Translator for HPLC HINTS and TIPS for Chromatographers

Saturday, December 8, 2012

Determining the Data Acquisition Rate (Sampling Rate) For Your HPLC Detector

Another common question I am asked is how to set-up the HPLC detector’s sampling rate. This article is specific to commonly used UV/VIS, not mass selective detectors (Mass Spectrometer detectors are set-up in a similar manner, but you also want to take into account the numbers of MRM transitions for each peak and dwell time to account for the scanning delay. Typical values for MS are >10 points with 15-20 being best). 

Most HPLC (UHPLC) instrument manufacturer’s provide default sampling rate values within their software packages. Please do not use them as the values shown were just put there to fill in the data field and may not apply to your application or method. Many chromatographer's use these values without first understanding if they are appropriate for their own methods. This is a common mistake. Just as the manufacturer does not know what wavelength, flow rate or mobile phase you will use, they also do not know what sample(s), method and/or conditions are appropriate for your specific application. As such, they provide numerous default values in these data entry fields to satisfy the software's requirement. Just as you select an appropriate wavelength and bandwidth, you should always calculate and enter the correct detector data acquisition rate value yourself which is appropriate for your specific application, detector type and method. 

The Peak shape's role during integration: For each chromatographic analysis you must determine the optimum sampling rate for the chosen detector. An accurate value is critical for proper instrument set-up, quantification and integration of your sample(s) peaks. In the most basic sense, the area under a perfectly Gaussian peak requires at least ten points to describe it with some detail. Ten points will provide basic data about the shape of an ideal peak to the computer. Since peaks are rarely perfectly symmetrical, a larger number of points will provide more accurate integration of the peak’s actual shape and total area. This will improve run-to-run reproducibility and quantification. We suggest you include twenty to thirty data points to allow for a more detailed fit to the peak. Too few points across a peak and you lose detail and sacrifice reproducibility. Too many points and you start to introduce noise into the system. 

With these facts in mind we can next think about calculating the detector’s data acquisition rate. You must select a data rate (sampling rate) that is sure to provide the recommended 20 to 30 data points across the peak width (we use the commonly calculated peak width at half height as the time measurement). Select a detector sampling rate that will provide you with this degree of detail and resolution. This is best accomplished by initially looking at an actual chromatogram of your sample. Look at the chromatogram and use the narrowest sample or standard peak past the void time, with good retention as an example to determine the best acquisition rate. The narrowest peak will be the worst-case scenario and will insure that you have enough points across all of the remaining peaks in the sample. It's width is often measured in units of time (seconds/minutes). This data can often be read directly off of a generated data acquisition report.


(a) If your narrowest peak has a peak width of 1.00 minute (60 seconds), then divide 30 points into 60 seconds for a result of 2 seconds per data point. The preferred sampling rate would be 2 seconds, 0.03 minutes or 0.5 Hz (depending on the units used by your detector).
(b) If your narrowest peak has a peak width of 0.20 minutes (12 seconds), then divide 30 points into 12 seconds  for a result of 0.4 seconds per data point. This equals a sampling rate of 2.5 samples per second or 2.5 Hz.


     To Determine the Data Acquisition Rate For Your Detector You Need To:
  • Calculate the best data rate for each method and not use a generalized value (though similar methods will often use the same rate).
  • Use your existing sample integration data results to identify the narrowest chromatographic peak in your analysis (at the baseline or half-height).
  • Record the width value of this peak (usually in units of time).
  • Divide this number by thirty (30) to determine the preferred sampling rate.
  • Use this value, or a value close to it, for your detector’s sampling rate.

Thursday, October 25, 2012

HPLC Capillary Tubing Connection Volumes:

The length and internal diameter of the HPLC interconnecting tubing used in your system really does matter. The total volume contained in the tubing can dilute your sample or separated peaks. This can effectively undue the work of separating the peak(s) on a column. Extra volume in the tubing can also have the effect of increasing the gradient delay factor for your method (the greater the volume of the tubing from the pump head to the column inlet, the greater the delay in the solvent mixture arriving at the column). In general, keep the the total delay volume as low as possible. This is accomplished by connecting the various modules together using the shortest lengths of tubing possible. For systems which use standard sized HPLC columns (e.g. I.D.'s of 3.0 to 4.6mm and lengths from 100mm to 300mm) the tubing internal diameter should be 0.17mm (0.007"). For systems which use very short, mini or micro bore sized HPLC columns (e.g. I.D.'s of 1.0 to 2.1 mm and lengths from 50mm to 250mm) the tubing internal diameter should be 0.12mm (0.005"). Looked at another way, if the total column volume is less than 750 ul, consider using the smaller internal diameter tubing (0.17mm) to reduce band broadening. 

Here are some tubing volumes to help you evaluate the effect changing the I.D. or length has on the tubing that you use.

I.D. (mm)
I.D. (inches)

ul / cm
ul / inch






Monday, September 24, 2012

HPLC Mobile Phase Filtering & Solvent Inlet Filters

HPLC Mobile Phase Filtering: 

The tubing and valve passageways of the HPLC system are very narrow and clogs can result from using solutions which have not been properly filtered. Columns are expensive and will also clog up with particulate matter causing increased back pressure and/or changes in retention times. Running clean, particulate free HPLC grade solvents through your chromatograph is a basic maintenance requirement. High grade chromatography solvents (and ultra pure water) are often pre-filtered through 0.2 micron filters by the manufacturer to meet their grade for use in chromatographic systems. However, there are times when you also prepare (mix) your own mobile phases using theses solvents with or without chemical reagents and additives. When you prepare mobile phase using these reagent grade chemicals or additives you should also take the extra time to filter the final mixture through a 0.2 micron glass or steel filter prior to use. This helps to insure that you start with as clean a solution as possible. *This is a critical procedure to follow with buffer solutions. When using aqueous solutions, possible bacterial and algae growth can occur so remember to date the solutions and dispose of them after a suitable time period (Make up only what you will use in one week). Do not re-filter these solutions and then use them again.

HPLC Solvent Inlet Filters:

Most HPLC manufacturer's supply solvent inlet filters on the lines which draw solvent into the pump head. To protect the pump and components downstream, these lines often incorporate a filter. These solvent pre-filters are usually made from plastic (PEEK or PEAK), glass or stainless steel. Their porosity is typically ten or twenty microns. A smaller porosity could be used, but it would restrict the lines ability to draw up fresh solvent into the pump head at the required flow rate so a compromise in pore size is necessary. The filter is primarily designed to stop the pump from drawing up any large particles or debris which could cause damage to the system and is NOT used to filter the solution (as mentioned above, the solutions used should be pre-filtered). These filters can clog up over time and so should be monitored for restrictions. Stainless steel filters can be cleaned using sonication and heat. Plastic filters should usually be replaced with new ones. Glass filters, which are often made of sintered glass, can be washed, but should never be sonicated to clean them as this can cause the glass to fracture and plug them up even worse. When in doubt, replace them with new filters. Filters used with clean organic solvents often last for many years. Filters which are used with aqueous solutions last for shorter times due to build up of undesirable biological matter.

  • Another way in which you can insure a clean source of liquid for your HPLC system is to make sure that your mobile phase reservoir bottles are clean and free of dirt and dust during use. Keep them covered. Always wipe off any dust and debris from the solvent bottles before you uncap them and pour them into another container (much of the dust in the mobile phase comes from dirt that falls into the bottles). Instead of 'topping-off' bottles, replace them with clean bottles containing new solution.

Friday, August 24, 2012


Many vendors offer an HPLC Pump "Seal Wash" option. If you often operate your instrument with high concentrations of aqueous salt buffers (e.g. Protein, Peptide Separations), then an optional seal wash system might be something you want on your HPLC system. When combined with daily flushing of the HPLC system to remove buffers, it can extend the life of and reduce the maintenance needed on your HPLC system. 

NOTE: If your HPLC system has a piston seal wash feature installed, then failure to utilize it (leaving it "dry"), may result in decreased lifetime of the wash seals and piston(s) due to the added friction they exert. If you have a seal wash system, but do not need it (i.e. running only NP solvents), then replace it with a non-seal wash system or utilize the seal wash feature to prevent damage.

To prevent the build up of salt crystals inside of the narrow bore tubing, pump and other HPLC components we strongly recommend that you wash the system down each day, after use. We routinely see HPLC systems with white fluffy crystals built up around the pump heads, pistons and various fittings from lack of maintenance on a daily basis. High concentrations of mobile phase buffer in your system (e.g. 0.1 M is considered 'high', but all buffers should be flushed out) can damage the pump pistons, pump seals, injector parts and are corrosive to the stainless steel used. The resulting damage can lead to expensive repairs.

  • Two types of flushing techniques can be employed to reduce the damage caused by these salt buffers and extend the life of the system. Flushing the entire HPLC flow path with a solution which does not contain any buffers (to rinse it) and optionally, flushing the back of the pump pistons using a "seal wash" system.

(1) Flushing the HPLC Flow Path: Potential damage from salts can be avoided if you remember to always flush down the entire flow path of your HPLC each day (and anytime it may sit unused) with a proper mixture of HPLC grade water and some organic (to prevent the growth of bacteria and/or mold). Flush the column down first with an appropriate solution and then remove it from the flow path. Next flush the entire HPLC system down to rinse it of any remaining deposits (sometimes the column can be left in-line and flushed with the system. Consult your column manufacturer for advice). The exact mixture to use will depend on the exact type of mobile phase you are using. You want to select something which will dissolve the buffer used in your mobile phase into the solution plus incorporate some organic solvent component to reduce the surface tension and also deter the growth of bacteria over time. For example: A common Reverse Phase (RP) wash solution of 80% HPLC Grade water and 20% Methanol can be used in many applications. If you have an automated HPLC system, then this entire process can be stored as a "Flush" method and programmed to run at the end of each day's sequence or series of runs so you do not have to remember to do it manually.

(2) Seal Wash System Use: When run with buffers, the HPLC pump's pistons are coated with buffer solution. Over time, the liquid evaporates and a film of buffer salts is deposit on the pistons. These salts accumulate and can scratch the piston surface allowing air to enter the system and/or leaks to occur (drips from behind the piston seal). Premature replacement of the pump head seals and pistons often results from this damage. Washing the internal flow path of the HPLC system (as described in section #1 above) does not wash away these salt deposits. A "seal wash" system can be employed to assist to deal with the problem. The seal wash pump's inlet line can be placed in a bottle with fresh wash solution and through either an automatic timer feature set in the pump's software or through the operator manually turning the wash pump on and off, it can wash the back of the piston area to rinse these deposits away. The rinse solution used to wash the pistons will again depend on the type of mobile phase you are using (just like the HPLC flushing solvent). For most RP applications, I recommend a mixture of HPLC Grade water and Methanol (50/50 to 80/20). Other common seal wash solutions are: 90% HPLC Grade water and 10% IPA or 80% HPLC Grade water and 20% ACN. For most applications, I prefer using Methanol over IPA because it is much better at dissolving many of the buffers used. A third option would be to use a wash solvent which is the same as your mobile phase, but without any buffers added (try to include at least 20% organic content). Again, you must review your own method to determine which wash solution is best as their is no such thing as a 'universal' wash solution that can be used with all methods.

If you are running Normal Phase (NP) applications, then the seal wash can also be employed to keep the pistons 'wet' during operation and avoid excessive high pitched piston squeal noise, which is common when running dry solvents (e.g. Hexane). Manufacturers often provide special piston seals designed for use with normal phase solvents, but sometime the incorporation of the mobile phase as a seal wash solvent can lubricate the pistons well. IPA can often be employed as a NP seal wash solvent choice too. In any case, always make sure that the tubing used in your seal wash pumps is fully compatible with the wash solution you choose.

  • Seal Wash SEALS: One final reminder about HPLC system which use a"Seal Wash". Some designs (not all) incorporate a separate piston seal, behind the main pump head seal, to seal the rinse solution inside the wash area. Just like the piston seals at the front of the pump head, these wash seals require regular replacement. If your HPLC system uses a wash seal, be sure and have some extras on hand so they can be replaced when you service the pump head. Failure to replace these worn seals usually results in liquid leaking out the back of the pump head. This may be mistaken for a seal failure at the front of the pump head, so you need to be aware of their use to diagnose and repair any leaks correctly.

Friday, July 20, 2012

Column Temperature in HPLC / UHPLC / LC-MS

Let us not forget the role of temperature in liquid chromatography. Just as mobile phase composition changes are used to develop better methods, column temperature is an important chromatography variable which must be addressed. I would like to call to your attention to a few different ways temperature can change your chromatography in this "hint and tip".

(1) Stability & Reproducibility of the Method: 
Maintaining a stable column temperature during a separation is important. Excellent temperature stability can lead to a high degree of reproducibility (*Their are of course many other factors to consider as well). For a typical analysis, temperature stability of 1.0 °C / hour (over the course of the analysis) is usually enough. If you are not using a thermostatted column compartment to perform your chromatography you may have already noticed the hour-to-hour or day-to-day fluctuations which can result from running samples under ambient temperature conditions. The normal changes in room temperature can be several degrees C over an eight hour period. These types of temperatures changes can make it impossible to achieve reproducible results for some samples. It is for this reason that it is critical that you include some type of temperature control as part of your method. Always record the temperature at the start and end of each run and include this data with your report. Most of the automated chromatography data systems provide this data as standard today and it is very valuable in reproducing the data as well as for troubleshooting, if needed.

(2) Back Pressure:
Column back pressure is directly changed by temperature. As the temperature rises, the column back pressure decreases. As the temperature decreases, the back pressure increases. This can be a useful variable when working with some of the newest sub-two micron particles on the market. The very high back pressures produced by these particles can be significantly reduced by increasing the column temperature [See "Pressure Drop Across an HPLC Column"]. 

When practical, try experimenting with your method by increasing the temperature, in increments of 5°C, to measure the change. You may discover an improved method with lower back pressures, a shorter run time and sharper peaks.

(3) Viscosity: 
Viscous mobile phase systems can take advantage of using higher temperatures to reduce the overall system back pressure. Since efficiency often improves with higher temperatures a double bonus of higher efficiency (sharper peaks) and lower back pressure can be achieved just by increasing the column temperature (peaks sometimes change elution order too so use standards to check this). 

(4) Practical Considerations:
Their are limits to using higher temperatures in chromatography which must be respected. The stability and solubility of your sample, the boiling point of your solvent, the maximum temperature setting of your column heater (mobile phase, flow cell and the rest of the HPLC system) and the stability of your column over time will determine how far you can safely push this.

(5) Specifications: 
One other issue worth mentioning here is that many traditional silica columns can loose their bonded phase at temperatures above 60°C. Some specialty silica phases (i.e. Waters XBridge & Zorbax StableBond) have temperature ratings to ~ 90°C. The more exotic non-silica based supports (e.g. Zirconium, graphitized carbon and/or PSDVB) often provide poor efficiency compared to the silica based products, but can handle temperatures in excess of 100°C

*Always consult with the column and/or instrument manufacturer to determine what the correct and safe operating conditions are before using any instrument, column or chemical.

Tuesday, June 19, 2012

HPLC Hints & Tips Web Page

If you would like to see some of these tips in a tabular format on a single web page, then check out this link:  

   HPLC HINTS & TIPS for Chromatographers:

   HPLC BLOG link, which is updated more frequently, can be found here:

Note: The web page and blog versions present some of the same tips, but some of the tips are only shown on one or the other page so it pays to check them both to stay up-to-date on all of the tips offered.

Monday, May 21, 2012

Common LC/MS ESI Tune Compounds:





Wednesday, April 25, 2012

Windows 7 Shortcuts & Tips

Here are some of My Favorite Helpful Shortcuts/Tips For Use With Microsoft Windows 7.0 

  Do you miss the 'Quick Launch Bar' ? The bar is absent in Windows 7, but it can be put back.
  1.   Use your mouse to right click on the Windows taskbar and then choose Toolbars; New Toolbar.
  2.   The system will ask you for the path of the new folder. Type:   %userprofile%\AppData\Roaming\Microsoft\Internet Explorer\Quick Launch
  3.   Select 'folder'. A new link to the quick launch bar will be added to your current task bar. 
  Are you using a laptop and want to know how the power is being used ? There is a built-in application which will create a file containing a power efficiency report for you.
  1. From the command line type ("Folder" is the name you supply where you want the report to go): powercfg -energy -output \Folder\Energy_Report.html
  Would you like to minimize all of the running application windows in one shot instead of minimizing them one at a time ? Windows 7 has a feature for this called " shake". The window that you are currently using will stay active and the rest will be minimized. Here is how to use it.

  1. Click and hold the title bar of the current active window you want to stay on-top. 
  2. While holding it with the mouse, shake the item back and forth until all of the other windows are minimized. 
  3. Once they are, let go of the mouse button. 
  4. Shake the title bar once again to bring them all back.

Tuesday, March 20, 2012

Hydrophilic Interaction Chromatography (HILIC)

Perhaps you have a polar sample which shows poor or no retention under reverse phase conditions. HILIC may provide you with an alternative method for retention and separation. HILIC is a unique mode of chromatography which uses numerous retention mechanisms. The most important mechanisms involve surface layer liquid-liquid partitioning, adsorption and various types of ionic interactions.

Sometimes referred to as aqueous normal phase chromatography, this hybrid technique utilizes a stationary phase which is very polar (e.g. silica, amino or a diol column) and a mobile phase which is made up mostly of organic phase with some water added. The retention mechanism is based on the idea that adding a low percentage of polar phase (water in this case) to a polar surface will result in a water layer forming. Typically this hydrophilic layer results when as little as 2 or 3% water is added to the mobile phase. The remainder of the mobile phase is an organic solvent (ACN is the most popular). The polar charged analyte(s) will partition into and out of this adsorbed water layer (a cation exchange process takes place, but their also can be a purely electrostatic mechanism going on as well). Unlike conventional reverse phase chromatography, in HILIC increasing the organic content of the mobile phase increases the retention! Put another way, increasing the water content of the mobile phase and decreasing the organic portion (as in an HILIC gradient method) results in retention and then elution of very polar analytes. 

With HILIC mode, sample elution (retention) decreases as you increase the polarity of the organic solvent. Based on this information, good HILIC column wash solutions usually use alcohols in place of ACN  (IPA, Ethanol and Methanol; with Methanol being a stronger eluter).

The use of additives, buffers and pH can all play a role in retention and separation plus improve reproducibility. When developing methods, be sure and evaluate their role. Because of the low water content of most methods, buffers must be chosen carefully to insure full solubility. Ammonium formate and acetate are popular as are acids such as formic acid. Regarding pH, the low aqueous portion will mean that the actual pH of the final solution will be much closer to neutral.

Tuesday, February 21, 2012

Techniques To Enhance Negative Mode ESI in LC/MS

Many sample types require MS analysis using negative ion electrospray mass spectrometry (ES MS) mode. Sensitivity can be less in this mode, compared to positive mode, as they employ mostly non-polar solvents which do not promote ion formation. In the past we discussed how adduct formation can be employed to enhance ion formation. There are other techniques which can be used as well. Here are a few tips which can be used to improve the quality of the signal obtained under negative mode ES MS conditions.

(1) Negative ion formation and signal response can be improved by choosing the right solution chemistry. One method to improve solvent desolvation and reduce the electrical discharge (noise) is to add isopropyl alcohol (2-Propanol) to the mobile phase. Reported in the literature nearly twenty years ago, as little as a 10% solution has been found to increase the signal level and decrease the noise level under many conditions. The addition of methanol to the mobile phase also can improve the signal, though usually not to the same degree as IPA.

(2) Another technique used to improve ionization involves the pH of the solution or mobile phase used. Higher pH values are often better. Post column addition of a basic solution which adds proton acceptors to the mix, such as ammonium hydroxide (20 or 30 mM), can also improve signal response and stability.

(3) APCI mode: If running nonpolar to semi-polar small molecular weight compounds, especially those which are volatile, this is still the source of choice. *Conventional ESI mode is best for polar to neutral molecules in small to large Mw ranges.

Tuesday, January 3, 2012

Popular Microsoft Windows® Short Cuts:

Here is a short list of some of the most popular Windows short cuts. Hopefully, you will spot a few that you do not know about and can use.

  • Windows Keyboard Logo Symbol + L: Lock the computer (without using CTRL+ALT+DELETE).

  • ALT+TAB: Easily switch between open programs.
  • ALT+F4: Quit the program.
  • ALT+F4: Closes the current window.

  • SHIFT+DELETE: Delete an item permanently.
  • SHIFT: Press and hold down the SHIFT key while you insert a CD-ROM to bypass the automatic-run feature.

  • CTRL+ESC: Open Start menu.
  • CTRL+C: Copy.
  • CTRL+X: Cut.
  • CTRL+V: Paste.
  • CTRL+Z: Undo.
  • CTRL+B: Bold Font.
  • CTRL+U: Underline Font.
  • CTRL+I: Italic Font.
  • CTRL+Z: Undo the last command

A Full List of Microsoft Short Cut Commands Can Be Found In This Key Directory (Listed by Application):