METABOLOMICS IN 2015:

01//15

www.is-x.com

Renton (Ewan McGregor) // Trainspotting

LOVE IT OR LEAVE IT?

TABLE OF CONTENTS

Cover article News Pages 3-13

01 02Reflections Xtandards

Pages 14-17

03Network News ure X Pages 18-20

04News Flasha Pages 21-24

05Gadgets & Innovations Pages 25-33

PART 1

Cover article

4

THE OVER-EXAGGERATED HYPE

Metabolomics is often described as the study of

“the complete set of low molecular weight

intermediates, which are context dependent,

varying according to the physiology,

developmental or pathological state of the

cell, tissue, organ or organism”.

In fact, metabolomics is a new term for an old

science in which classical biochemical concepts

are investigated.

New and unique to the current research that is

being conducted is the combination with

genomics information and full system biology.

5

The molecules involved in metabolic analysis are

chemically very diverse, consisting of a broad

range of polarities, chemistries and size.

Additionally, metabolites are present at a wide

range of concentrations within a particular

sample.

These two facts, next to the large number of

metabolites that have to be detected

comprehensively in certain metabolic

experiments, contribute to the major challenges of

performing this type of analyses and studies.

OR NOT?

6

METABOLITE TYPES

Primary metabolite

Directly involved in normal growth,

development and reproduction.

Strongly conserved among species.

Secondary metabolite

Not directly involved in normal

growth, development and

reproduction. The absence of

secondary metabolites does not

result in immediate death, rather in

long term impairment of the

organism’s survivability. Secundary

metabolites are often restricted to

a narrow set of species within a

phylogenetic group. They often

occur in low concentrations.

There are estimated to be approximately 2.000 primary metabolites in humans with this number increasing by 10-fold or more if secondary metabolites are considered as well.

“

7

RESEARCH AREAS

Target compound analysis:

Carried out to determine and quantify specific

metabolites of interest in a consistent & accurate

manner.

Metabolite profiling:

Used to determine, qualitatively or quantitatively, a

group of related compounds or associated specific

metabolic pathways, such as carbohydrates, amino acids,

etc.

Metabolomics:

Comprehensive analysis of the whole metabolome under

a given set of conditions. Carried out quantitatively as

well as semi-quantitatively.

Metabolomic fingerprinting:

Metabolic fingerprinting is not aimed at the identification

of individual compounds but rather at the comparison of

patterns or fingerprints of metabolites and how they

change in response of disease or exposure to toxins.

Indicative

²²²

Accurate, validated & reliable

8

DISCUSSION

Critical to obtaining valid metabolomic data is understanding the question

behind a study. This means knowledge of and/or hypotheses on the metabolic

pathways that could be involved in the particular question under investigation.

Once these hypotheses are described and particular metabolites have been

identified, it is much easier to develop analytical procedures that accurately

target these analytes. For example, many secondary metabolites are easier to

analyze by LC/MS methods whereas most primary metabolites can readily be

quantified by GC/MS. In the same respect, it is evenly important to identify the

chemical classes of compounds that should be targeted, because this has a

determining influence on the analytical strategy that is finally opted for.

Metabolomics has to be considered an extension of classical target-driven analytical chemistry.

“

?

9

DISCUSSION

The identification of metabolites must always be based on at least two orthogonal physicochemical

characteristics, such as retention index and mass spectrum. Identifications that are based on authentic

chemical standards are generally more trustworthy than annotations based on calculated characteristics.

Nevertheless, the metabolome itself is an unrestricted entity that clearly comprises more than the suite of

known compounds to be found in classical textbooks or that can be purchased from chemical

manufacturers. The metabolome cannot be simply computed from reconstructed biochemical pathways

due to enzymatic diversity, substrate ambiguity and variation in regulatory mechanisms. The sheer

complexity of natural products, including isomeric compounds, renders the use of accurate masses and

database queries often insufficient for correct metabolite annotation.

 

Quality control is important.

This means that short as well as long-term influence of matrix effects is carefully evaluated. Only if

quantification of a range of well-known target metabolites validates a specific analytical protocol, can

unbiased analysis be furthered to the level of metabolomics and comprise novel metabolite signals.

QC/QA has to include randomized sample sequences, blank controls and bracketing samples with external

calibration standards.

0 25 50 75 100 125 1500

50

100

150

200

250

300

Comparison of smoker’s and non smoker’s breath

Acetone Ethanol Isoprene AcetonitrileTime / seconds

Con

cent

ratio

n / p

pb

Non smoker Smoker

WHAT CAN WE DO FOR YOU?

Selected-ion Flow Tube MS

SIFT-MS is a dedicated MS technique that uses

soft chemical ionization with three reagent ions in

a flow tube. The technique is particularly well

suited for real-time analysis of volatile compounds

(organic as well as inorganic) without the need for

external calibration (absolute quantification).

We use SIFT-MS in exhaled breath analysis:

SCAN analysis: biomarker discovery

SIM analysis: in-situ quantitative analysis

of biomarkers

11

WHAT CAN WE DO FOR YOU?

GC/MSMS in full scan/SRM mode

Current state-of-the-art in GC/MSMS technology permits

quantitative target analysis of several hundreds of

compounds at ultratrace levels and with short cycle times.

Typical workflow:

 

Extraction/derivatization (methoxyamination +

silylation)

SCAN analysis: untargeted analysis; biomarker

discovery

autoSRM analysis: determination of MS/MS

transitions

SCAN/SRM: discovery & quantitative analysis

12

Automated Sample Preparation

Sample preparation for metabolomics is tedious, time-consuming and therefore highly prone to variability

induced errors.

A suite of modular Lego-type solutions exist that enable full automation of sample preparation prior to

GC/MS and LC/MS analysis.

Solutions include:

In-vial extraction

Two-phase derivatization

Centrifugation

Filtration

Solid phase extraction

…

WHAT CAN WE DO FOR YOU?

13

Data analysis

We provide training & consultancy in data analysis for biomarker

discovery.

Design of experiments (DOE)

Data pre-processing: smoothing, baseline correction,

normalization

Data alignment: peak warping

Comparative analysis: surface maps, peak matching, peak

picking

Statistical analylis: univariate and multivariate

WHAT CAN WE MEAN DO YOU?

PART 2

Reflections

SYFT LAB IN THE PICTURE

A couple of weeks ago a new Voice200 Ultra was installed in our laboratory in Breda. The new

instrument is not only equipped with a heated transfer line for standard VOC applications but also with

the new swab desorber interface for introducing semi-volatile components into the instrument. The new

Voice200 Ultra combines state-of-the-art SIFT-MS technology with optimized sample introduction

hardware for demanding applications at PPT levels.

These multidisciplinary studies have been initiated in the wake of the new installation:

Geographical differentiation of olive oils

Analysis of residual solvents in contaminated soils

Direct measurement of printer emissions

Monitoring of apple sauce production

Analysis of beer aroma

Analysis of plant emissions when treated with biocides

PAL ARROW – A NEW TYPE OF SPME ANALYSIS

Since its development by Belardi and Pawliszyn in 1989, Solid

Phase Microextraction (SPME) has become one of the most

popular extraction technologies for environmental, food and

health analyses. However, the technique remained almost

unchanged with some significant drawbacks, such as the limited

mechanical stability and small phase volumes of the fibers. All

attempts to overcome these limitations have until now been a

trade-off between versatility and labor-intense handling. With the

PAL SPME Arrow we present a new technology for micro-

extraction, offering trace level sensitivity combined with high

mechanical robustness. The PAL SPME Arrow features an outer

diameter of max. 1.5mm, which allows the enclosure of a large

sorption phase volumes with a highly resistant and stabilizing

inner rod. The arrow-shaped tip allows smooth penetration of vial

septa and injector. In contrast to traditional SPME fibers, the

Arrow design fully protects the sorptive material, minimizing

adverse influences and loss of analytes during transfer processes.

PAL HEATEX STIRRER

The efficient mixing of reagents is required for many operations in

the laboratory, like sample homogenization, the dissolving of solids

or liquid/liquid extraction. For the efficient headspace analysis of

liquid samples a rapid exchange between the liquid and the gas

phase (headspace) is required. Often magnetic stirrers are applied

to achieve mixing. However, especially at higher speeds stir bars

tend to loose contact to the magnet and stop turning. This

problem is aggravated when solids are added to the sample liquid

which is common practice, e.g. the addition of salts to the liquid to

shift the equilibrium. Furthermore stir bars make autosampling

cumbersome since a bar has to be added to every sample vial

manually. Vortex mixers offer effective stirring, but cannot be used

for SPME sampling.

The powerful PAL Heatex Stirrer mixes samples rapidly applying

cycloid shaped mixing pattern without the need for stir bars. For

SPME headspace and immersion sampling the special design (pat.

pending) ensures that the delicate fiber is not damaged.

PART 3

Network news

http://www.ncbi.nlm.nih.gov/pubmed/25549013

IMDO @ VUB PUBLISHES FIRST SIFT-MS ARTICLE

The IMDO group of Prof De Vuyst at VUBrussels has published their first peer reviewed SIFT-MS article.

The article discussed the set-up they have designed for on-line monitoring of fermentation processes. The

feasibility of this technique was demonstrated using the case of the production of ethanol during

sourdough fermentation. The potential of SIFT-MS as an online monitoring device for food fermentations

was further demonstrated by the detection of acetoin in certain sourdough fermentations. This allowed

discrimination between sourdough fermentation processes and illustrated the importance of real-time

monitoring of food fermentations.

In their recent publication, Vergeynst, Van Langenhove and Demeestere discuss the use of

modern high-resolution MS for full spectrum trace level analysis of emerging environmental

organic contaminants.

Modern HRMS raises the opportunity for post-acquisition suspect screening when no reference standards

are a priori available. When setting up a conventional screening identification train based on successively

different identification criteria including mass error and isotope fit, the false negative rate typically

accumulates upon advancing through the decision tree. The challenge is thus to elaborate a well-balanced

screening, in which the different criteria are equally stringent, leading to a controllable number of false

negatives.

Presented is a novel suspect screening approach using liquid-chromatography Orbitrap HRMS. Based on

a multivariate statistical model, the screening takes into account the accurate mass error of the mono

isotopic ion and up to three isotopes, isotope ratios, and a peak/noise filter. As such, for the first time,

controlling the overall false negative rate of the screening algorithm to a desired level (5% in this study)

is achieved. Simultaneously, a well-balanced identification decision is guaranteed taking the different

identification criteria as a whole in a holistic statistical approach.http://pubs.acs.org/doi/abs/10.1021/ac503426k

HIGH-RESOLUTION MS

PART 4

News flash

TRACE DETECTION OF ENDOGENOUS VOCFOR SEARCH & RESCUE APPLICATIONS

Since Pauling's paper in the 1970s, interest has

increased in volatile organic compounds (VOCs)

released from different bio-fluids, such as skin,

breath, blood and urine. A number of VOCs reflect

internal biochemical pathways occurring in the

human body and their chemical pattern may serve

as the chemical platform for tracing human VOCs.

Monitoring endogenous human VOCs is proposed

as an alternative method to the use of canines for

search, rescue and emergency applications.

Tracing humans VOCs requires robust, rapid,

reliable and sensitive analytical instruments.

Instrumentation currently used to study human

VOC biomarkers (e.g. GC-MS, PTR-MS, SIFT-MS,

MCC-IMS, FAIMS and sensor based systems) has

significant clinical potential, but has yet to receive

widespread consideration for emergency search

applications.

http://www.sciencedirect.com/science/article/pii/S0165993615000199

Product ion yields for a suite of hydrocarbons associated with motor vehicle exhaust including alkenes,

alkanes, cycloalkanes, and aromatic compounds are reported for a PTR-MS instrument operated at an

E/N ratio of 80 and 120 Td. At 120 Td many of the compounds tested underwent dissociative proton

transfer reactions complicating the interpretation of the vehicle exhaust mass spectrum. However at 80

Td most aromatic and alkene compounds tested yielded M + H product ions at near 100% yield and alkyl

substituted cyclohexanes and C9-C12 branched alkanes yielded M-H ions as the major product ion. The

PTR-MS response factors to dimethyl and trimethyl cyclohexane compounds were about a third of that

expected if they reacted at the collisional rate limit with H3O+. Analysis of gasoline at 80 Td showed that

the major peaks in the mass spectrum could be reasonably accounted for from known hydrocarbon

abundance and their product ion yields, including the alkyl substituted cyclohexane compounds which

yielded M-H ions at m/z 97, 111, and 125. Operation at lower E/N ratios would enable the PTR-MS to

measure alkyl substituted cyclohexanes and larger alkane compounds in urban air at their M-H product

ion.

http://www.sciencedirect.com/science/article/pii/S1387380615000196

PTR FRAGMENTATION OF GASOLINE

Recently, thermally-assisted hydrolysis and methylation followed by gas chromatography–mass

spectrometry (THM–GC–MS) in combination with chemometrics has been used to develop a 20-compound

model for fast differentiation of Mycobacterium tuberculosis (MTB) from Non-tuberculous mycobacteria

(NTM) in bacterial cultures. This model provided better than 95% accuracy. In our current work a

hexane/methanol/water extraction followed by a solid phase extraction (SPE) clean-up procedure was

developed for use before THM–GC–MS, to make the test suitable for the identification of mycobacteria in

sputum. The 20 biomarker model had to be adapted since many compounds were also found in the

sputum of non-tuberculosis patients. An algorithm was established based on tuberculostearic acid,

hexacosanoic acid and mycoserosates.

http://www.sciencedirect.com/science/article/pii/S1570023215000914

DIRECT DETECTION OF MYCOBACTERIUM TUBERCULOSIS IN SPUTUM

The detection limit of the method was

approximately 1 × 104 bacteria/mL sputum.

Sputum specimens from 32 patients from South

Africa who were suspected of having tuberculosis

were blindly tested using the new method. Eight

of the nine culture-positive sputum specimens

were detected by the new SPE–THM–GC–MS

method, resulting in a sensitivity of 89%. The

specimen that was missed by the new method was

also microscopy negative.

PART 5

Gadgets & innovations

BACTERIA CAN’T CLING TO NEW NANOSURFACE

http://www.futurity.org/bacteria-biofilm-nanopores-838502/

Bacteria can’t stick to a new type of nanoscale surface that could prove useful in food processing,

medical, and shipping industries. The technology uses an electrochemical process called anodization to

create nanoscale pores that change the electrical charge and surface energy of a metal surface, which in

turn exerts a repulsive force on bacterial cells and prevents attachment and biofilm formation. Whereas a

sheet of paper is about 100,000 nanometers thick, these pores can be as small as just 15 nanometers.

When the researchers applied the anodization process to aluminum, it created a nanoporous surface

called alumina, which proved effective in preventing surrogates of two well-known pathogens, Escherichia

coli O157:H7 and Listeria monocytogenes, from attaching, according to the study in Biofouling. The study

also investigates how the size of the nanopores changes the repulsive forces on bacteria.

It’s probably one of the lowest-cost possibilities to manufacture a nanostructure on a metallic surface,” says senior author Carmen Moraru, professor of food science at

Cornell University.

“

In this publication the authors present a proof-of-concept demonstration of an all-printed temporary

tattoo-based glucose sensor for noninvasive glycemic monitoring. The sensor represents the first example

of an easy-to-wear flexible tattoo-based epidermal diagnostic device combining reverse iontophoretic

extraction of interstitial glucose and an enzyme-based amperometric biosensor. In-vitro studies reveal the

tattoo sensor’s linear response toward physiologically relevant glucose levels with negligible

interferences from common coexisting electroactive species. The iontophoretic-biosensing tattoo platform

is reduced to practice by applying the device on human subjects and monitoring variations in glycemic

levels due to food consumption. Correlation of the sensor response with that of a commercial glucose

meter underscores the promise of the tattoo sensor to detect glucose levels in a noninvasive fashion.

Control on-body experiments demonstrate the

importance of the reverse iontophoresis operation and

validate the sensor specificity. This preliminary

investigation indicates that the tattoo-based

iontophoresis-sensor platform holds considerable

promise for efficient diabetes management and can be

extended toward noninvasive monitoring of other

physiologically relevant analytes present in the

interstitial fluid.http://pubs.acs.org/doi/abs/10.1021/ac504300n

TATTOO-BASED NONINVASIVE MONITORING

CALL CENTERS REPLACED BY WHATSAPP

Haptik is a mobile messaging assistant from India which enables customers to receive real-time support

and information for over 200 international companies, including American Express, BMW, British Airways

and many more. Users begin by downloading the app to their smartphone or tablet. They then send a

query to Haptik via the WhatsApp-style platform and an assistant will respond within six minutes. The

platform’s experts — who specialize in specific areas such as wireless and telecom or food and delivery —

offer a huge range of services from finding a mobile plan, to locating a nearby ATM, to troubleshooting a

customer’s IT problem. Users simply browse the categories in the app to see if Haptik can help with their

particular problem. As more companies come on board, potential services offered will continue to expand.

http://www.wired.com/2015/01/getac-v110/

LAPTOP BUILT FOR MILITARY BEATDOWNS

“Ruggedness” is about more than just surviving stress tests. It’s about performing when there’s every

excuse not to, and that’s just what Getac’s ultra-rugged, nearly indestructible V110 convertible PC does.

With an array of essential crunch-time features and improved performance and functionality over its

predecessor, Getac’s V110 is something of a must-have for anyone whose worksite conditions skew

toward the extreme. Weighing just 4.6 pounds (relatively light; rugged notebooks usually weigh between

7 and 10 pounds), the V110 sports a 11.6-inch display and a full-size mechanical keyboard. The machine

also doubles as a tablet—the touchscreen swivels around and folds down flat. There are many

convertibles out there, but this one’s built to be virtually fail-proof in high-pressure environments. Hard

knocks and occasional drops are dispelled by the magnesium alloy chassis and shock-absorbing rugged

polymers and hardened rubbers. Spills can’t harm it—the ports and modules are all sealed behind hinged

door-flaps, and the keyboard is sealed by a membrane that’s fully waterproof.

http://www.springwise.com/smart-acupuncture-pen-checks-vitamins/

SMART PEN CHECKS VITAMINE LEVELS

Vitastiq allows anyone to track their vitamin and mineral levels through a handheld device and app that

blends scientific data with thousands of years of acupuncture wisdom. The device itself is a consumer-

friendly handheld electrode which enables users to examine their vitamin levels and spot deficiencies

before physical symptoms occur. It plugs straight into the headphone socket of any smartphone and

works by sending a small electrical current through acupuncture points on the user’s body. This may

sound painful, but it isn’t. In fact, it’s a standard element of the EAV — electroacupuncture —

methodology, which has been used worldwide for over 20 years.

When people press the Vitastiq against their skin, the data is logged to the user’s smartphone

through the free app, where they can monitor up to 30 changing vitamin and mineral requirements.

An in-app tutorial guides users through the relevant reading spots one at a time to ensure they get

an accurate and complete reading of the body.

http://www.springwise.com/smart-handlebars-haptic-feedback-enable-screen-free-navigation/

SMART HANDLEBARS USE HAPTIC FEEDBACK TO ENABLE SCREEN-FREE NAVIGATION

The humble bicycle may be one of our oldest forms of transport but it is also one the greenest and most

fulfilling ways to get from A to B. The relative simplicity of its structure has recently made it ripe for

additional smart features and add-ons. We have already seen Merge from New York and COBI from

Germany attempt to offer cyclists the “ultimate” bike. Now, smrtGRiPs is a three-in-one bike upgrade that

can make any bike smarter, safer and easier to locate. Users insert a pair of smrtGRiPs into their

handlebars and connect them with their smartphone via bluetooth. Haptic and audible feedback guide

cyclists through their journey safely without the need for screens or taking their eyes off the road. The

handlebars vibrate to indicate left and right turns and separation alerts can inform cycling partners if

someone has been left behind. The connected app can also be used to locate missing bikes in a busy bike

rack by making the handlebars ring with the “ring your ride” feature, and if a bike is stolen the app

notifies the crowdGPS network to be on the lookout.

SMART PATCH LAUNCHES CROWDFUNDING CAMPAIGN

STEMP was designed to solve issues related to thermometers currently on the market, especially those

designed for small children and their parents, who comprise a large share of first-time thermometer

consumers. Especially when you have children that get sick, STEMP is a great way to continuously

monitor your child’s temperature continuously by simply putting the STEMP on with the provided patch.

It syncs to your smart phone so you can collect data, see trends, and make smarter decisions, over hours,

days, or even weeks (one charge lasts up to 30 days). You can even share the information with your

healthcare provider in the cloud.

http://www.springwise.com/green-computer-server-heats-homes-free/

GREEN SERVER HEATS HOMES FOR FREE

By turning servers into electrical heaters for homes, Nerdalize does not need the building and expensive

cooling equipment normal datacenters need. Not using a building and cooling systems adds up to about

60% in savings! The beauty of our idea is that our servers get just as warm as a normal heater, so we can

heat the homeowner’s house with them. In return for allowing us to do that we pay for the homeowner’s

heating bill. This way computing users get affordable computing power and homeowners get a free

heating bill.

Hope you enjoyed it.Please keep sharing.

More atwww.is-x.com