to compare spectra. Note the match factor in the lower left hand window, which is indicative of the confidence or quality of the match between the suggested spectrum and the unknown.

 

Figure 24: Typical library search results from the NIST EI GCMS 2008 library.

Many modern spectral libraries and specialist software offer the opportunity for spectral deconvolution - that is to extract spectra of individual compounds from overlapping or poorly resolved peaks.

 
 

Step 3 - Introduction to Logical Interpretation

If the spectrum obtained from an unknown compound is not found within a spectral library, or the ‘match’ between the library spectrum and our unknown is poor spectral interpretation will be required. This type of interpretation falls into three broad categories:

  • It is used to ‘confirm’ the structure of a sample — for example from an organic synthesis.
  • Identify the differences between a suggested library match or an unknown spectrum — such as when the library has given an indication of the analyte ‘type’ which must then be refine.
  • There are no ‘clues’ as to the identity of the compound and it must be characterized from the spectrum (often known as ab initio interpretation).

The art and science of spectral interpretation is a vast subject.  As a general introduction, a logical approach to the task of interpretation is described as follows: 12-13

  1. Obtain a “good” quality spectrum of the component.
  2. Identify the molecular ion.
  3. Consider the general appearance.
  4. Postulate a molecular formula using isotopic normalization/nitrogen rule/rings and double bonds formula.
  5. Identify significant structural fragment ions and elucidate/rationalize.
  6. Identify significant neutral losses and elucidate/rationalize.
  7. Combine information and propose a potential structure.
 
 

Step 4 - Identifying the Molecular Ion

The presence of a molecular ion (radical cation of the intact analyte) within a mass spectrum gives a host of information and possibilities:

  • Indicates the molecular weight of the species being analyzed.
  • If a high mass accuracy analyzer is being used it will be possible to postulate a molecular formula from the instrument data system (as mass accuracy decreases, the number of possible formulae suggested will increase).
  • If a low mass accuracy analyzer is being used the isotopic pattern around the molecular ion can help to postulate an empirical formulae (using a technique known as isotopic normalization).
  • The molecular weight may give an indication of the presence of nitrogen within the molecule, i.e. a compound with an odd molecular weight will contain an odd number of nitrogen atoms.  Compounds with an even molecular weight will either contain no nitrogen atoms or an even number of nitrogen atoms,
  • Fragments at lower mass than the molecular ion and the mass loss can be used to look for major structural components and check for logical or illogical mass losses.
  • The rings and double bonds formula (Equation 1) can be used to check the degree of unsaturation within the molecule and double check the molecular ion. If the answer to the rings and double bonds formula is an integer then the proposed formula will be an odd electron molecule and may be the molecular ion; if the answer is a non-integer then it is NOT the molecular ion.

Equation 1


Where:
X = Carbon and silicon
Y = Hydrogen, chlorine, fluorine, and iodine
Z = Nitrogen and phosphrous

 

If the structure presents

Rings + Unsaturations

One ring

1

One double bond

1

One triple bond

2

Table 4: Rings + Unsaturations values.

 
 

The molecular ion will not necessarily be the highest molecular weight ion within the spectrum - especially if there is a noisy spectral background (Figure 25). Under these circumstances the source of the noise should be eliminated if possible or the sampling threshold of the detector/data system combination should be increased in order to eliminate the noise (take care not to raise the threshold too high or important structural ions may be eliminated).

 

Figure 25: It cannot be assumed that the ion at m/z 142 is the molecular ion (and, therefore, represents the molecular mass of the analyte assuming z = 1), several checks are available to help understand the validity of the molecular ion.

 
 

It has been shown previously that the molecular ion intensity will depend upon the energy of the radical cation formed during the ionization process, and the ability of the analyte to stabilize this energy through various electronic effects (inductive stabilization, delocalization of charge, etc., etc.). Therefore, the intensity of the molecular ion tends to be stronger for the following compound classes (Figure 26):

  • Aromatic
  • Highly unsaturated (conjugated)
  • Cyclic
  • Higher order of substitution (i.e. tertiary carbocations are more stable than their primary analogues)
 

Figure 26: Molecular ions can be more easily identified as the stability of the cation ion increases.
Top: EI mass spectrum of benzene.  Bottom: EI mass spectrum of 3-ethyl octane.

 
 

Perhaps the quickest way to check for the presence of a molecular ion is to reduce the energy of the ionizing electrons below 70 eV in an attempt to reduce the degree of fragmentation induced. As always, this has to be balanced with the loss in absolute sensitivity and is not always achievable.

A second approach is to use a ‘softer’ ionization approach such as chemical ionization (CI), in which the degree of fragmentation of the radical cation is greatly reduced through the use of a ‘reagent gas’ which ionizes the analyte molecules via proton transfer and other related processes.

The final, simple check that can be carried out is to look for illogical losses from the molecular ion. Examination of the proposed molecular ion, the next highest mass fragments, and the mass difference between the sets of signals can sometimes reveal that the proposed mass difference (mass loss) is not logical (Figure 27).

 

Figure 27: The difference between the proposed molecular ion signal at m/z 84 and the fragment ion at m/z 69 is 15 Da — representing the fragmentation of the intact molecule to lose the terminal methyl group from the molecule. This ‘logical loss’ indicates the ion at m/z 84 MAY be the molecular ion (other ‘losses’ from the molecular ion should be checked, however, take care not to go too low in mass (half of the proposed molecular weight is a good guide), otherwise we may fall into the trap of considering second generation fragments (fragments of fragments), which is not a valid approach).

 

While Figure 27 considers a ‘logical’ mass loss from the proposed molecular ion, there are illogical losses which are impossible to lose from a compound containing C, H, N or O. If ‘losses’ from a proposed molecular ion of these amounts (Table 5) are observed, then the proposed molecular ion probably is not the molecular ion.

 

Mass

Illogical Fragment

3

H3

4

He

5

HeH

6

C/2

7

Li

8

LiH, He2

9

Be

10

BeH

11

B

12

BH, C

13

CH

14

N, CH2

21

NeH

22

B2

23

BC

24

C2

Table 5: The use of illogical losses to test the validity of a proposed molecular ion in GC–EI-MS.

 
  • Losses of between 5 and 13 Daltons AND 21 and 25 Daltons CANNOT easily occur.  This should be considered when attempting to identify a molecular ion
  • To illustrate the unlikely losses – some ‘outrageous’ losses are proposed opposite. NOTE: if an analyte contains lithium or beryllium then these losses MAY occur

For more information on spectral interpretation see the following CHROMacademy module:

Mass Spec > MS Interpretation > General Interpretation Strategies

 
 

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Isotopes are atoms with the same atomic number but different atomic weights.  The difference in weight between isotopes of the same elements is caused by a difference in the number of neutrons.  The relative abundance of an isotope in nature, compared to isotopes of the same element, is relatively constant (Figure 28).
The isotopic abundances of the elements can be classified into general categories:

  • A - elements with one natural isotope
  • A+1 - elements with two natural isotopes, the second being 1 mass unit heavier than the most abundant isotope
  • A+2 - elements with two natural isotopes the second being two mass units heavier than the most abundant isotope
 

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Figure 28: Relative abundances of selected isotopes. 14
 
 

Once the molecular ion has been identified then a normalization process must be carried out.  Isotopic lines must be referred to as a percentage of the molecular ion.  The halogens are particularly useful as their isotope patterns are very characteristic and easy to recognize.

The normalization process can be carried out as follows (Figure 29):

  1. Identify the molecular ion
  2. Calculate a normalization factor (NF) (Equation 2)
  3. Normalize high mass region signals (multiply all intensities by NF)
  4. Compare spectrum (if possible) with generic high mass spectrums
 

Equation 2



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Figure 29: Isotopic normalization.
 
 

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There has been a large amount of focus on the use of alternatives to helium as a GC carrier gas, in particular, the use of hydrogen.  When using hydrogen as the carrier gas in a GC-MS system there are some practical considerations that must be taken into account.

Perhaps the most widely used interface design for the GC-MS coupling is the 'capillary direct' interface.  In this design, the column is inserted directly into the ionization chamber of the mass spectrometer.  Therefore, the column’s effluent (analyte plus carrier gas) is fully delivered inside the MS source.

For optimum sensitivity, the carrier gas must be pumped away by the MS vacuum system.  Most bench-top MS detectors can pump 2-4 cm3/s of helium carrier gas but somewhat less with hydrogen.  Changes in vacuum levels within the ion source may cause changes to ionization efficiency, reduce the resolving power of the mass analyzer/detector and change fragmentation patterns due to collisional effects.  It is important to consult manufacturers as changes to pumps, instrument hardware, or firmware may be required.

Problems may be experienced with the ionization of “fragile” compounds, compounds at trace levels, and reactive compounds (alcohols, aldehydes, ketones) due to the reactive nature of hydrogen.  This will result in a change in ion ratio, extra peaks in the chromatogram, or reduced sensitivity (Figure 30).
The use of methylene chloride can also be problematic due to the formation of HCl at higher temperatures (> 280 oC), which may cause unwanted reactions with analyte molecules.

 

Figure 30:  Mass spectra of Lindane in helium (top) and hydrogen (bottom). 15

 

When converting a standard GC-MS system to work with hydrogen it is always best to consult with the manufacturer to determine component compatibility with H2, i.e. magnet and draw out lens.

A characteristic background spectrum will be seen when using hydrogen (Figure 31), however, this will reduce over time. Most manufacturers have protocols which reduce the ‘background depletion’ time to a few hours after switchover. 

 

Figure 31: Hydrogen background spectrum.

 
 

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  1. Ralph Elliot Mayo and Edward B. Delany. “Ion Source for a Mass Spectrometer” United States Patent # 3,557,365. Jan 19, 1971.
  2. Kuo-Chin Lin and Prederick P. Pickett. “Electron Ionization Ion Source for Trace Analysis” United States Patent # 4689574. Aug. 25, 1987
  3. Marvin McMaster and Christopher McMaster.  “GC-MS A Practiocal User’s Guide” Wiley-VCH, USA, 1988.
  4. Robert L. Grob and Eugene F. Barry. “Moderm Practice of Gas Chromatography” Chapter 6. Fourth Edition. Published by John Wiley & Sons, Inc., Hoboken, New 2004.
  5. John McMurry. “Organic Chemsitry”. Brooks/Cole Publishing Company. Third Edition. Ch 5. California, USA 1992
  6. Rolf Ekman, Jerzy Silberring, Ann Westman-Brinkmalm and Agnieszka Kraj. “Mass Spectrommetry Instrumentation, Interpretation, and Applications” Ch 5. John Wiley & Sons. New Jersey, USA 2009.
  7. Milton Orchin, Roger S. Macomber, Allan R. Pinhas, R. Marshall Wilson “The Vocabulary And Concepts of Organic Chemistry” Second Edition. Ch 17. A John Wiley & Sons, Inc., Publication. New Jersey 2005.
  8. Jürgen H. Gross “Mass Spectrometry” 2nd Ed. Springer, 2011, Chapter 7.
  9. Stephen E. Stein, Donald R. Scott. “Optimization and Testing of Mass Spectral Library Search Algorithms for Compound Identification” American Society for Mass Spectrometry 1994, 5, 859-866
  10. Fred W. McLafferty, Mei-Yi, Douglas B. Stauffer and Stanton Y. Loh. “Comparison of Algorithms and Databases for Matching Unknown Mass Spectra” American Society for Mass Spectrometry 1998, 9, 92-95
  11. James Barker. “Mass Spectrometry” John Wiley and Sons 1999, 19-35.
  12. J. Throck Watson and O. David Sparkman. “Introduction to Mass Spectrometry -Instrumentation, Applications and Strategies for Data Interpretation” John Wiley & Sons Ltd, West Sussex PO19 8SQ, England. Chapters 3, 6 and 7. March 2008
  13. F. W. McLafferty. “Interpretation of Mass Spectra.” 3rd Edition. University Science Books: Mill Valley, (1980), 15.
  14. Lide, D. R. ed., CRC Handbook of Chemistry and Physics, Internet Version 2005, <http://www.hbcpnetbase.com>, CRC Press, Boca Raton, FL, 2005.
  15. http://www.chem.agilent.com/Library/slidepresentation/Public/ASTS_MidAmerica_Converting_Agilent_GCMSD_To_Hydrogen_Carrier_Gas.pdf
 
 

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The focus of this month’s Essential Guide webcast is GC-MS ionization processes.  The two main forms of ionization, Electron Ionization (EI) and Chemical Ionization (CI), will be discussed in depth.  The molecular reactions which occur within the ion source to produce ions will be examined along with which form of ionization should be used for particular analytes.  Finally, our speakers Dr. John Langley (Southampton University) and Scott Fletcher (Crawford Scientific) will impart some of their expert knowledge regarding optimization of the GC-MS process and some general interpretation strategies. 

Topics covered include:

  • Why use GC-MS
  • Anatomy of a typical ion source
  • Electron and Chemical Ionization – explanation of key parameters and how they effect your analysis
  • How to improve sensitivity and specificity by manually tuning source parameters
  • Recognizing ionization problems in your chromatographic and mass spectral data
  • Analyte fragmentation and basic interpretation strategies

Key Learning Objectives:

  • Explore the mechanisms of ion formation in both Electron and Chemical Ionization processes
  • Understand which ionization process should be used for particular analytes
  • Understand the anatomy of the ion source and how the components function they function
  • Examine the effects of changing electron energy on the resulting mass spectrum (Electron Ionization)
  • Determine the effect of the reagent gas on the mass spectrum obtained (Chemical Ionization)

Who Should Attend:

  • Anyone working with GC-MS who would like to further understand the ionization process
  • Anyone using GC who would like to utilize GC-MS in their laboratory
  • Anyone involved in developing GC and GC-MS methods

Scott
Fletcher

Technical Manager
Crawford Scientific

John Langley

Dr. John Langley
Head of Mass Spectrometry
School of Chemistry, University of Southampton