Gerstel Dynamic Headspace Sampler

Last month our new Agilent GC-MS was installed! Shortly after it was commissioned I had to watch nervously as the Gerstel engineer cut bits out of it so that he could enhance it further with a new Dynamic Headspace Sampling [DHS] system, including Thermal Desorption Unit [TDU] and Cooled Injection System [CIS]. This was dramatic but very rewarding as we now have the first and only DHS system in New Zealand.


DHS is a very sophisticated way of getting all of the volatile compounds out of a solid or liquid sample and into a GC-MS. It uses the same principle as static headspace analysis but, instead of just injecting a volume of the headspace or using an SPME fibre to trap the volatile components, DHS uses a flow of gas (your choice of helium, nitrogen or air) through the vial’s headspace to continuously remove volatiles from the headspace and collect them on a sorbent trap. The sorbent trap is then transferred to the TDU and the volatiles desorbed onto the CIS for analysis. The whole process is automated and highly customisable. Because volatiles are constantly removed from the headspace you can capture the entire volatile component from a given sample, making the technique much more sensitive than SPME and a massive step beyond static headspace analysis.

The applications for this technology are primarily in the field of food science, where flavour and fragrance volatiles are common characterisation targets. Gerstel have some more elaborate suggestions for applications, which interest me more, such as the characterisation of volatiles emitted by brown marmorated stink bugs. This application note describes how you can put a live animal into the DHS vial to analyse its volatile profile in vivo! The procedure seems entirely harmless to the subjects (beyond the mild irritation they might experience from being confined within a glass vial), providing volatiles are extracted at ambient temperatures using air.

Screenshot from 2016-07-14 21:50:01

Another very useful new technique which is available to anyone with a TDU is Thermal Extraction [TE]. This can be applied to solid or liquid samples placed inside the glass TDU tubes. In practice you can use TE to analyse almost anything, providing you can get it into the tiny glass tubes. So far I have analysed lyophilised lamb meat and abalone tissue, a tissue snip from a snapper ovary, honey and even a piece of a leaf. My new PhD student is now applying the technique to the desorption of PAHs from particulate filters to characterise the prevalence of these notorious carcinogens in the air around New Zealand and in his native Rwanda.


Making Size Exclusion Chromatography columns

My summer student, Kalita, has been digesting oligosaccharides, derivatising them and injecting them into the mass spectrometers in an effort to derive structural information from these complex molecules. We had hoped to use acrylamide gel electrophoresis to visualise the performance of our digests, in the way of Pomin et al (2005).

Screenshot from 2016-03-03 20:30:41.png

This figure from the paper shows the effect of their hydrolysis technique upon the molecular weight of the oligomer. Note the banding patterns resulting from selective hydrolysis of certain glycosidic bonds. This produces a regular reduction in size of the fragments. We wanted to use this feature to produce polymeric fragments in the <10kDa size rage. These would be amenable to LC-MS/MS, as in Lang et al (2014), allowing us to infer the sequence, functionalisation and bonding of the monomers within the oligomer.

As it turned out our acrylamide gels got lost somewhere amidst The Great Bureaucracy and so, with time running out we cast around for alternate technologies. Enter Yang, et al (2009), who used a similar technique in their paper, but also deployed Size Exclusion Chromatography to illustrate the size-class of fragments produced.

Screenshot from 2016-03-03 21:11:31.png

The thing is we didn’t have any GPC or SEC columns.  😦


So we decided to try making our own!  😀


Fortunately or chemical store had a shelf of old bottles of dextran and other GPC or ion-exchange substrates. We dug up a protocol from an MSc thesis by Wilfred Mak in which he’d used an anion exchange substrate to determine the molecular weight of intact sulfated fucan oligosaccharides, rifled through the stores to find some substrates that looked about right and away we went!

We started out with a biuret:


At the bottom, hidden by the blue compression screw, is a plug of deactivated glass wool with a few mL of sand on top of that and then the white dextran gel. This was the first addition of substrate and settling. After topping it up we have a column of about 40cm length. This type of column is purely gravity-fed. You add sample and running buffer at the top and wait for the head of fluid to pass through the column, collecting fractions through the tap at the bottom. This can take hours.

While Kalita was putting this together I was looking at some of the old silica particle LC columns I had and wondering if I might dismantle them, remove the packing and repack them with the dextran to give a real, high-pressure column. This could be plumbed into one of our conventional LC setups, allowing us to push samples through at a faster rate and giving the option of automated sample injection, data and fraction collection. I had something of a brain wave and realised that I had some Swagelok fittings which would allow me to fit a piece of 1/4″ polypropylene air line with pressure-tight caps and LC fittings at either end to fulfil exactly that function. A couple of hours later Kalita and I were the proud parents of monstrous creation on the left!


The white tube held between the two clamps on the left hand retort is the air line packed with hydrated dextran. The line at the top comes from the Shimadzu LC pump on the right, which is pumping Tris buffer through the column to settle the packing material. We can get a flow of 2 mL/min through the column with a back pressure of about 5 bar. Plenty for LC!

For now our creation is parked until we can get round to doing something cool with it on Monday but watch this space to see the outcome. Our intention is to add an autosampler to the front for sample injection, a Refractive Index Detector and maybe even an electrochemical detector on the outflow to detect what came off the column and possibly even a fraction collector for downstream LC-MS/MS analysis of the fractions! Fun!

Our first goal is to validate the SEC function by injecting a range of proteins stained with Bradford Reagent. We can also try some di- and tri-saccharides along with our oligo digests.


References cited

Lang et al (2014). Applications of Mass Spectrometry to Structural Analysis of
Marine Oligosaccharides. Mar. Drugs 2014, 12, 4005-4030

Pomin et al (2005). Mild acid hydrolysis of sulfated fucans: a selective 2-desulfation reaction and an alternative approach for preparing tailored sulfated oligosaccharides. Glycobiology vol. 15 no. 12 pp. 1376–1385, 2005

Yang et al (2009). Mechanism of mild acid hydrolysis of galactan polysaccharides with highly ordered disaccharide repeats leading to a complete series of exclusively odd-numbered oligosaccharides. FEBS Journal 276 (2009) 2125–2137

Bee hive mass logger

11-03-2016: This project hit a problem. See update at the bottom.

Following on from my bathroom scales hack I spent this evening sawing and screwing together the platform for it to sit on. This was an urgent task as the bee hive is being moved to a new location tomorrow and so this would be an ideal opportunity to get the scales in place without having to arrange another movement of the hive. Bees are incredibly precise creatures, I am discovering. If you move their hive a just a few meters away when foragers are out, they will return to the location they are familiar with and won’t be able to find their way home! If beekeepers have to move their hives such a short distance they’ll move them a couple of kilometers away for a week and then move them to the new spot.

The scales will sit on a plywood deck raised off the roof’s surface to provide a thermal insulation gap for the hive. I drew up the rough schematic below to illustrate this.

beehive mass monitor schematic

My final design was slightly different, with the pallet being a little smaller than the plywood shelf. This is because, as well as the four strips of ply that keep the shelf securely fitted over the scales, I also added a plywood curtain around the edge of the shelf that hung down below the pallet to prevent rain being driven in to the scales. The ply is 12mm and very solid. I sized it to be ever so slightly smaller than the footprint of the hive so that it will fit perfectly on top. Here’s some build pics:

shelf (upside down), scales, pallet


scales on the pallet


This next one is upside down but illustrates how the four strips of ply keep the top shelf secure. You can also see the curtains. The notches at the back are for wires to exit.


final assembly



Looking forward to testing this!


Update, 11-03-2016

Unfortunately there is a major flaw with my design. When Matt went to put the bee hive on top of it it turned out to be unstable due to the small footprint of the scales relative to the hive. The hive is only one box at the moment but Matt intends to add another soon and that would definitely make it vulnerable to being blown over by a gust of wind! Not a desirable situation. I am going to have to look at designing a larger platform to the corners of which I can attach the load cells. This is contrary to the advice on the MakeZine blog that inspired this project, however I cannot see any other solution besides buying an industrial-size set of scales. I want to try the DIY option first before I spend a couple of hundred dollars.

Hacking bathroom scales with an HX711 breakout

Hopefully this will be the start of a series of posts on the Internet of Bees, or the #IOBee. In case you didn’t realise, this is a play on the Internet of Things, or IoT. My intent with the IOBee is to document my application of some basic sensor technology to monitoring the health of bee hives.

There is an excellent writeup here of a conversion of a set of luggage scales to a real-time bee hive mass monitor. I have been wondering if I can do the same thing to monitor the mass of experimental bee hives in some research I’m planning looking at the effects of neonicotinoids upon honey bee colonies. In order to test this out I ventured onto eBay and bought a couple of HX711 breakouts, which you can get for just a couple of dollars.

HX711 breakout

I also bought a cheap set of bathroom scales from the Warehouse, despite the advice on MakeZine, which advised not to skimp. I intended this to be a proof-of-concept so I wasn’t going to be spending big bucks just yet.

bathroom scales

This turned out to be an excellent hacking subject. After taking the back off I found a circuit board carrying the integrated circuit, some components and some wires.


The two black pads you can see are the rubber feet on the bottom of the load cells. I prised one out to show you the other side.


The red white and blue wires coming from each of the four load cells needed to be joined together carefully according to the first image in this excellent post on StackExchange that I located after a modest amount of googling. I also found this how-to from SparkFun to be informative.

Once I had soldered the blue and white wires together to mimic the pattern shown and the red ones to the appropriate pads on the HX711 breakout I was left with this:


I also soldered the wires from a length of USB cable from an old mouse to the other side of the breakout. The four tabs and their wires were to VCC (red), GND (black), CLK (white) and SDA (green). I drilled a hole in the plastic chassis to pass the cable through and put a cable tie around it on the inside to prevent the wires being pulled off the board. The mount holes in the breakout board ( I love mount holes!) happened to be just the right width to allow me to screw it to the chassis through two of the holes that the original PCB was mounted on. The white thing is a piece of polyethylene milk bottle wall that I cut out and used to insulate the connections of the breakout and to hold it down as the screw heads were nearly as small as the holes. This arrangement allowed the breakout to be seen through the glass window where the LCD used to be. A nice touch. 😀


Having wired everything together I needed an electronic brain for my creation to talk to so I hooked it up to the Arduino Nano I’ve been using as a receiver for my solar-powered, wireless monitoring testbed. Ignore the BME280 and the NRF24 coming off it. VCC went to 5V, GND to GND, SCK to D4 and SDA to D5.


I downloaded the HX711 library written by bogde (thanks!) and also the HX711 breakout sketches from the SparkFun how-to linked above. I was pretty impressed to see numbers appear straight away on the serial monitor although this turned to mild disappointment when I placed a mass on the scales and the number went negative! Apparently I had got the polarity of the signal wires the wrong way around. 😦

Five minutes of soldering later I was back reading numbers and this time they went up with the mass on the scales. According to the instructions on the test sketch I kept adjusting the calibration factor until the scales read the correct mass for the object I’d put on it. Then came the acid test: now it was calibrated, would it get my mass right?


As you can see it worked almost perfectly. And I am somewhat overweight. :-/

A useful edit I made to the SparkFun code was to change the line

Serial.print(scale.get_units(), 1);


Serial.print(scale.get_units(), 3);

This gave me three decimal places instead of one and significantly more information. I was particularly pleased to see that these scales read quite consistently. The numbers for my weight jump about quite a lot because I wasn’t too worried about keeping still to get a stable reading but when I placed a fixed mass on the scales the second decimal place was pretty stable and only the third flicked up and down by 1-3 units. These scales were advertised as being accurate to +/- 100g so my results indicate I can do much better than that. And that’s without any of the tricks you can use with microprocessors to improve the accuracy of otherwise low resolution tools, such as polling them and taking a moving average.

More on the application of this very cool hack another day, once I’ve validated the calibration as described on MakeZine.

Jake Martin’s Citizen Science Spectrophotometer

Jake Martin was an MSc student at the University of Auckland School of Chemical Sciences, now a PhD candidate at Cambridge University in the UK. Jake has developed a simple spectrophotometer– a device which measures the transmittance or absorbance of light at specific wavelengths- made from lasercut plastic and a handful of electronic components. Jake has been kind enough to share his design with me because I have a background and ongoing professional interest in environmental monitoring. I am very impressed with the potential of this technology and am keen to promote it further to any public body or community interested in doing their own environmental monitoring.

Jake’s initial application was measuring nitrate concentration in water. This is a highly topical issue in New Zealand, where freshwater habitats have suffered significant degradation in recent years, often due to increasing nitrate inputsassociated with the expansion of dairy farming. The urine from thousands of cattle and the fertilisers used to stimulate pasture growth for them to graze on raises the concentration of nitrate and nitrite in streams, rivers, lakes, wetlands and groundwater. This causes nuisance algal and microbial growth, such as rock slime, phytoplankton and cyanobacteria blooms and periphyton growth. These compounds can also have sublethal and lethal effects upon animals if their concentrations rise high enough.

The ability for members of the public to go out and measure nitrogen concentrations in their own back yard is a huge step in connecting people and communities with their environments. It is also a valuable tool for farmers, many of whom are concerned about the consequences of nitrate emissions from their farms.  In order to develop practices to minimise fluxes of nitrate into freshwater habitats, such as planting riparian margins, farmers need to be able to measure it cheaply and rapidly.

Jake’s design is wonderfully simple anyone can pick it up in about two minutes. I am going to be demonstrating it and handing out free kits at the Sea Week 2016 event at Cornwallis on Saturday 5th March. Anyone who is interested in the quality of freshwater and marine habitats in New Zealand should come down and check it out. On the day we also hope to be able to show people how to measure phosphate concentrations and water turbidity, two other major water quality parameters that can indicate just how clean and safe your environment is.

I will present my testing of the spectrophotometer and a detailed how-to in another post.

nonstructural carbohydrates and FTIR

Non-structural carbohydrates [NSC] are important to tree growth and survival. Their quantification can be achieved by several analytical methodologies of varying accuracy. I am currently applying one of these – LC-MS – to elucidate the structure of algal oligosaccharides. However, these advanced analytical techniques require some fairly high-tech equipment and some careful sample preparation.

Recently it has been proposed that near-infrared spectroscopy can be used to quantify NSC with no sample preparation beyond homogenisation in a ball mill, or similar (Ramirez et al 2015). One of my students wants to try this method so I showed her how to put samples into the Fourier Transform InfraRed [FTIR] spectroscope. The referenced paper used a rigorous process of parallel biochemical analysis to determine the NSC content of the samples analysed and used these to determine the relationship between the NSC content and the FTIR properties. I have proposed a standard analytical process to eliminate this complex validation process, known as Standard Addition. Using this technique the student will add varying concentrations of the different NSC components to her samples and determine how this addition affects their FTIR properties. This should obviate the need to conduct biochemical or chemical analysis in parallel.



Ramirez et al, 2015: Near-infrared spectroscopy (NIRS) predicts non-structural carbohydrate concentrations in different tissue types of a broad range of tree speciesMethods in Ecology and Evolution 2015, 6, 1018–1025 doi: 10.1111/2041-210X.12391