puriFlash-MS Targeted Isolation of Natural Products Under Normal Phase Conditions


The improvement of analytical techniques and methodological tools plays an important role in the characterization and isolation of bioactive secondary metabolites in natural product research. Reverse-phase liquid chromatography-mass spectrometry (RP-LC-MS) is widely used for metabolite profiling of complex natural extracts at the analytical level and is increasingly being used for targeted MS isolation of biomarkers. Normal-phase chromatography (NP-LC) is well suited for the purification of polar secondary metabolites offering also some advantages compared to RP like low operating pressures and cheapest stationary phases.

NP-LC however is typically not well-suited for MS coupling. The potential of NP-LC-APCI-MS for metabolite purification at the preparative scale using generic separation methods has been investigated on an Advion X Interchim PuriFlash® – CMS system in view of its application for targeted MS isolation of lipophilic secondary metabolite. A mixture of three representative apolar natural products was used to optimize separation, splitting and MS ionization in conditions mimicking real isolation cases. Finally, successful isolation of the apolar constituents of the dichloromethane roots extract of Angelica archangelica was performed.

Rapid Isolation of a Representative Apolar Natural Product Mixture by Normal-Phase Flash-CMS

Purification of a Natural Products Mixture on 12 g and 25 g Normal Phase Flash Columns

Three commercially available standards (caryophyllene oxide, khellin, and alpha-santonin) were used to evaluate the applicability of the puriFlash-CMS system as a tool for rapid purification of lipophilic compounds from crude plant extracts.

The four chromatograms show the mixture profile at the preparative scale with rapid gradients on two column sizes with a good overlap of the UV and MS signals.

All parameters were carefully optimized for both separation and detection. Special care was taken to find ionization and splitting conditions that would provide good detection and

Flash-MS Guided Purification of a Given Compound

Scheme of the Post Column Makeup Pump Dilution

puriFlash-CMS System

Solvents from the normal phase are highly flammable for the APCI source and should be avoided because of the heating process.

Optimized post-column dilution was mandatory in order to have an efficient and safe ionization.  The solvent mixture when it reached the MS detector was at > 99% either ACN or MeOH.

APCI-MS detection with optimized splitting conditions and post-column elution of appropriate solvent was found robust and well suited for this type of purification.

Normal-Phase puriFlash-CMS Purification of Angelica archangelica Roots Extract

Analytical HPLC-UV

Analytical Scale:

Preparative Scale:

Flash Preparative UV-ELSD-MS

The roots of Angelica archangelica are rich in coumarin derivatives. MS-ELSD detection in addition to UV detection enabled the monitoring of secondary metabolites with no or weak chromophores and the selectivity of the MS was of great help for a precise collection of partially coeluting compounds.


Normal-phase flash purification represents an efficient strategy for a rational isolation of specific lipophilic biomarkers or bio-active compounds based on metabolite profiling results. MS-triggered fractionation and ELSD monitoring in addition to standard UV detection is a powerful tool for precise collection and to estimate the amount of separated compounds. MS is particularly useful for the specific collection of any given m/z in case of coelution that often occurs in crude extracts using high loading and low peak capacity chromatographic methodologies.

This fast and rational approach can be widely used for single step purifications and isolation of synthetic and natural mixtures. It is also compatible for the detection of apolar compounds that lack chromophores which is very common in natural product research. Separation performed at the preparative scale allows to purify tens to hundreds mg of compounds for further structural identification and assessment of their bioactivities.


Davide Righi1, Antonio Azzollini1, Emerson Ferreira Queiroz1, Jean-Luc Wolfender1
School of pharmaceutical sciences, University of Geneva, University of Lausanne, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
[1] Davy Guillarme, Dao T.T. Nguyen, Serge Rudaz, Jean-Luc Veuthey, Eur. J. Pharma. Biopharma. 2008, 68, 430

Peptide Purification: Flash-MS Coupling using the puriFlash 5.250P and expression CMS

In order to adapt, Interchim set up a laboratory to be able to perform online demonstrations. These demonstrations can be articulated around purifications of “standard” products in order to demonstrate the potential of our instruments. This example demonstrates the capabilities of a flash-ms system featuring the Interchim puriFlash 5.250 and Advion expression Compact Mass Spectrometer (CMS) for the purification of a peptide.


For the purification of a peptide resulting from chemical synthesis, we used the puriFlash 5.250P. To monitor this purification, we used a UV detector and Advion expression CMS.

The detection of peptides by mass spectrometry is done with an ESI source, which is ideal for the detection of large molecules such as peptides. A small amount of product is “diverted” by the MS interface for detection.

Flow Injection Analysis (FIA)

Direct Injection of Crude Sample on the expression CMS.

Here is the resulting mass spectra:

We observe a peak at m/z 643, which corresponds to the molecule of interested charged 3 times (M+3H)3+, as well as a peak at m/z 964.3, which corresponds to the molecule of interest charged 2 times (M+2H)2+.

HPLC Conditions

Here are the results:

Transposition & Purification

A peptide column with a preparative column was used: PFB5C18T-150/212.

First, the analytical HPLC method was transposed to a preparative HPLC method.

Then, the concentration of the injected sample was increased to be able to purify the maximum amount of the product in a single run.

Thanks to the puriFlash 5.250P system coupled with the expression CMS, the product of interest was purified and collected based on its mass.

Better Chemistry from Intelligent Flash Purification

<< Click here to check out our latest whitepaper:
Breaking Through Bottlenecks in Organic Synthesis with a Streamlined Purification Workflow >>

We have all been there: You want to do a simple Flash purification.

Easy, right?

You then begin to prepare your reaction mixture, think about monitoring the reaction, confirming the product, developing the Flash method…

This post highlights some ways to make Flash purification easier than ever before. Read on for tips on reaction monitoring, purification and fraction ID.

<<click infographic to zoom>>

Pre-Flash Run: Performing (and monitoring) your reaction
Starting off you are faced with several decisions to make – decisions that can turn the simple purification process in to a half-day adventure in sample preparation and scrolling through social media while you wait for your LC/MS results.

The first decision you need to make is how you can quickly and easily make your compound and get that compound over to the Flash system. Pronto!

Tip #1: Reduce wait times.
If you think, “LC/MS is best!” you may want to reconsider. Reaction monitoring can be done much faster and easier using alternative technologies like TLC. Consider what you truly need – a quick answer to, ‘Did I make my compound?” Seek to find that answer in the easiest way possible, using the most straightforward (even basic) technology that you have on hand in your lab.

Tip #2: Reduce your sample preparation.
If you choose to use the TLC route over LC/MS (Bravo!) to monitor the reaction, you’ll still have a few steps between you and the Flash run. Namely, the annoyance of scraping spots, preparing them in a solvent for direct injection in to the mass spectrometer. It may be an opportunity to explore additional technologies available on the market, such as a TLC Plate Reader. This newer technology gives you push-button analysis of TLC plates. No scraping. No sample prep. No cleanup. Just results in seconds.

Imagine – your reaction complete and your compound of interest identified with only the push of a button!

<<click here for more information on reaction monitoring from Advion>>

During the Flash Run: Use the Tools at Hand
The nice thing is that (generally) technology is on our side. Thanks to AI and auto-runs and the ‘set-it-and-forget-it’ mentality of several tedious chemistry processes, we have luckily evolved to a time where many industry-leading experts have done the work for you.

Tip #3: Simplify Flash method development.
Several questions come up during method development in Flash that, unless you are an expert, you may not know definitively. What are your Rf values? Which column should you choose? If your Flash system offers the ability to simplify method development with suggested details, it is a good starting point and can help your routine purification run smoothly.

<<click here for more information on intelligent flash purification from Advion x interchim>>

After the Flash Run: Identifying Fractions

You’ve made it though your purification and feel confident about the work you put in so far. Hopefully you spent no time at all monitoring your reaction and preparing your method, and you feel confident that you let the Flash system help with method development. But what now? Is it finally time to dust off the old LC/MS?

Tip #4: Simplify Fraction ID
There is not one way to ID a compound. As we learned before, TLC is an ideal alternative to LC/MS for reaction monitoring. Now, we look at it from a different angle – how to quickly ID the fractions in your tubes without wasting any of your precious time?

Tools like the Advion ASAP liquids and solids probe are ideal fo this. The simple probe is dipped in to one of the tubes and then inserted in to the APCI ion source of the mass spec. This allows for prep-free sampling – and another way to skip the LC/MS.

<<click here for more information about the ASAP probe from Advion>>

Have any tips (or headaches) to add to this list? Email us, info@advion.com and make yourself known! We are happy to connect you with a Flash expert on our team.

Interested in a streamlined TLC to Flash to ASAP workflow system? Advion x Interchim is currently offering a free Flash system with the purchase of a mass spectrometer. Click here to learn more about the latest special offers.

Video more your style? Watch a full Flash workflow, from reaction to fraction in our latest clip:

Combined Atomic and Molecular (CAM) Ionization: The Diversity of the Liquid Sampling – Atmospheric Pressure Glow Discharge

Authors: Tyler Williams1, Jacob R. Bills1, Jamey Jones2, and R. Kenneth Marcus1
1Clemson University, Department of Chemistry, Clemson, SC 29634
2Advion Inc, Ithaca, NY 14850

Mass spectrometric techniques are typically divided into two distinct fields: atomic and molecular. Liquid sampling – atmospheric pressure glow discharge (LS-APGD) has been developed as a versatile ionization source capable of combined atomic and molecular (CAM) analysis. To date, the LS-APGD has demonstrated impressive results in U isotope ratio analysis as well as molecular analysis across a wide range of instrument platforms.1-3 While molecular sampling has been demonstrated on this source, these samples fall into the realm of ESI-type samples, larger, polar compounds, most commonly LC-relevant drug targets. Presented here will be the demonstration of the wider versatility of the LS-APGD as a CAM ionization source using the Advion expression Compact Mass Spectrometer (CMS).

This poster was presented at the ASMS 2020 Reboot.

This research was also published in the Journal of Analytical Atomic Spectrometry (JAAS)*.
*This article is not open access.

Advion COVID-19 Update: Dedicated to Science – Dedicated to You

Dear Customers and Partners,

During this global pandemic, the health and safety of you and our employees is our highest priority. In parallel, we remain committed to delivering solutions and providing the SERVICE to which you have grown accustomed and distinguishes us from all others. As such, we have implemented proactive measures protecting, while still serving all stakeholders during this rapidly-evolving and challenging period.

  • Order Processing: We will continue to receive and process orders, ensuring their timely delivery – in strict compliance with all health regulations and with fully-maintained and executed quality processes.
  • Customer Service: Our global team is fully committed to providing any support you need. But, like you, we are also subject to near-hourly changes in global travel restrictions based upon country directives, border restrictions, federal and state guidelines. In a growing number of instances, we are being denied entrance into customer facilities – which is frustrating for all involved. As an alternative, we also provide remote support via a number of digital support technologies. All incoming support inquiries will be managed with the same speed and efficiency you have come to expect from our world-class experts.
  • Headquarter Visits and Entry: Under approved conditions, we will support demonstrations and training. Advion facilities are being maintained in accordance with state health compliance to meet and exceed recommendations for a safe and sanitary environment.
  • Staff: Advion has implemented a flexible work policy, including the ability to work from home for all employees that are able to do so, and modifications for those who are not. This has been put in place in an effort to improve social distancing techniques to suppress the spread of COVID-19, while also allowing Advion to maintain its necessary business functions.

Our commitment to our customers and partners is unwavering. We are dedicated to you and your team; ensuring your future success. If you have any questions please contact Kristy Licari, klicari@advion.com or call 607-882-9903.


Your Advion Family

Advion Inc. Dedicated to Science – Dedicated to You

Mass Spectrometry for the Teaching Lab

Teaching Mass Spectrometry: The Basics

Developing a curriculum for any course is taxing: lecture content, lab materials, take-home packets and more.

Our team at Advion understands that while teaching mass spectrometry to your students may be a priority for you, it may not be something that you are ready to do without significant preparation. That’s why we have developed a teaching package, featuring the following:

  • The expression® Compact Mass Spectrometer (CMS) – an instrument with the simplicity for teaching students, and the performance to support your own research
  • ESI and APCI ionization techniques
  • Easy to use sample inlet techniques such as the Plate Express automated TLC plate reader, and the one-touch ASAP liquid and solids probe
  • Over 10 hours of recorded lectures from industry expert and Advion co-founder, Dr. Jack Henion
  • Lecture slides to share or adapt to your own teaching style
  • Simple, intuitive, student-friendly CheMS Software

From introductory mass spectrometry principles to in-depth research projects, Advion’s teaching package provides a wide array of hands-on experience opportunities essential for teaching mass spectrometry to chemists.


Learn more about the easy, prep-free sample introduction techniques that make learning mass spectrometry with the expression CMS stimulating and easy for both professors and students:


Plate Express Push-Button TLC Plate Reader

• Couple the Plate Express TLC plate reader to the expression CMS for push-button TLC plate analysis

• No scraping or sample preparation required

• Identify spots in <1 minute



ASAP Atmospheric Solids Analysis Probe

• Ideal for student use, the ASAP probe provides the easiest sample inlet technique for liquid and solid samples with no prep

• Insert the probe into the mass spectrometer for answers in seconds



LC/CMS – Learning the Basics of (U)HPLC

• Gain expertise in LC/MS by adding the Advion AVANT (U)HPLC system, or connect the expression CMS to your lab’s current LC using our integrated software options



CheMS Software for a simplified user experience

• Quickly select the workflow and type of compounds to be analyzed without needing to be an expert in mass spectrometry

• Effortless method and instrument setup for a range of sample introduction techniques




expression CMS

The expression CMS is a research-grade benchtop mass spectrometer designed with the chemist in mind. When class is not in session, the system is ideal to support research projects. With electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources and an extended mass range option for large molecules, the expression CMS is an easy-to-use versatile mass detector for a variety of research applications and in the teaching lab. Its ease-of-use, versatility, and one-click software make the expression CMS ideal for undergraduate and graduate teaching chemistry programs.



Comprehensive Lecture Materials

Developed by Cornell Professor Emeritus, Jack Henion, PhD, along with leading chemistry departments, a ready-to-teach curriculum on mass spectrometry is included in the teaching package. Share as is or adapt to your teaching style. The curriculum includes pre-recorded lectures and accompanying slides on the fundamentals of mass spectrometry, sample inlet techniques, and real-world examples used in the chemistry workplace for hands-on learning. Lectures include:

  • Introduction to Mass Spectrometry
  • Flow Injection Analysis, ESI and APCI Ionization Techniques
  • Direct Analysis Probe for Liquids and Solids (ASAP)
  • Plate Express TLC Plate Reader
  • Touch Express Open Port Sampling Interface (OPSI)
  • LC/MS Techniques
  • Other CMS Applications & Techniques

Comprehensive Reaction Monitoring & Flow Chemistry Resources

Did I make my compound?”


It’s a common phrase that may follow you around the lab daily. With time-sensitive reactions coupled with the time-sensitive need to confirm data, fast reaction monitoring is essential for bench chemists looking for the most streamlined daily workflow.

The expression Compact Mass Spectrometer (CMS) addresses the need of organic and synthetic chemists to understand the optimal time to quench a reaction mixture. They can obtain answers within minutes rather than hours or days. Additionally, multiple inlet techniques like the atmospheric samples analysis probe (ASAP), Plate Express TLC plate reader, direct injection and more provides the ultimate in flexibility for sample analysis without the need for complex sample preparation. In addition, the use of the expression CMS in flow chemistry applications is an ideal reaction monitoring tool.

Learn more about the essential tools for fast reaction monitoring in this comprehensive resource guide:


Whitepaper: Compact Mass Spectrometry – A Complete Reaction Monitoring Solution

• Learn different sample techniques and ionization methods  based on your compounds

• See how prep-free, 30 second analysis can benefit your lab

• Find out how an optimized flow chemistry tool for fast reaction monitoring can take some burden off high resolution instruments with long run times



Webinar: Self-Optimizing Flow Reactors, Chris Horbaczewskyj, University of Leeds

• Learn advantages and disadvantages of both batch and flow chemistry

• Find out how on-line analytics within continuous flow chemistry allow reactions to be monitored in real-time allowing immediate characterization and the ability to optimize



Application Note: Real-Time Reaction Monitoring of a Solution-Phase Peptide Synthesis using the Plate Express and expression TLC/CMS

• Read how a combination of thin-layer chromatography (TLC) and compact mass spectrometry (CMS) is a simple and quick way for chemists to overcome synthetic challenges and optimize chemical reactions

• Learn how peptides of pharmaceutical interest can be readily synthesized following a rapid, continuous solution-phase synthesis strategy




Application Note: Analysis of Two Reaction Products by Direct Analysis Probe on a Compact Mass Spectrometer

• Find out how, with one swipe, a liquid or solid can be introduced in to the mass spec for reaction monitoring results in seconds

• Read how the ASAP with the CMS is used in identification of the products of a reaction where two products are possible




Application Note: Suzuki Reaction Monitoring Using Compact Mass Spectrometry with TLC Interface

• Learn how anonline thin-layer chromatography TLC/CMS technique using the Advion expression compact mass spectrometer (CMS) and Plate Express™ interface tcan provide compound structural information without sample preparation after TLC separation




Publication: A Novel Internet-Based Reaction Monitoring, Control and Autonomous Self-Optimization Platform for Chemical Synthesis (Open Access)

• Learn how the expression CMS was integrated in to a new workflow developed by the University of Cambridge Ley Lab that offers a modular software system that enables researchers to monitor and control chemical reactions via the Internet, using any device from any location in the world




Publication: Controlling an organic synthesis robot with machine learning to search for new reactivity (Open Access)

• Using the Advion expression Compact Mass Spectrometer and developments in robotics and AI, learn how chemical reactions can be performed faster than they can be performed manually. Not only is speed a benefit, the development also can predict the reactivity of possible reagent combinations after conducting only a small number of experiments




BONUS SOFTWARE WEBINAR: New Developments in Mass Spectrometry – Peak Express

• Find out if you made your compound with a new type of mass spectrum: the Delta Spectrum (ΔS). The patented ΔS is able to look beyond chemical noise and automatically detect even the smallest peaks without knowing the m/z

• How to easily find adducts, dimers, fragments, side-reactions and other unexpected compounds at the click of a button, in real-time or with post-processing

• How to use Peak Express software to highlight minor components in complex mixtures and dirty matrices, and can give you the ability to control mass-directed purification without providing the compound mass

• How to easily acquire XIC-quality data while scanning the entire mass range, allowing Peak Express™ to tell you the m/z


AI robot mixes chemicals to discover reactions – publication and video

Publication Alert: Controlling an organic synthesis robot with machine learning to search for new reactivity
Jarosław M. Granda, Liva Donina, Vincenza Dragone, De-Liang Long, and Leroy Cronin / Nature, Published online 2018 Jul 18

Using the Advion expression Compact Mass Spectrometer and developments in robotics and AI, learn how chemical reactions can be performed faster than they can be performed manually. Not only is speed a benefit, the development also can predict the reactivity of possible reagent combinations after conducting only a small number of experiments.

Video Alert: Not only was this development published in Nature, but a video featuring the system at work is also available:

Reporter Adam Levy talks to chemist Lee Cronin about his team’s search1 for new chemical reactions.

“It’s very difficult when you ask a chemist in the lab to go discover something. It’s a bit like asking someone to go in a boat now and find a new continent,” Cronin said.

Join our Webinar: Self-optimising Continuous Flow Reactors

Join us for a webinar with Chris Horbaczewskyj from the University of Leeds and Jack Henion, Advion’s Chief Scientific Founder on Thursday, April 26, 2018. Chris is working on the self-optimisation of continuous flow reactions using online mass spectrometry. Continuous flow and process optimisation are relatively new methods involved in chemical synthesis. This webinar outlines the workflow of the Bourne group at the University of Leeds for process development applications.

Register for this webinar to learn more!

Self-Optimising Continuous Flow Reactors Webinar

Join us for a Webinar with Chris Horbaczewskyj of the University of Leeds and Jack Henion, Advion’s Chief Scientific Founder, on Thursday, April 26, 2018 at 10am EST / 3PM GMT.

This presentation outlines the work carried out within the Bourne group at the University of Leeds for process development applications:

  1. Use of flow chemistry with online HPLC in the self-optimisation of reactions
  2. Use of online mass spectrometry for the optimisation of continuous flow reactions using an experimental design approach
  3. The development of new algorithms for multiple variable optimisation in chemical systems