What is Different about Prep LC? (Versus Analytical HPLC)

prep column 

The goal of prep LC is not to produce the best looking chromatogram.

Prep LC can be used to purify a material for manufacturing or research purposes, or it can also be used for sample cleanup prior to analytical measurement, such as in gel permeation chromatography. Most Restek customers are more involved with using it for purification processes, so I will stick to that for this discussion. Products purified by prep LC might include pharmaceutical products, test materials for research or industrial chemicals, to name a few. What surprises some analysts is that the separation criteria are often not as stringent for prep LC as compared to its analytical counterpart. Perfectly symmetric peak shape and baseline resolution are often not required. The goal is not to produce an aesthetically pleasing graph, but to produce a purified product in a way that is overall the most economical and most expedient.


Column eluent is at least partially recovered and used, not sent to waste.

A very big difference in prep LC is that usually the column eluent is separated into timed intervals to make “cuts” of the sample for purification. This is typically done by attaching a fraction collector immediately following the detector and a non-destructive detector, such as UV. Often a switching valve is used to direct flow either to a waste container or to the fraction collector, or the fraction collector itself may contain the switching valve. The system or its components are programmed to begin collecting fractions as soon as analyte peaks become visible on the detector. The collected fractions are usually concentrated/ solvent exchanged to produce a final product or to perhaps to allow analysis by HPLC, GC, or other techniques for an intermediate product. Often multiple aliquots of the same sample are injected repeatedly to purify more of the starting material. Under this scenario, the desired fractions from each chromatographic run would likely be combined to produce the final product. It would be quite common to analyze aliquots from intermediate products or perhaps from individual fractions to monitor progress prior to combining them at the end.


Requires larger column IDs.

The size of the column in prep LC is obviously much larger than analytical LC. For these applications, this is needed to accommodate a larger sample size and also to make using it most cost effective. Column IDs for our prep columns are from 10 -30 mm, whereas the maximum ID for analytical scale is 4.6 mm. Our selection of prep columns can be found here on our website:



Requires method development on analytical scale first.

Since prep HPLC columns are more expensive and have limited availability, we ask that you first develop your method on an analytical column of the same phase. It makes sense to confirm that your compounds of interest can be separated sufficiently before you “graduate” to prep scale. Often analysts will start with a 4.6 mm ID column first. Please do make sure you do this with the exact same column phase to make it worthwhile. In other words, if you plan to use an Ultra C18 prep column, perform your method development on an Ultra C18 analytical column with an ID of 4.6 mm or smaller.


Requires specialized hardware.

Using a prep LC column brings with it certain requirements in terms of LC system hardware. For that reason, many analysts will use a system specifically designed for prep chromatography. Here are some examples of components that would be different:

  • Solvent pumps capable of higher flow rates, up to 150 mL/min
  • Larger sample loops
  • Higher pressure rating valves and components
  • Detectors with prep size flow cells


For example, here are links to information on systems available from Shimadzu and Waters:




I hope this post has helped to give you a better idea of what is involved with prep LC and how it is different. Please stay tuned for the next post, where we will discuss scaling up from analytical scale to prep scale LC. Thank you for reading!


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