Guidelines for Routine Use and Maintenance of Ultra Performance Size-Exclusion and Ion-Exchange Chromatography Systems


The Application Notebook

The Application NotebookThe Application Notebook-03-02-2012
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Waters Application Note


For the analysis of biotherapeutics, size-exclusion (SEC) and ion-exchange (IEX) chromatography are typically conducted under native separation conditions, requiring high ionic strength, 100% aqueous eluents. For high performance liquid chromatography systems, these conditions can be problematic: in the absence of bactericides, lack of proper maintenance can lead to bacterial contamination within hours. The presence of high salt concentrations increases the potential of particulates in the mobile phases. However, with the proper setup and care of a chromatographic system, robust and reproducible chromatography can be achieved with minimal downtime.1,2


The care and use of a size-exclusion and/or ion-exchange chromatographic system requires many of the same standard practices as any other system. However, there are some additional protocols that are required for high salt, aqueous mobile phases. While the practices outlined in this document are described for ACQUITY UPLC Systems, the principles apply to any chromatographic system. Overall system recommendations include:

  • If using a steel system, modify according to the manufacturer's recommendations. For use with a Waters UPLC System, detailed guidelines are available.

  • Clean laboratory glassware properly.

  • If possible, use mobile phases containing a bacteriostat (i.e. 0.02% sodium azide) to prevent microbial growth.

Additional recommendations are listed below by component. These considerations are for microbial growth, system suitability and/or protein stability.

Solvent Delivery System

The buffers used in SEC and IEX can favour microbial growth leading to contamination of the column and system. Other recommendations include:

  • Always filter aqueous mobile phase through compatible 0.22 µm or smaller membrane filters. The use of sterile filters and containers is also recommended.

  • Use only high purity water (18.2 MΩ cm). Bottled water should be opened the day of use.

  • Never 'top-off' mobile-phase bottles. Always change bottles when replacing mobile phase.

  • Replace eluents on a regular basis.

  • All eluent bottles should be visually inspected daily for microbial growth and/or particulates. Microbial growth can be a film on the bottle surface or may be observed by swirling the bottle.

  • If microbial growth has occurred in the eluent bottle, replace the mobile-phase filter or flush it with a 70% isopropanol solution. Microbes can contaminate mobilephase filters.

  • The solvent manager should never be left idle in either high salt mobile phases or 100% water.

Sample Manager

SEC and IEX conditions often require high-ionic-strength solutions in the sample manager wash lines (wash/purge, strong and weak needle). However, these eluents may have a detrimental effect on the sample syringe and/or needle. Recommendations include:

  • Ensure the sample is soluble in the mobile-phase and sample manager washes.

  • Follow the manufacturer's recommendations for wash solvents.

  • If the sample manager is idle, purge needle and/or wash lines with high purity water, preferably containing a bacteriostat.

UV Detectors

Waters recommends titanium or stainless steel optical flow cells when performing SEC or IEX under aqueous conditions. The standard ACQUITY optical flow cell contains Teflon AF in the fluidic path. Under native conditions, some proteins may interact with the flow cell surface, resulting in peak tailing and sloped baseline. Recommendations for detectors include:

  • Use titanium or stainless steel flow cells to reduce proteinsurface interactions. Other flow cell material (i.e. Teflon) may cause peak tailing.

  • Never leave the detector idle in high salt eluents. Flush thoroughly with water followed by a higher organic eluent.

Column Storage

To maintain long column lifetimes and minimize the risk of microbial contamination, the following recommendations should be followed:

  • Flush and store columns following the manufacturer's recommendations. Typical recommendations are 10–20% methanol or with a bactericide (i.e. 0.1% sodium azide).

  • Size-exclusion columns can typically be stored at 4–8 °C to reduce microbial growth. Ion-exchange columns are usually stored at room temperature. Check the manufacturer's recommendations for details.


SEC and IEX chromatography are performed under native conditions, requiring high-ionic strength, 100% aqueous eluents. To minimize protein-surface interactions, these conditions may require the use of a bio-compatible chromatographic system specifically designed for these applications. Precautions must be taken to prevent and minimize bacterial contamination. Signs of such contamination3 , which can occur within hours include: deteriorating peak shape, resolution and column lifetime. Unfortunately, once the column has been contaminated, regeneration is difficult. To decrease the frequency of system repairs and contamination, a series of steps have been outlined for maintenance and care of a chromatographic system and columns used for the analysis of biomolecules. These recommendations include maintenance for the solvent manager, sample manager, detector and column. Using these procedures in combination with good laboratory practices ensures a robust, reproducible system for ultra-performance-size-exclusion and ion-exchange chromatography.

Figure 1


1. "Size-Exclusion and Ion-Exchange Chromatography of Proteins using the ACQUITY UPLC System", Waters User Manual, Rev A, Part Number 715002147 (2010).

2. "Size-Exclusion and Ion-Exchange Chromatography of Proteins using the ACQUITY UPLC H-Class System", Waters User Manual, Rev A, Part Number 715002909 (2010).

3. "Controlling Contamination in LC/MS and HPLC/MS Systems", Waters User Manual, Part Number 715001307.

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