Capillary Electrophoresis (CE) Troubleshooting Tips:

What follows is a short list of problems, "observations" followed by a list of areas that should be investigated, as appropriate in parenthesis (), to troubleshoot common problems seen when using the analytical technique of capillary electrophoresis, CE, CZE.

 Observation (Investigate for cause):

            Excessive Baseline Drifting up or down

·         Temperature is not stable (stabilize room and/or capillary temperature).

·         Fouling of capillary (replace or clean and wash capillary with fresh, filtered solution).

·         Current levels unstable (loose connections, partial obstruction in capillary or running out of buffer solutions).

·         Capillary may have poorly cut ends resulting in poor connections or flow (replace capillary).

Excessive Signal Noise

·         Detector has air in flow cell (purge capillary and wash flow path).

·         Current level may be too high (reduce current).

·         Detection parameters, wavelength and bandwidth, may be inappropriate for buffer solution (select appropriate detection settings which are appropriate for the buffer used and selective for the analyte).

Loss of Signal

·         Voltage/Current has turned off (turn ON or investigate if system is in “alarm” state due to an error).

·         Detector parameters not selected.

·         Capillary has not been fully equilibrated (equilibrate capillary and auto-zero the scale).

·         Baseline offset may be off-scale (after equilibration, adjust scale or auto-zero).

·         Detector lamp(s) off, not ignited or due for replacement (verify lamp operation).

Signal Peak Shape Issues

·         Truncated, clipped or ‘square’ peaks (sample overload, reduce concentration 10x, shorten load time and re-evaluate).

·         Tailing peaks often result from very high current or when the concentration of buffer is too high (lower the current and/or reduce the buffer concentration, then re-evaluate).

·         Sampling rate may be too low (measure the peak width in units of time (i.e. seconds), then configure the detector to insure that the sampling rate allows for at least 20 points to be collected per average peak width (30 points is a better target # to use).

·         No peaks observed (Many possible causes, including: Partially or fully obstructed capillary, broken capillary, out of buffer, no injection, detector settings inappropriate for analysis, current too low, pressure too low. Look for a small peak from the injection along the start of the baseline to confirm that an analysis was started, then troubleshoot the method and settings).

            General Stability and Noise Issues 

·   When the CE system has not been used in a few days, salts from the buffer solution(s) may deposit on and clog the capillary line, flow cell and/or sensors. To avoid these problems, be sure to thoroughly clean, flush and wash down the flow path before use. Take the time to prepare fresh filtered solutions (each day) and allow time for the system to equilibrate. Taking these basic steps will avoid many hours/days of frustration.

UV / VIS, VWD, DAD, PDA HPLC DETECTOR SIGNAL BANDWIDTH (bw) SELECTION

Modern chromatography UV/VIS detectors offer the operator a choice of one to several hundred different signal wavelength choices (as is the case for Diode Array Detectors). Besides being able to specify a single wavelength, you can often choose a signal BANDWIDTH (bw) to associate with each wavelength [e.g. for a 280 nm signal with 10 nm bandwidth. This is often written as: 280 (10) or [280:10]. In many detectors, Signal Bandwidth is a variable, not fixed and represents the total number of nanometers across the specified signal value chosen. For example: If you select a signal wavelength of 280 nm and choose a bandwidth value of 10 nm, then you are actually gathering all signal data between 275 nm and 285 nm (5 nm to the left of the apex and 5 nm to the right for a total of 10 nm). Using a narrow bandwidth has the advantage of increasing the signal selectivity of the detector as you are only collecting data within a tight window. If you were to increase the bandwidth to 60 nm in the same example you would now be collecting data between 250 nm and 310 nm. The additional data collected over this wider range may reduce the total noise (by averaging it over a wide range), improve the S/N ratio (which may increase sensitivity), but it also reduces the selectivity. Large bandwidths also increase the chance you may include peak signal data from other co-eluting components into your signal data. You must select a bandwidth range for each signal wavelength which is located 'safely' away from any other potentially interfering peak. As with many things in life, balance is important. In this case, bandwidth choice is the balance between selectivity and sensitivity.

• When developing new methods we recommend that you choose an initial bandwidth value of 10 nm for each signal. This provides a nice balance between selectivity and sensitivity. It is also a common bandwidth value used on many older UV/VIS detectors which have a fixed signal bandwidth (such as many single or variable wavelength detectors).

• If you have determined the exact signal maximum for your sample and you would like to gain additional sensitivity for your sample (and thus decrease selectivity), re-run the analysis using several different, but increasing signal bandwidth values (e.g. 10, 20, 30, 50 and 100 nm). Choose bw values that are safely within the range of the detector, within the limits of the mobile phase's absorption region and also away from any potential co-eluting peaks. *To confirm which value is best, be sure and calculate the actual measured signal to noise ratio of the peak of interest after each analysis. This is a critical step! Do not be fooled by increases in the peak height or area alone as these changes are not always synonymous with better signal to noise ratios. Only by measuring the actual baseline noise level for each run and comparing it with the actual peak signal obtained will you be able to determine if increasing the bandwidth has provided you with better noise reduction and signal strength.

• To increase spectral signal selectivity choose a bw value that is very narrow. A value such as 2 or 4 nm would allow the detector to collect only signal data that is at or near the apex of your selected wavelength. This can be very useful when trying to discriminate your signal from nearby signal peaks, especially at low wavelengths such as 210 nm.

• When reporting your method conditions always include the wavelength AND bandwidth used for each signal. In order to accurately reproduce your method, this information is needed. *The flow cell dimensions, wavelength and bandwidth should always be included in your method.

REFERENCE WAVELENGTHS (as used in HPLC UV/VIS):

One of the most common problems that I see as a consultant in laboratories which use chromatography for sample analysis relates to how to choose appropriate settings for the modern UV/VIS detectors. In addition to selecting scientifically appropriate UV/VIS wavelength(s) and Bandwidth signal values, selecting one optional feature may invalidate an entire HPLC method. This software feature, found in many Multi-Wavelength and Scanning Diode Array UV/VIS detectors (aka: "DAD" or a "PDA") is known as the “ReferenceWavelength” .

• Please do not confuse this specific software feature ("Reference Wavelength") with the initial reference scan ('zero') which the detector takes at the start of the analysis and is subtracted from your desired signal to show only one initial signal plot (and which is used as the initial signal value to compare to the measured signal during the rest of the analysis run. This is usually known as "zeroing" the detector and occurs just once, at the start of each run. When you manually press the 'Auto-zero', you are adjusting the displayed signal plot to a know reference point (often 0.0 volts). This is a one-time zero of the signal and has nothing to do with the special software feature we discuss in this article.

"Reference Wavelength" [Usually written as: Signal Wavelength/Bandwidth: Ref Wavelength/Bandwidth]. Most manufacturers of advanced HPLC UV/VIS (esp. DAD/PDA) detectors provide this extra software feature in their chromatography software, but its use and function are a mystery to most chromatographers. As with all advanced features, proper training is required to understand and use them successfully. Using advanced features without proper training can result in analysis errors, invalid methods and perhaps very expensive product recalls.

Allow me to provide a brief explanation of the “Reference Wavelength” software feature as seen and used with many DAD and/or PDA detectors (e.g. HP/Agilent and Waters brand HPLC systems).

If you are running a gradient analysis, then the change in solvent properties (RI and light absorption/transmission) and temperature over time can cause noticeable baseline drift during the run. This drift up or down relative to the starting baseline reference point is normal, but may cause a number of quantification problems with the analysis reporting software (as flat baselines are more easily and accurately integrated than sloped ones). 

Two scientifically correct methods were developed to deal with this slippery slope of a problem. Each proposed method has some limitations, but if optimized can improve the quality of the resulting baseline (flatter, allowing for better peak integration) and preserve the original acquired signal data for compliance.

(Method # 1) Run the same method again, but this time with no sample (a blank of mobile phase) and subtract the resulting signal to produce a "blank subtracted run". This preserves the original data and removes the observed drift from the resulting signal ('A' - 'B'  = 'C'), but due to the time difference between injections, you are unable to confirm if anything has changed between the time of the first and second injection. It is not perfect.

(Method # 2) Set up the detector to collect a second channel of data (2nd wavelength signal) that is close to the original wavelength selection, BUT far enough away from the original signal such that it will not overlap any of the peak spectra of interest or other compounds in the sample. This is tricky as you want it close enough to show the drift, but far enough away to not show any sample signal. If selected carefully, it can be used as a pseudo blank run for post-run baseline subtraction. You can then subtract the second acquired ‘blank’ signal run from your original signal run and the resulting chromatogram should have a flatter baseline (less drift) for quantification purposes. With this method, two separate signals, 'A' and 'B', are collected at the same time (this is the key). A third, baseline subtracted signal, 'C', can be generated from them. This method preserves the raw data obtained from all three signals (i.e. Original, Secondary, and Subtracted signals). The benefit of this method is that the signals are all acquired using the same time base (unlike Method #1).

Using the concept of Method # 2 described above, many HPLC manufactures added a software feature known as a the ‘Reference Wavelength’ to their systems. This feature allowed a chromatographer to include with each signal choice, 'A', a second wavelength value, 'B', (and bandwidth) as part of the method which would be used to subtract out raw data from the primary wavelength during the analysis. This subtraction occurs in real-time, on your raw data gathered from the detector and the resulting data reported to the user is in fact the result of the subtraction only. The original signal data is destroyed. You will never know what the original data looked like before the reference wavelength was subtracted from it (it has been destroyed). Only the newly manipulated (subtracted) result is provided, 'C'. If any sample peak(s) or impurities appeared in the region where you selected a reference wavelength/bandwidth, then the resulting data would have been subtracted from your actual sample and you would never know it happened or have any record of it! This brings up a serious validation issue as you are modifying the original data with no way of knowing (or documenting) how you have changed it. It is for this reason alone that we teach chromatographers to always turn this feature 'OFF' by default. If they want to make use of the feature, then we suggest that they simultaneously collect data from a second, separate wavelength channel such that the two raw data streams are preserved for validation purposes (Method # 2). IOW: To acquire scientifically useful data, turn 'OFF' the Reference Wavelength software feature and record all of the signal data. The separate signals can be compared, subtracted or manipulated as needed for integration and reporting purposes, but the original signal sample data, 'A', is left unchanged and secure. This allows you to monitor for contamination, impurities, problems or changes during the run. It also allows others to verify your method for accuracy.

Observational Notes:  I am often called in to diagnose what the client's refer to as 'a strange problem' where the area of a known sample peak changes in an unexpected way. That "way" often includes going NEGATIVE, below the baseline. Or even increasing in area, mass or decreasing in mass.The column is clean, pumps work fine, retention times are stable and everything appears to be working fine. *This anomaly is due to the reference wavelength software feature being turned 'ON' and another compound (peak) absorbing in the user selected Reference bandwidth region. Its absorption contributes to the final signal. If the data collected (area) for the 'reference peak' is larger than the sample peak the resulting chromatogram will show a negative peak (this tends to be noticed by most users as it is illogical and indicates a serious problem!), whereas if the reference peak is smaller than the sample peak, the resulting area signal decreases, which may or may not be noticed (incorrectly interpreted as a lower concentration sample). You can see the obvious danger posed by this situation. Companies can be put in a situation where all of their past data is found to be invalid and product recalls may result from this finding. The cause is directly related to a lack of understanding and proper training in the use of the software and/or HPLC system.

 
How to Solve The Problem: The reason we see this feature cause so many problems in laboratories appears to be due to the fact that the Reference Wavelength software feature is being turned 'ON' by default in the software for most DAD/ PDA modules (The real default value for "Reference Wavelength" should always be: 'OFF', not on).  To make matters worse, the default values for the wavelength and bandwidths often supplied by the manufacturers are actually used by most chromatographers (what are the odds that the random values placed in the system are even relevant to your analysis? Why would you use them?). We suggest using a ‘canned’ method template in most laboratories which includes a new default value for this feature... 'OFF' for all analysis methods. Most importantly of all, please obtain formal training in the use of a specialty detector such as a diode-array detector before using one for sample analysis.

Notes

1. The bandwidth chosen for each wavelength is also very important and if chosen poorly, can result in adding noise to your signal, reducing it or even enhancing it. Please refer to this article for more info: http://hplctips.blogspot.com/2011/09/uv-vis-hplc-detector-signal-bandwidth.html 
2. If you are still running HPLC methods with the “Reference Wavelength” turned 'ON' while awaiting approval to turn it 'OFF', then you can ADD additional signals to your method with the same primary settings as before, but with “Reference Wavelength” now set to 'OFF'. Adding the same signal w/o the “Reference Wavelength” will provide you with the original signal data for future comparison to the "collected/modified" signal (allowing you to see if the data was changed). Make sure you configure these extra channels to be saved with the analysis.