Home » Instruments and Tools » Preparative and Process Chromatography

Preparative and Process Chromatography

How to commence successful prep or process chromatography?

The sole purpose of preparative and process chromatography is to arrive fast at the purest compound at highest yield and competitive price.

Every additional gram of compound is additional income. Sometimes this could also mean additional risks. Most process specialists sign confidentiality agreements with their employers. This makes them scared to take risks, It is easier not to maximize yield and to reduce risks.

As a rule of thumb chemist prefer re-crystallization or distillation over chromatography as purification method. Biochemist, Biotechnologist, Food technologist know that they have almost no alternative in molecular purification / separation processes than chromatography.

Chromatography is still a young process industry that is continuously being advanced with new materials and process methods. Competition in the market is driving the industry towards specialised niche products. Niche product have smaler but high added value markets.

Many new molecules used as API or exipients. They are highly active compounds produced in small quantities. An incewasing amount of novel compounds can’t be crystallized. Thus demand for high yielding low cost chromatography methods is growing.

Prep & Production Scale Chromatography is used to extract, fractionate,separate and purify molecules in

Fine chemical production
Manufacture of pharmaceutical compounds
Food processing

The field of Prep and Process Scale Chromatography is very wide and diverse. Standardized plants or standardized turnkey processes do not produce the purest compound fast at the highest yield for the most competitive price! The best strategy is to assess all requirement and then to select the best components that fit the requirements.

Necomer clients often commence looking around for low cost producers or branded products suppliers. This is a risky strategy because consumable and labour cost are often higher than assest depreciation costs. Consequently we start by asking our clients technical questions. We also want to understand overt and covert needs of the clients. Based on the answers we can gage whether or not we are the right partner to help our client achieving his ambition. If there is compatibility it is common practice to sign mutual confidential disclosure agreements. After that we put together a proposal that is being discussed with our clients.  

We are a network of independent partners and highly innovative chromatography pioneers. All of us have built through the years our own process technologies, created  unique particles, plants, equipment and software tools. Pooling our skills and knowledge enables us to move production scale chromatography into a new era.

We are determined to systematically evolve liquid chromatography as the most competitive of all purification methods. With our accumulated skills we enable our clients to manufacture the most competitive compounds! Don’t hesitate to contact us for help.

Important questions to be asked!

The biggest problem today are people that collect addresses, spread SPAMS fake news or attempt to hack your system. Many companies have installed a wide range of protection systems that scan mails at server level.  If you are a serious potential client make sure your E-Mail is genuine.  For your first contact make sure your first contact contains the following address details:

  • Company/Institution Name :
  • Owners:
  • Address:
  • Website Address:
  • Contact Person:
  • E-Mail Address of Contact Person
  • Direct Tel No. of Contact

What kind of compounds to be purified / separated?

  1. Organic Synthetic Compounds (MW<2000) (Heterocycles, Vitamins, Organometallics, Hormones, Pesticides,)
  2. Natural Products (MW <2000) (Saccharides, Lipids, Phospholipids, Isoprenoids, Steroids, Alkaloids, Flavonoids, Terpenes, Polyphenols, Saponins, Proanthocyanidins, Tannins etc. from a wide range of matrixes)
  3. Amino Acids, Peptides, Oligonucleotides
  4. Large scale race mate purification
  5. Inorganics Separation (Cations and Anions, Metals, Metal oxides, Nobel Metals, Acids, Alkalis, Industrial Waste,
  6. Hydrometallurgical- samples refines, leachates, extracts, precipitants )
  7. Protein, Biomarkers and Bio therapeutic Proteins , (Enzymes, Membrane Proteins, Recombinant Proteins, Antibodies, extracts from mammalian Tissue, Erythrocytes, Yeast, Bacteria)

What is your sample preparation method in prep and process chromatography?

Please describe.

Your preferred sample separation and purification method in prep or process chromatography?

Please describe.

You’re Process Perspective

Every process can be looked at from three perspectives. It is important to write down and to quantify the various anticipations.

  1. Upstream Perspective

Is a description of origin of sample (E.g. Sap from a plant XYZ that growth in A, Animal feed named ABC from company X or slurry from a chemical process A, retentate of a membrane process in a communal waste water treatment plant, piece of tissue from a biopsy from Z etc.) and a description of how the sample was harvested or synthesized and prepared prior separation / purification / modification process.

  1. Project Perspective

The project encompasses either purification / separation / fractionation / alteration or all of those processes. It requires a precise description of process steps to be undertaken. Important is to write down the anticipated quantification of the output results.
People with low job security and no expertise avoid formulating such parameters. They often go out to search internet forums and lend up with many different opinion

  1. Downstream Perspective

Every process output has to go through downstream processes. This requires a description of what should happen with the sample, what downstream processes the sample will be exposed too, what upper / lower level of purity are required, what productivity and target cost should be achieved. In a commercial environment the ultimate arbiter of success is productivity.

 Start-up Data

Please supply start up data such as analytical chromatograms. Make-up of liquid extract, Bio-broth, chemical raw material analysis etc.

Factors of Success in Prep and Process Chromatography?

Most processes comprise of a number of steps and involve a number of persons with different perspectives and skills. Frustration and money can be saved by gathering the process responsible people to invest time to go through the Upstream, Project and Downstream perspective. It is important that everybody understands the requirements and commits to it. Sample preparation is often over or under designed, conducted by unskilled labor, badly communicated or simply not given the respect it deserves. Sample preparation means for everybody something different! We have to simply consider it as a process step within a chain of many sequential or parallel processes. In this chain we have to look back in time, upstream and to learn what happened to the sample before it reached us. Sample preparation is important. All participants have to know from to what state the sample has to be converted and which method (physical separation, pulverization, dissolution, filtration, membrane filtration, solvent extraction, soxhlet extraction, distillation, adsorption, precipitation, centrifuging, chelating, masking, reacting etc. (If you need help please don’t hesitate to contact us!)
People often assume that everybody knows what will and should happen in the following process stage or they don’t care. In some industries people simply don’t talk to each other’s because they consider this as not their territory or concern. They work toward a specification and think that will suffice. Many specifications are not complete or ambivalent. Discussing the downstream process people may also trigger new ideas how to handle the project best. Furthermore it is also improving relationships and responsibilities between the parties.
The bottom line in chromatography cost efficiency and effectiveness (Yield, throughput and purity) and they are influenced by the following factors:

Environmental factors

There is quite a difference in cost whether or not you are using organic solvent or water and this in turn is dependent on what infrastructure is available. Some companies do have infrastructures to recycles solvents but some don’t. Some chromatography separation materials don’t use as much solvent as others. Please ask us for advice at the start of your project. Compatibility of target molecules with water or solvents is an important aspect. Availability of solvent is another important issue and so is purity of solvents.
Sometimes it may be necessary to design your plant according to ATEX regulations! The cost difference between ATEX or not ATEX conform plants is substantial. Let us know we may have intelligent solutions to get around ATEX costs!

Process selection

Process selection commences with definition of:

Anticipated Production volume (mg, g, kg or tons per day / week or month output). Sales and marketing people should normally provide such information. Often they don’t know and keep quiet. The Japanese taught us to design processes that break even with satisfying local demand. Every additional export can be done at fixed cost. This enables to build up a very competitive global market.
1 to 20 g/8h
20 to 100 g/ 8h
100 to 500 g / 8 h
500 to 1000 g / 8 h
1 Kg to 10 Kg/ 8 h
10 to 100 Kg / 8 h
100 to 1000 Kg/ 8 h
> 1 T / 8 h

Type /chemistry of molecules / particles to be processed

(This is important for assessing availability of raw materials and environmental cost and precautions)
Level of purity to be achieved. (We don’t over or under design the process. Regulatory authorities and clients define this dimension. It is often possible to increase market share with more pure compounds for similar costs)

Envisaged process life

Envisaged process cost and maintenance costs
Envisaged capital requirements and form of financing the capital investment.
In which industrial sector are you working? Some industries operate with low cost high trough put conditions others deals in highly differentiated specialty products e.g.
Pharma Research & Development (FDA, Local regulations)
Generic API Production (EMEA, FDA , Local regulations)
Fine chemical Production (Environmental regulations)
Food & Cosmetic Industry (Food regulation )
Others (No governing regulation)
Who is responsible for process validation
Plant – supplier
Component supplier
Everybody wants to possess the very best plants/ components. Unfortunately everybody has a different perception of what he considers to be the best.  Some prefer to buy branded turn-key plants from the largest supply companies.
Some prefer to buy from suppliers that show us plant-/component configurations which result in low cost final products. (This may include high investment but low running costs and process licensing)
Some buy what they are told to buy.
Some collect a number of quotations and select the cheapest one.
Some buy branded components and plants that they bought before.
Some procure the latest and most automated technology.
Some buy components and develop their own plant in-house.

Process Modus

Chromatography (LC, Flash, MPLC, HPLC).
Flash/MPLC/Membrane Purity (for intermediates, industrial grade raw materials)
99 % Purity (HPLC, SMB)
Patient injectable quality (Enantiomer pure, selective solvents)
Solid Phase Extraction,
Expanded Bed Adsorption
Chemical Synthesis (Heterogeneous Catalysts, SPPS, SPOS, Scavenging etc.)

Separation materials to be used

A large cost component is the separation material. Low cost materials may not be the best solution particularly if costly materials are being lost in the separation process.
Process chromatographers tend to look for materials with large surface area because they take higher loadings. The basis for a large surface area is small pore diameters. Make sure that the pore diameter correlates with the molecular weight of the samples. Type of surface structure and ligand density has also a dramatic influence on available surface area

Process configuration and equipment selection

In process chromatography there are many different processes available – some unique and protected by intellectual proprietary rights and many are commodities that can be utilized by everybody. Make sure that you are using processes that provide sufficient “freedom to move” so as to avoid patent infringement. It is much more advisable to check-out the “freedom to operate” issue long before you invest large amount of money in process development. We are in contact with some “process developers” that have IPR protected processes. Process developers protect their processes because they use combination of factors that lead to better yield, better resolution or to faster processing. It is advisable to sign a CDA and to evaluate the process for its claimed benefits. Process developers have invested large sums and time in developing and protecting their processes so it is only logical that they demand a small royalty payment. Never ignore IPR because it is much cheaper to pay an agreed royalty than a fine for patent violation.
Large enterprises mistrust small enterprises or only for a short time. They rather buy from large suppliers and commodity equipment. The history books are full of purchases that finally led to noncompetitive products. Many small companies have highly innovative process equipment and some don’t even try to collaborate with large life science enterprises from bad experiences.

The list of process configuration is endless here just a few:

Batch (Every batch a different sample )
Single columns chromatography (Flash, MPLC, HPLC, Expanded Bed Purification, new experimental processes)
Parallel column chromatography
Discontinuous processes
Touching band
Sample overload mode
Displacement mode
Flip-flop process
Column Recycling
Continuous column processes
SMB (Simulated Moving Bed)
SSR (Steady State Recycling) and Varicol®
Fauquet Process etc
Please let us know if you are interested in some of above processes we can help you with the appropriate IPR and contact persons and of course to provide some of the relevant components and software

Additional considerations

Column Loading Capacity:

Being able to get enough from the column in a given period of time is one of the most important factors in prep chromatography. What are our yield and cost objectives? You should know how long it takes to get satisfy your objectives with regards to sample quantity. Sometime solvents are chosen that are not optimal and load ability is decrease or intra column crystallization occur. One has to find appropriate diluent solvents to match the mobile phase. Every column has its own load capacity. Please enquire with us.

Cost per sample:

If the column cost is very high as in the case of chiral materials all parameters have to be looked at including costs of time, solvents used column replacement costs etc. . . . You will realize this is a very important criterion in prep chromatography since there are large differences in yield and costs.

Cost of solvents.

Cost of solvent varies from type and purity of solvents used and from country to country. There are large differences in solvent usage between the different chromatography materials and methods.


ml / minute – some column have reduced run times.
Equilibration time, ml / minute – some columns use very small quantities of solvents for column equilibration. Please enquire.

Cost of wastage and disposal,

Total volume – use less, dispose of less.


Less equilibration time, more runtime per day – Due to time saving in equilibration time. There are columns that require only 1 column volume to equilibrate and they are columns that use 20 column volume for equilibration

Column lifetime.

There are columns that last up to 10 times longer than ordinary columns.

Column cleaning procedures

Column live can be extended if they are serviced properly. This can be done quickly and hysteresis effects avoided. Its cost has to be included.

Preferred surface chemistries.

Some columns allow running a number of modalities (RP, HILIC, ANP etc.) This enables diverse use of solvents to improve solubility range for the column / sample match or to reduce conditioning time.

On-column degradation.

Some compounds require extreme conditions (low / high pH, Temp etc.) that may lead to accelerated column degradation. In reverse extreme conditions may also hydrolyze, modify compounds or lead to in-column crystallization. Change process or columns chemistry!

Availability of bulk separation materials

Some suppliers manufacture only small quantities of separation materials for analytical applications. In the past 10 years we have seen a departure from in-house packed to professionally packed columns. Column packing is not trivial – particularly new type B, C and hybrid materials are much more sensitive to be packed. The market is today very price and quality competitive and so it makes sense to let the material manufacturer pack your column.

Cost of Hardware / Systems

Technical people often avoid talking about costs, – its complex and based on many variables. They rather fish around for low cost suppliers because they don’t understand that cost is part of the productivity equation. In large enterprises technical people often look for performance properties of a particular process component and then submit a capital expenditure form to the finance department together with a debate about importance and benefits of the proposed acquisition. The finance department either approve or disapproves the acquisition. In smaller enterprises new equipment/plant acquisition is often debated between general, finance a technical management. Size of investment and productivity gains are important issues. It often helps technical people to get some overall cost related data and demands from their superiors. That includes

Anticipated Costs

What is the cost of raw materials or feed and how can we controll this cost?

What is the anticipated maximum / minimum cost for the process or cost of producing compound X?

What is the capital expenditure budget for the procurement of plant / Equipment?

Do we have a budget for consumables (Solvents, Columns, and Materials etc.)?

What is our business model (How do we make money?)

Cash flow is everything in business. From where does the cash come to finance business development?

Registration time is unpredictable and government authorities can’t be accelerated.  How do we finance the business if registration authorities are not in a hurry?

Who are our potential clients and why should they buy our products?

Is there an anticipated sales price for the final compound?

What are our potential competitors and what are their strength?

What are we doing if suddenly a low cost supplier appears?

Investment Strategy

The productivity of purification / separation depends largely on process configurations and consumables used and to a lesser degree on plant / component costs.

Location is another issue. In some countries government supports investment in new technologies with special grants or taxation benefits.

Depreciation rulings also vary from country to country, from province to province. There are a number of patented processes that result in high productivity.

With high cost yield is an important issue. Paying small amounts of royalties may be very profitable particularly if the purification / separation technology can be made part of the compound IPR so as to extend the patent life for a few years. Patent life is between 20 and 25 years. Towards the end of patent life the largest profits are made. Extending patent life is thus very attractive. Unfortunately external influencers in large multinational enterprises such as investors and finance analysts have a huge influence on management behavior and career lifetime. In the past 20 years many billions were destroyed by purchasing managers that did not understand how to deal with IPR protected products. They wanted to impress their shareholders by gaining a few percent with low cost procurements but at the same time they lost patent extension that had additional revenue potential in the billions. Penny-wise and Dollar-foolish – unfortunately this topic is a taboo. The situation if often quite different in small privately owned enterprises

Environmental and Safety Cost Issues

Many processes use large quantities of solvents (organic and aqueous) that may cause environmental problems. Environmental and safety cost may have a huge impact on overall costs and productivity. In purification / separation organic solvents are very popular as mobile phases. To avoid unexpected surprised you should prose the following questions:

Do we have earthed solvent storage tanks?
What solvents will be use?
What are the cost of solvents?
Do the supplied pants / components have to be EX-Protected?
Could some operations be done outside the Ex-Protected area?
Do we dispose off or recycle the spend organic solvent?
Are solvent reduction strategies of interest?
There are also questions for water based system users

Do your raw materials come directly from a sterile bio process?
Can you legally discard the spent eluent into the waste water system without post process treatment?
Would you have to incinerate the spent eluent?

Branded chromatography systems:

Large pharmaceutical manufacturing companies prefer branded equipment from the large system suppliers. They assume that large system suppliers are here to stay and will offer better service. History has shown that this is not the case because large companies grow by acquiring smaller technology suppliers and their competitors.
After the acquisition is completed they often have to pay for the acquisition and this is traditionally done by streamlining the product range and releasing the competent technical people.
Small privately owned companies do lots of custom based development work. This way they advance the industry. Some also manufacture for large system manufacturer branded products. Privately owned specialty engineering and manufacturing enterprises such as ours are generally very stable suppliers particularly those that supply reliable quality products. To survive small specialty product manufacturer are forced to offer very competitive pricing and functional products. Our clients are primarily small and expanding companies and research institution with limited budgets.

Conservative engineering

Small companies have much to lose and so many use conservative designs or over design their products. Large enterprises have large overheads and are under pressure to maximize their income some manufacturers cut down on raw material cost on their products (low cost steel, thin steel for housing and base plates). Our components are heavier and sturdier and run for many years without maintenance. Our components and systems are being used not only in chromatography but also in heavy engineering environment such as in oil exploration. Prep Chromatography systems are working horses. They have to be designed conservatively and have to be mechanically robust.

Turn-key system vs. evolving system

There are two kinds of end-users those who prefer turn-key systems and those who want to evolve a system. Turnkey systems can’t be altered and fine-tuned very much. The client has to know precisely what he needs. In turbulent times chromatographers often have to modify or extend their processes.