Top 10 Things Users Can Do to Minimize Contamination of LC/MS Systems

日付: 05/21/2021

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For research use only. Not for use in diagnostic procedures.


Several things can be done to reduce contamination of LC/MS systems that require minimal time but increase uptime and robustness. Here, we present a list (in no particular ranking) of the top ten things to consider when trying to lower instrument contamination.

  1. Chose high-quality solvents and reagents.
    1. Do not use aqueous mobile phases that are more than 1-week old. They should be freshly prepared each week.
    2. Use LC/MS-grade solvents. Ideally, bottled LC/MS water should be purchased; but if in-house filtered water is used, a procedure should be in place to ensure that the filters are changed regularly (as part of a preventative maintenance plan), that total organic content is less than 5 ppb, and that the conductivity is acceptable (18.2 megaohm/cm2).
    3. Add as little as 5% organic content to the aqueous mobile phase to prevent bacterial or algae growth and prevent contamination.
    4. Never top off mobile phases by pouring the remaining volume of one solvent into a newly-opened solvent bottle. The best practice is to replace the entire bottle of mobile phase.
    5. Do not use detergents to wash mobile phase bottles. This can lead to residue build-up and can present as contamination.
    6. Prepare mobile phases in a clean part of the lab. (Separate-air handling can be helpful if your analyte(s) are volatile.) It is also good practice to prepare mobile phases and diluent prior to handling your compounds of interest.
    7. Purchase small volumes of reagents. We prefer the single-use ampules (where applicable), stored in a desiccator away from general laboratory chemicals.
    8. Do not use solvents from squeeze bottles. Similarly, plastics such as parafilm can also contribute to contamination.
  2. Select the appropriate level of sample dilution.
    1. When using a dilute-and-shoot method, the level of sample dilution can become a critical factor because insufficient dilution can lead to neutrals/contaminants entering the mass spectrometer. Properly diluted samples and standards will reduce the cause of this issue.
    2. Properly tuning the compound(s) of interest as well as the source settings can help reduce contamination in dilute-and-shoot methods.
  3. Enhance sample prep with additional filtration steps.
    1. Consider changing the sample preparation workflow. Adding steps such as solid-phase extraction can boost the removal of contaminants.
    2. Consider centrifuging your samples at an appropriate speed for long enough. We have found that 21,000 x g for 15 min is a great way to obtain a nicely defined pellet of material on the bottom of the sample container.
  4. Inject a lower volume.
    1. Lowering the injection volume can help prevent neutrals/contaminants from entering the system simply by reducing the amount of these species.
    2. Properly tuning the compound(s) of interest as well as the source settings can help reduce contamination in dilute-and-shoot methods.
  5. Reduce the concentration used during syringe infusion.
    1. Many users are unsure of what concentration to use for compound optimization. For SCIEX instrumentation, the ideal signal intensity for the Q1 mass falls approximately mid e5low e6 cps when adding 1025 scans together.
    2. To determine the appropriate concentration, consult this schema:
  1. Optimize curtain gas settings.
    1. The curtain gas should be optimized as part of method development or when transferring a method. To find the optimal curtain gas, set up a tee-infusion (or perform on-column optimization) and monitor the analyte signal to find the point when signal degradation affects the assay. Set the curtain gas to the highest setting that does not have a detrimental impact on signal intensity.
  2. Use a divert valve.
    1. The use of a divert valve is critical to keeping neutrals/contaminants from entering the system. A divert valve can be used to redirect effluent to waste from the regions of the chromatogram where analytes are not eluting.
    2. To set up a divert valve, please visit this link for a video tutorial:
  3. Use scheduled ionization.
    1. Analyst® 1.7 or Sciex OS 2.0 Software or later versions feature the option for scheduled ionization, which can be utilized to schedule when the source is operating.
    2. Whey using scheduled ionization, the ion spray voltage is only applied during a portion of the data acquisition. This reduces contamination from neutrals/contaminants that elute in different chromatographic regions from the analytes of interest.
    3. This link describes how to set up a method with scheduled ionization:
    4. This Tech Note describes how this feature was tested:  
  4. Evaluate the autosampler needle depth.
    1. When samples are centrifuged, a pellet of particulate matter is often present at the bottom of the vial/well. Ensure that the needle depth of your autosampler is set to aspirate sample from the top and not the bottom of the vial/well.
    2. Some autosamplers use a bottom-sensing feature to ensure the needle penetrates far enough into the well when sample volumes are low. This is a great feature if you decant the sample prior to analysis; however, this can also cause those samples with pellets to become disturbed and cause particulate matter to enter the system.
  5. Practice routine cleaning and maintenance.
    1. Routine cleaning is paramount to reducing contamination. Here are two links that describe how to clean the front end of your MS.
    2. Follow the vendor's recommendations on when to replace guard and/or analytical columns.
    3. Consider implementing a shutdown method to flush the system at the end of each batch.
      1. There is some evidence that having a shutdown method in the opposite polarity is even more helpful. For example, if your method uses positive polarity, having the shutdown method in negative polarity can help reduce contamination.  
      2. The shutdown method can be a long, isocratic HPLC method that injects water or some other solvent applicable to your assay. By having high GS1, GS2, TEM and CUR settings, this can help keep the system clean by performing a mini bake-out at the end of each batch.
      3. In addition to helping clean the system, this can also flush out any contaminants that are present still on the column.
    4. Consider leaving the mass spectrometer on in standby at the end of the day. This allows the temperature and gas flows to stay on in the mass spectrometer after the LC system goes into standby mode. This option can be selected in the queue settings in Analyst software.  


Posted: Jun 23, 2021