No thanks! I would like to know more about CHROMacademy

 Over 3000 E-Learning topics / 5000 Articles & Applications
GC-MS Contamination

Contamination is usually identified by excessive background ions in the mass spectrum.  Contamination can originate from GC or MS components in the system. 
The source of the contamination can sometimes be determined by identifying the contaminant.  Some contaminants are much more likely to originate in the GC, some others in the MS (Table 1).

GC Contamination Sources
Column or septum bleed
Dirty injection port
Injection port liner
Contaminated syringe
Poor quality carrier gas
Dirty carrier gas tubing
Finger prints
Air leaks
Cleaning solvents and material
MS Contamination Sources
Air leak
Cleaning solvents and materials
Diffusion pump fluid
Foreline pump oil
Fingerprints inside the manifold

Table 1: GC-MS contamination sources.

Contamination can be caused when non-ionized solute molecules adosrb to the surface of the ion source and contaminate electrostatic components; the degree of contamination is dependent on the concentration and nature of the sample with systems becoming increasingly contaminated over time.  To avoid contamination from non-ionized sample components, it is good practice to screen unknown samples using an alternative detector (e.g. FID) to assess exactly what is being introduced into the mass spectrometer - the chromatogram is a good indicator of all sample peaks.  Poor sensitivity, loss of sensitivity at high masses, or high multiplier gain during an auto tune are all indicators that your mass spectrometer source may need to be cleaned.

The action required to remove the contamination depends on the type and level of contamination.  Minor contamination by water or solvents can usually be removed by allowing the system to pump (with a flow of clean carrier gas) overnight.  Serious contamination by rough pump oil, diffusion pump fluid, or fingerprints is much more difficult to remove and may require extensive cleaning.


With GC-MS most of the contamination issues come from the sample, therefore, it is important to utilize sample preparation in order to minimize the amount of contamination being injected into the GC-MS system.  The type of sample preparation used will depend on the sample type and the analytical requirements of the method. 

Strategies to reduce contamination from the sample include the use of solid phase extraction (SPE), sample dilution, lower injection volumes, higher split ratio etc.  If the sample load cannot be reduced due to sensitivity issues, look at improving sensitivity by reducing the scan range (usually chopping the lower end of the mass range) or using SIM with qualifier ions, or using a high sensitivity tune (rather than standard tune used for NIST searches).

Air leaks

Air leaks are particularly problematic for any instrument which requires vacuum to operate.  Leaks are generally caused by damaged or incorrectly fastened vacuum seals.  The proper column nut and ferrule combination are critical for a leak tight seal.  The correct ferrule choice is dependent on the column outer diameter (the ferrule should only be slightly larger than the column outer diameter).
Air leaks will also allow contaminants to enter the system which could adversely affect analysis.  Symptoms of leaks include:

  • Higher than normal vacuum manifold pressure or foreline pressure
  • Higher than normal background
  • Peaks characteristic of air (m/z 18, 28, 32, and 44 or m/z 14 and 16, Figure 1)
  • Poor sensitivity
  • Low relative abundance of m/z 502

Leaks can occur in the GC or MS, with GC leaks most commonly occurring in the injection port septum, injection port column nut, or from a broken or cracked capillary column.  There are many more locations in the MS where leaks can occur:

  • GC-MS interface column nut
  • Side/top plate o-ring (all the way around)
  • Vent valve o-ring
  • Calibration valve
  • High vacuum gauge tube fitting
  • Cracked ion gauge tube
  • Front and rear end plate o-rings
  • GC-MS interface o-ring (where the interface attaches to the vacuum manifold)
  • Diffusion pump co-seal and/or baffle adapter o-ring
  • Turbomolecular pump o-ring
  • New Vespel/graphite ferrules contract when heated

By far the most common place for a leak is the transfer line ferrule due to the Vespel shrinking, with the next most common place being the ferrule on the GC.  The first step in leak testing is to use a blanking plug on the transfer line of the MS.  If it is not leaking when blanked then this indicates that the problem is further upstream.  If it does leak then it highlights that the problem is related to the MS and could be any one of the numerous seals.  

At this point, an easy way to check for leaks is to use a dust removal aerosol (also often known as a leak detector spray, which contains either compressed air or chlorodifluoromethane).  With the mass spec pumped down look at masses between m/z 35 and 75, spray the aerosol (chlorodifluoromethane) and look for peaks to appear at m/z 51, 52, and 67.  If the dust removal spray contains compressed air monitor the nitrogen (m/z 28) and oxygen (m/z 32) ions.  Spray short bursts at fittings in the interface oven, around the separator, and in the GC allowing time for the peaks to show up in the mass spectrum. Tightening or replacing any fittings or ferrules that appear to be leaking should fix the problem.  If helium is being used as the carrier gas a helium detector can be used to check for leaks.  You should also spray around all the seals on the MS - the door, the tune compound valve, and vent to the foreline pump are common leak sites.  There will be a delay between using the spray and a signal appearing in the tune window.

If the leak is isolated to the MS then fixing it may be a job for the service engineer.

For more information see this article GC-MS Leak Detection.

Figure 1: Spectra showing no air/water leak (top left), a small leak (top right), and a large leak (bottom).

Oil and cleaning solvents

Following ion source cleaning, spectra will often exhibit solvent contamination peaks (Figure 2).  To avoid solvent contamination, dry all cleaned metal parts in the GC oven prior to reassembling and reinstalling them.  Use a temperature above the boiling point of the solvent but below the limit of the column.

Operating the diffusion pump without a flow of carrier gas into the vacuum system will result in vapor from the pump fluid drifting into the vacuum manifold.  A more serious problem is back streaming of fluid into the vacuum manifold caused by sudden or improper venting of the vacuum system.  Back streamed fluid will be evidenced by a prominent peak at m/z 446 and increased background noise - this type of contamination may need engineer intervention (Figure 2).

Contamination by foreline pump oil is characterized by peaks spaced 14 Da apart (hydrocarbons).  Contamination with foreline pump oil is less common than contamination with diffusion pump fluid.  

Figure 2: MS spectrum pump oil (top, m/z 39, 41, 43, 55, 57), pump oil contamination (middle), and trichloroethylene (TCE) contamination. 

When vacuum pumps are used in mass spectrometers, all the residual organic chemicals analyzed by the MS are trapped in the vacuum pump oil.  Eventually these contaminants are expelled out of the oil and can contribute to system contamination.  Regular pump maintenance and gas ballasting (Figure 3) will help to keep pumps running and reduce contamination.

Content on this page requires a newer version of Adobe Flash Player.

Get Adobe Flash player

Figure 3: Vacuum pump elements, oil contamination, and gas ballasting.

Column bleed

To maintain MS performance and reduce the frequency of required ion source maintenance, it is important to choose a phase for your application with the lowest amount of column bleed – the background generated by all columns (Figure 4 and 5).  Column bleed increases with temperature, column length, film thickness, and polarity.  Special low bleed phases exist with silphenylene chemistry and many manufacturers offer ‘MS’ designated phases.  Specially immobilized PLOT columns should be used to prevent evolution of particulate material into the ion-source

Figure 4: Characteristic column bleed ions.


For GC-MS applications low bleed stationary phases reduce column contribution to background noise which results in improved mass spectral purity and more accurate library identification (Figure 5). 

Figure 5: Improved spectral purity using GC-MS column.

Proper column conditioning can also help to reduce column bleed.

See this article for more information GC-MS Columns for GC Methods.


Fingerprints contain hydrocarbons which can appear in mass spectra.  Hydrocarbon contamination is evidenced by a series of peaks spaced 14 Da apart.  The abundance of these peaks decreases as the peak mass increases.  Fingerprint contamination is usually caused by failure to wear lint-free, nylon gloves during ion source cleaning, GC inlet maintenance, or from installing the column.

Common contaniment ions

Table 2 lists common GC-MS contaminants, their characteristic ions, and the likely contamination source.

Ions (m/z) Compound Possible Source
13, 14, 15, 16 Methane Chemical ionization (CI) gas
18, 28, 32, 44 or 14, 16 H2O, N2, O2 CO2 or N, O Residual air and water, air leaks
28, 44 CO, CO2 Hydrocarbon fragments
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
105, 106 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, 335, 429 Dimethylpolysiloxane Septum bleed or methyl silicone column coating
77, 94, 115, 141, 168, 170, 262, 354, 446 Diffusion pump fluid and related ions Diffusion pump fluid
149 Plasticizer (phthalates) Vacuum seals (o-rings) damaged by high temperature, use of vinyl or plastic gloves
Peaks spaced 14 Da apart Hydrocarbons Fingerprints, foreline pump oil

Table 2: Common GC-MS contaminant ions.

Maintenance schedules

Regular GC-MS system maintenance will help to prevent many problems including contamination (Table 3 and 4).
Use clean tools when performing maintenance on the MS system to avoid contamination. 
Always wear lint-free, nylon gloves during ion source maintenance, GC inlet maintenance, or when installing the column.

Task Daily Weekly Monthly Every 3 Months Yearly As Needed
Check/replace septum          
Check injection port liners          
Check column nut tightness          
Check foreline pump oil level          
Check diffusion pump fluid          
Change injection port liners and o-rings          
Gas ballast the foreline pump          
Clean split/splitless split vent trap          
Check for leaks (inlet and column connections)          
Replace gas cylinders (when below 500 psig)          
Recondition or replace internal and external traps and chemical filters on the GC          
Replace carrier gas traps          
Replace column          
Lubricate seals          

Table 3: GC maintenance schedule.

Task Every Week Every 3 Months Every 6 Months As Needed
Autotune or manual tune (save results)      
Cabinet Maintenance        
Clean cabinet      
Inspect hoses and cords      
Vacuum the fan filter      
Vacuum System Maintenance        
Check mechanical pump oil      
Replace mechanical pump oil      
Replace mechanical pump traps      
Check diffusion pump fluid      
Degas ion gauge tube      
Replace ion gauge tube      
Replace seals and o-rings      
Analyzer Maintenance        
Clean ion source      
Replace filament      
Replace ion source heater      
Replace mass filter heater      
Replace electron multiplier horn      
GC-MS Interface Maintenance        
Refill EI calibration vial      
Refill CI calibration vial      
Replace interface heater      

Table 4: MS maintenance schedule.



You may also like...

Quick Guides

GC-MS Quick Quiz »

Improving Sensitivity of Environmental GC-MS Analysis »

Do You Know What’s In Your Beer? »

Fundamentals of GC-MS Ionization Techniques »

Webcasts & Tutorials

What GC-MS Operators Need to Know »

GC-MS Ionization Processes »

GC-MS/MS Analysis - What You Need to Know »

The Secrets of Optimizing GC-MS Methods »


Fundamental GC-MS - Introduction »

Fundamental GC-MS - GC Considerations »

loading data
loading data
loading data
loading data
loading data

Dr. Dawn Watson

This article was written by Dr. Dawn Watson.

Dawn received her PhD in synthetic inorganic chemistry from the University of Strathclyde, Glasgow. The focus of her PhD thesis was the synthesis and application of soft scorpionate ligands. As well as synthetic skills, this work relied on the use of a wide variety of analytical techniques, such as, NMR, mass spectrometry (MS), Raman spectroscopy, infrared spectroscopy (IR), UV-visible spectroscopy, electrochemistry, and thermogravimetric analysis.

Following her PhD she spent two years as a postdoctoral research fellow at Princeton University studying the reaction kinetics of small molecule oxidation by catalysts based on Cytochrome P450. In order to monitor these reactions stopped-flow kinetics, NMR, HPLC, GC-MS, and LC-MS techniques were utilized.

Prior to joining the Crawford Scientific and CHROMacademy technical team she worked for Gilson providing sales and support for the entire product range including, HPLC (both analytical and preparative), solid phase extraction, automated liquid handling, mass spec, pipettes, and laboratory consumables.

group  subsCHROMacademy can deliver to corporate clients on a multi-user subscription basis.
Served up from secure servers to the corporate intranet or individual desktops.

  • Microsite - your own learning site powered by CHROMacademy
  • Your Landing Pages -with your logo and branding
  • Customized Assessments - Based on content agreed upon Certificate of Completion
  • Certification Programs - Offer your learners a goal to strive towards
  • Our Learning Management System is S.C.O.R.M. compliant and will connect to your system
  • Engagement Package - E-newsletter stimulation program derived from your content and ours
  • Full archive of Essential Guide webcasts & tutorials
  • 1000’s of eLearning topics - HPLC / GC / Sample Prep / Mass Spec
  • Ask the Expert - our experts will answer your chromatography questions within 24 hrs.
  • Assessments - test your knowledge
  • Application notes & LCGC articles
  • Troubleshooting and virtual lab tools

Request a quote


 Home | About UsContact Us | SubscribeTerms and Conditions | Advertise | Privacy Policy 

  • loading data

loading data

loading data


loading data

loading data