GC-MS Contamination Identification and Sources

Over the past few months I have received a number of questions regarding the identification and possible sources of contamination observed in GC-MS systems (GC/MSD, EI). Contamination can be sourced to the instrument itself or to materials used in the preparation of samples. We shall review a few of the most common types of contamination observed and how you can use the MS detector data to identify them in this article.

Air Leaks / Contamination: The GC-MS detector operates under vacuum conditions so air must be kept to a minimum detectable level. 

• Common Sources: Improper fitting connections; improper fitting materials/age; damaged or worn vacuum seals. 
• Identification: High background noise levels (poor S/N of stds); Peaks associated with air (i.e. m/z 18, 28, 32, 44).

Acetone Cleaning Fluid Contamination: Often used to clean the metal parts of the source, acetone may appear in the signal. Look for peaks at m/z 43 & 58.

Dimethylpolysiloxane Contamination/Bleed: Silicone from the various seals and septa may appear and depending on the chemical source, are often detected at m/z 147, 207,221, 281,295,355 & 429. *Always use high quality seals & inject blanks often to check for contamination.

Plasticizer Contamination: Many plastics are used in the seals found in the GC-MS instrument. These plastics may eventually bleed into the system and be detected (due to normal wear, heat stress or even poor sample preparation). It is critical to identify which ones result from worn out seals vs. use of plastics as part of improper sample preparation procedures (e.g. improper handling techniques, glove material, plastic sample tubes, washing glassware with soaps etc). One of the most common peaks observed will be m/z 149 (Phthalate).

Diffusion Pump Oil Fluid Contamination: Turning off the carrier gas flow may allow for some of the diffusion pump oil to back-stream. *Maintain carrier gas flow when this system is ON. If diffusion pump oil has entered the source, you should observe a strong signal peak (e.g. m/z 262, 446 for the oil).

Foreline Pump Oil Fluid Contamination: Look up the specific chemical composition of the oil used to obtain applicable m/z values to check for (e.g. hydrocarbons, m/z 69 ...).

*Avoid GC-MS contamination and trouble by first receiving the proper training to operate, use and maintain the GC-MS system. This includes making sure the entire system is fully maintained, seals changed, performance monitored regularly, insuring all of the vacuum pump oils are changed on a regular schedule and always use high quality replacement parts. Maintenance is something that most users can perform themselves, especially if they have completed a formal hands-on training class using their own GC-MS system (Most manufacturers offer basic on-site Maintenance classes).

Tips and Advice for Priming your HPLC PUMP (or similar pumps, FPLC or UHPLC Pump)

The single most important component of any HPLC system is the Pump module. We often refer to it as "the heart of the HPLC system". 

• You may have the most sensitive HPLC detector, the best column, a perfect method of analysis, but none of this will matter unless the HPLC pump(s) that provide mobile phase to the system operate perfectly, all of the time. If you have a poor quality (or poorly maintained) system, then you will spend much of your time trying to establish reliable flow through the HPLC system, not running samples. 
• Before using an HPLC system, you should prime all of the lines in your HPLC pump. This is needed to purge any air from the tubing, introduce fresh mobile phase to each line and then to VERIFY that each channel delivers the reported amount of fluid to the column (measure it).
  

• NOTE: This is a LONG, detailed article with lots of information, Hints and Tips. It is available in PDF format for download, here.

The HPLC pump's ability (stability) to provide reliable operation depends on: 

(1) The Chemical, Physical and Miscibility properties of the Liquid(s) being pumped;

(2) The Amount of dissolved gas inside the liquid (must be minimized);

(3) The Temperature of the room (or HPLC) must be stable;

(4) The Position of the mobile phase bottles (relative to the pump, above or below);

(5) The Solvent Pickup Filters used (are clean and appropriate in material & porosity);

(6) The Fittings used are correctly installed & tightened;

(7) The types of Tubing used are chemically, temperature and pressure compatible (esp. the Inside Diameter of the tubing);

(8) The Selected Flow Rate(s) and Back-pressure are within the optimal range of the pump;

(9) All mobile phase solutions are Filtered, Freshly prepared and Degassed;

(10) How often the Pump is properly Inspected, Cleaned & Serviced.

 The HPLC pump is the most important part of your HPLC system. Take care of it. Neglect or abuse it, and you may lose time and money. Almost every problem you experience using an HPLC will be related in some way to the pump. Make sure you understand the flow path of the system in detail, and have the training to setup and use it properly. Take a hands-on training class (not a video or web based tutorial) to learn how to use the pump on your specific HPLC system. Learn how to run simple verification tests to check the flow rate (best done with a graduated cylinder). Never rely on the software values, check and verify everything yourself. Priming and flushing are needed any time air bubbles are present, mobile phase solutions are changed or the system has sat unused (this includes overnight). Always flush multi-channel pumps and valves (i.e. Binary, Ternary, Quaternary...) using a setting of 100% channel composition. Run one channel at a time at 100%, not 25% or 50% to flush channels (a common novice mistake). Flush ALL channels on a regular basis.

OK, so what can you do to make sure your HPLC pump is properly primed with fluid and operating to the best of its ability?

Start, by reading the operator's manual for your pump. Review the procedures for connecting it to the system, become familiar with the flow path and understand the procedures to prime the pump heads. Practice these procedures.

If an inline vacuum degasser is used, become familiar with the specifications, chemical compatibility (some are not compatible with solvents such as strong acids, strong bases, THF, chloroform, fluorinated additives and so on) and internal channel volume of each chamber used. It is useful to know what the degasser chamber volume is to figure out what the total channel priming volume is. This may be different for similar systems. Check, measure, verify, do not assume.

Priming Volume: The total volume contained in each channel's low-pressure line from the mobile phase bottle to the degasser + the degasser chamber channel volume + the total volume in the line from the degasser to the pump head (or multichannel valve) = the total minimum volume you must flush out before using the system. Because flushing just the minimum of volume (1x) of fluid through the channel is unreliable, flush 2x, 3x or more times this total volume, per channel (or as much fluid as it takes), to prime each channel. *If no degasser is present, then just calculate the volume contained in the low pressure tubing from the bottle to the pump head/valve. Set the pump to direct the flow to waste and use a high initial flow rate to speed up the priming process.

Use fresh mobile phase (prepared daily and filtered). Make sure the solvent pickup filters are clean. If possible, have the bottles placed higher than the pump's inlet (once flow has been established, this will allow natural siphoning to push liquid towards the pump head). Prime all of the lines used. The pumps run on liquid, not air so try and fill any of the lines with pure mobile phase before you connect them to the pump and/or degasser (If all of the lines are prefilled with fresh liquid, you can skip this part).  

There are two ways to PRIME EACH line (Flushing the Channels).

• *First, open any Prime/Purge or Waste Valve so the mobile phase is directed to waste, not the injector, column or detector. Our goal is to initially fill the lines with liquid, quickly, and we do not want these fluids to go through the entire HPLC system (i.e. column), just the HPLC pump.

(1) Wet Priming use a syringe fitted with a Luer-to-threaded fitting adapter (usually 1/4-28) to draw liquid through the tubing in the mobile phase bottle and into the pump's degasser and/or pump head's inlet. Be sure to have this type of syringe available (very useful). Never push fluid, only draw fluid through the tubing, just like the pump does. Connect the syringe to the mobile phase bottle lines, degasser ports and/or pump head multichannel valve or pump head inlet, as needed, to draw liquid through until all lines are filled.

(2) Dry Priming using the HPLC pump to draw the mobile phase out of the bottles, through the lines, degasser channels and to the pump head or multichannel valve. Note: "Dry" because the lines (low pressure tubing) are initially dry when we start. Always do this one channel at a time (e.g. A = 100%). This insures no miscibility or mixing problems and is standard procedure. Start with a modest flow rate to get the fluid moving through the lines, then increase the flow rate to speed up the process. The low pressure Teflon tubing is transparent so you can watch this process. Repeat with each channel. Note: Some HPLC pumps will struggle to perform this type of dry priming, as they will be unable to draw the liquid up from the bottle and/or pump the air out of the system. Pre-priming the lines using a syringe (as in #1 above) will help solve this. Running the pump with just air inside the lines may result in increased wear on the system (esp the piston seals) so if the system struggles to fill with liquid after one minute, discontinue and manually wet prime each line.

NOTES: 

• The back-pressure shown on the system readout should be very low during this initial  priming process (e.g. < 15 bars) as the HPLC system should not be plumbed with the column or detector inline, during the priming process (it should be by-passing those parts). Only the viscosity of the solution, the selected flow rate and the internal diameter of the tubing going into and out of the pump will contribute to the observed back-pressure, and this should be very low value.

• Once you have verified that liquid is exiting through the pump head waste port, you can increase the flow rate to speed up the priming process, but pay attention to the back-pressure. It should increase as the flow rate increases and drop as the flow rate drops. Continue to prime each channel in this way, one-at-a-time, until all channels are primed and flushed with liquid. You can gradually slow the flow rate down as you stop, to transition from one channel to another.
  

• If liquid has been drawn to the pump head, but the pump head still is not pumping liquid through it, it may be experiencing cavitation (air locked). If there is an outlet port on top of the pump head, the outlet fitting above the pump head can sometimes be briefly loosened with a wrench, allowing the system to push the air out (open it slightly with a wrench, then quickly close it after liquid comes out). Have a towel ready to soak up any fluid that comes out. Keep the area clean and dry. Alternatively, try drawing liquid through this port, while it is running, to gently fill the pump head chamber and remove the air.

• In some case, the inlet or especially the outlet check valve(s) can also become "stuck" open. When buffers are left in the system (they should be flushed out with water), crystals and particulate matter may deposit on the valve resulting in poor sealing, leaks or air being drawn through. Drawing liquid out of the pump head's outlet port with a syringe (or gently pushing it through the pump head) may remove the air bubble, debris and prime the valve, restoring function. Note: If needed, shut down the pump and clean/replace any contaminated or worn check valves before proceeding.
  

• In more extreme cases, you can change the mobile phase going into the pump head to a more viscous intermediate solvent to get things moving (an alcohol such as IPA might work well. If buffers have been used, then always first flush with pure water). 

• Degas all eluents / mobile phase solutions used. All of them. Degassing will help reduce the formation of bubbles inside the pump head. Failure to properly degas the solutions used may result in loss of prime, baseline and/or pressure instability. Make sure your degasser is operating properly (electronic vacuum degassers only last ~ 5 years at most. Be sure to have them professionally serviced). Sonicating fluids at the bench or using vacuum filtration to initially remove gas from the solution will only degas the solution for a short time (minutes). Gas will slowly diffuse back into the solution resulting in baseline noise, drift and pump problems (for HPLC, only use inline degassing or Helium sparging).
  

• Verify the flow rate. It may be unwise to rely on the indicated flow rate shown on the instrument screen or display. It is wise to measure the flow rate of each channel, separately, using a graduated cylinder and a timer. This is the most reliable way to determine what the actual flow rate is through the system (and is also the method we use during performance verification or qualification testing too). To check the flow, make sure the system has been primed and flushed. Install a flow restriction capillary in place of the column (to provide the required back pressure). Set the flow rate to a value which is appropriate for the pump and measure/record the volume delivered vs. time. Example: Using a flow rate of 1.000 mL/min obtain a 10 mL volume, glass laboratory grade graduated cylinder. At time zero, direct the flow from the restrictor's outlet into the graduated cylinder. Measure the volume of fluid collected in 8 minutes. *It should be 8.00 mLs.
  

If you continue to have priming problems and/or air bubbles disrupting the flow there are four more things you can check. 

1. Make sure the solvent pickup filters/frits are clean and unobstructed (these are maintenance items). If the filters are obstructed, then a vacuum may form on the line resulting in pump cavitation and loss of prime. One quick way to check if this might be a problem is to remove the suspect solvent pickup filter from the tubing, then try again. If flow is restored w/o the filter in place, then the filter may have been clogged. Install a new solvent filter as soon as possible. *Never run the HPLC without solvent filters installed. Those filters perform a very important job and protect the flow path of the system.  
2. Service the Pump Heads. Regular cleaning, inspection and replacement of worn parts must be done to maintain the function of the pump. Worn parts will result in failures, instability, lost time, plus invalid data. The pump has many mechanical parts which wear out and require replacement. Most pumps should be inspected/serviced every 6 months. Keep the pumps clean and fully serviced (replace: piston seals, pistons, frits, check valves as needed). Depending on the brand, model and applications, the types of parts needed and the frequency of repairs varies widely. *This is discussed in another article. 
3. If your HPLC system has an inline vacuum degasser (either a standalone or integrated module), it may be damaged, contaminated or broken. The typical service life of an electronic inline vacuum degasser is only five years (some models have even shorter lifespans). Degasser's with internal damage may result in contamination of the mobile phase. A failing or damaged HPLC vacuum degasser may directly contribute to analysis problems (ghost peaks, pressure instability, poor baseline stability...). Have your degasser professionally diagnostically tested and serviced often.  
4. Clean and/or replace any worn or damaged inlet or outlet pump head valves. Not flushing buffers out of the HPLC system on a regular basis or remain in contact with the solution for long periods of time can damage the valves. In some cases, cleaning is all that is needed, but in others, replacement is required to restore function. Be sure to have the system professionally serviced on a regular basis.
   

• Additional Troubleshooting Info can be found here:

Diagnosing & Troubleshooting HPLC Pressure Fluctuation Problems (Unstable Baseline)

Air Bubbles Exiting the HPLC PUMP, Reasons Why.

Reasons For Air Bubbles Exiting The HPLC Pump:

• Pump Cavitation: When the pump pressure fluctuates wildly up and down, at very low pressures, this is often due to 'pump cavitation'. It is caused by a loss of priming inside the pump (Air, instead of liquid is in the pump's flow path). The HPLC pump should be primed with fresh, degassed mobile phase (following proper procedures) to restore smooth, stable flow. Often, this can be accomplished using the pump, set to a high flow rate, to draw liquid from the bottles. In cases where the pump is not strog enough, manually priming the low pressure lines using a syringe (~ 20 mL) filled with mobile phase and opening (or disconnecting) a fitting at the pump's outlet may aid in priming the system. Note: Depending on the configuration of your HPLC system, to fully prime an HPLC pump, you may need to run 20 or more mLs of solution through EACH channel. Please keep this in mind every time you use the system and every time you prepare or change a mobile phase solution. This article on baseline/pressure fluctuations may assist you in troubleshooting.

• Loose Connections: If one or more of the low-pressure fittings (nuts and ferrules)  which secure the Teflon tubing to the pump (or vacuum degasser) are damaged or loose, air may enter the system resulting in bubbles. Most pumps use plastic finger-tight style fittings 1/4-28 (or 5/16-24). The threads are soft and can be deformed. When access to these fittings is difficult, sometimes the fittings are left loose and will allow small amounts of air to be drawn in. A build up of salts and/or buffers on the exposed fittings can also allow air into the system (and the presence of deposits on the fittings indicates poor maintenance and a LEAK !). Inspect the tubing and fittings used for proper type, seating depth, wear/condition, cleanliness and/or damage. Replace parts as needed and re-install using the correct amount of torque.

• Flow Rate Too High, Too Low or Not Enough Degasser Equilibration Time: Degassing efficiency is directly related to the flow rate. Lower flow rates increase the residence time of the mobile phase in the degassing membrane or tubing, improving the gas removal. Higher flow rates provide less time for gas extraction and result in lower degassing efficiency (which equals bubbles in the outlet line). Check with the manufacturer regarding the optimal flow rate range for your degasser to insure you are working  within an acceptable range. Allow enough time for the degasser to reach its set-point and stabilize before use. If the degasser is not operating properly or is unable to "keep up" with the flow rate, then bubbles may be frequently observed in the outlet lines. 

• Choice of Mobile Phase Liquid: The miscibility of the liquid is also important. If the new mobile phase is not compatible with the previously used mobile phase, pump cavitation may result. Always flush the pump with an intermediate liquid that will dissolve in both the old and new fluids to flush them out before introducing the new mobile phase solution. (such as pure water or IPA, as applicable). The solubility of air (gas) in the specific solution used also affects the efficiency of the vacuum degasser. Aqueous solutions usually hold less gas than popular organic solvents (though air bubbles can be harder to "push" through in water). The amount of dissolved gas inside the liquid relates directly to the time needed to reduce it to acceptable levels for use in HPLC. Be sure to allow enough time to properly degass the new solution.

• Dirty or Obstructed Solvent Pickup Filters (Bottle filters): Bottle filters should be cleaned or replaced at regular intervals, following routine maintenance SOPs. When they become fouled or obstructed, a vacuum may form as the liquid is drawn into the system. This may result in air being sucked into the tubing or through a fitting (remember that the low pressure Teflon tubing used to connect the bottles to the degasser and pump is porous and allows gas to diffuse through it). The pickup filters should not obstruct the normal flow of solvent (typically they are 10-20 u in porosity). * a quick troubleshooting tip to rule out an obstructed solvent pickup filter is to temporarily remove the filter from the bottle. Observe the back-pressure on the pump to see if it increases and priming is restored. If so, the filter may be clogged. Always replace the filter with a fresh, clean filter and never operate the HPLC without the solvent filters installed.

• A Sticking Check Valve: The pump's inlet and outlet check valves must function perfectly, all of the time, to maintain proper flow and pump function. If an inlet check valve is not fully closing properly to seal off the high pressures generated inside the pump, then the pump will not be able to maintain pressure or flow. Inspect the check valve. Remove and clean it, per the manufacturer's guidelines (often this involves placing the check valve assembly in a beaker with solvent such as IPA and sonicating for 20 minutes to remove any residues. If cleaning fails to restore proper valve function, then replace the check valve with a new one.

• Worn Pump Piston Seals (or Pistons): When the piston seals begin to leak, air is allowed into the system. Pump piston seals require regular replacement (they are normal wear items). Scratched or worn pistons may also result in leaks with air getting into the system. Inspect and Test them both for pressure tightness on a scheduled basis or anytime you suspect a problem. Flush the pump with a suitable liquid, then run a high-pressure test to determine if they pass or fail the manufacturer's leak tightness and high pressure tests. Be sure to perform a physical inspection too.

• Contaminated or Obstructed Pump Outlet Filter: Most HPLC pumps have a small disposable outlet filter installed at or near the pump outlet line (Note: In the case of most Agilent brand HPLC pumps, a small PTFE filter may be found at the outlet valve or inside of the prime-purge valve). These filters should be replaced at regular intervals (monthly is strongly recommended), especially if any aqueous buffers or solutions are used (a they contribute to contamination). Contaminated pump outlet filters may result in a number of pressure instability problems. Abnormally high back-pressure during operation OR when vented to waste are indications it is obstructed. Regular scheduled replacement is the best way to prevent lost time and reduce system contamination.

 Any of the above causes may contribute to valves not functioning properly or air being drawn into the HPLC system. Troubleshooting should begin with the easiest and obvious areas first. Check the condition of the low pressure tubing used to make the connections to and from the mobile phase bottles and pump. If it is kinked, twisted or damaged, replace it with new tubing. Check the fittings used (nuts and ferrules) for tightness and to insure they have been installed properly and are not leaking. Repair all leaks. Keep the system clean (it is easier to monitor and troubleshoot problems when it is clean). Replace any damaged fittings with new ones. Check the solvent pickup filters monthly to insure they are clean and not obstructed. Make sure the flow rate you are using is within the acceptable range for your degasser. 

Has your degasser module been professionally cleaned and serviced within the last 5 years? Are any degasser errors being generated? Is the vacuum degasser making any unusual sounds? Is liquid being emitted from the vacuum pump exhaust port? If any of the answers to these questions are 'yes', then have the HPLC vacuum degasser professionally diagnosed for problems so that repairs can be made to restore function.

Vacuum Pressure Units Conversion Table

Several of the questions I receive each week by email deal with scientific calculations or conversion of various units. One popular request relates to the conversion of micrograms, ppm and percent. Several years ago to address this question, I posted a table of weight to ppm units ("Conversion Factors microgram, nanogram, ppm, ppb and percent") which has proven to be very popular.

Because of the large number of vacuum pumps attached to HPLC and MS systems, another common conversion question relates to vacuum units. Due to the different applications and regions of the world, the desired unit often varies. It is for this reason that I develop unit conversion tables as I find these tables provide for a convenient way to print out and/or keep handy in a binder for future reference. Widespread computer use coupled to freely available page reader software (e.g. Adobe PDF) provides another means to store useful information as a pdf file too. I present this "Vacuum Pressure Units Conversion Table" in a viewable and an optionally available downloadable form [click HERE to download].

VACUUM PRESSURE UNITS CONVERSION TABLE:

*Some of the more commonly used values are shown in boldface type. ** Absolute Vacuum..

% Vacuum	Torr (mm Mercury)	kPa abs	Inches of Mercury	Micron	PSI
0.0	760.0	101.4	0.00	760,000	14.7
1.3	750.0	99.9	0.42	750,000	14.5
1.9	735.6	97.7	1.02	735,600	14.2
7.9	700.0	93.5	2.32	700,000	13.5
21.0	600.0	79.9	6.32	600,000	11.6
34.0	500.0	66.7	10.22	500,000	9.7
47.0	400.0	53.2	14.22	400,000	7.7
50.0	380.0	50.8	14.92	380,000	7.3
61.0	300.0	40	18.12	300,000	5.8
74.0	200.0	26.6	22.07	200,000	3.9
87.0	100.0	13.3	25.98	100,000	1.93
88.0	90.0	12	26.38	90,000	1.74
89.5	80.0	10.7	26.77	80,000	1.55
90.8	70.0	9.3	27.16	70,000	1.35
92.1	60.0	8	27.56	60,000	1.16
93.0	51.7	6.9	27.89	51,700	1.00
93.5	50.0	6.7	27.95	50,000	0.97
94.8	40.0	5.3	28.35	40,000	0.77
96.1	30.0	4	28.74	30,000	0.58
96.6	25.4	3.4	28.92	25,400	0.49
97.4	20.0	2.7	29.14	20,000	0.39
98.7	10.0	1.3	29.53	10,000	0.193
99.0	7.6	1.0	29.62	7,600	0.147
99.87	1.0	0.13	29.88	1,000	0.01934
99.90	0.75	0.1	29.89	750	0.0145
99.99	0.10	0.013	29.916	100	0.00193
99.999	0.01	0.0013	29.9196	10	0.000193
100	0.00	0	29.92	0	0