Pawel L. Urban

National Tsing Hua University | NTHU · Department of Chemistry

Background: Psoriasis is a chronic, immune-mediated inflammatory skin disease. Screening skin metabolites could unravel the pathophysiology of psoriasis and provide new diagnostic approaches. Due to the lack of suitable methodologies for collecting scarce amounts of skin excretions, the psoriatic skin metabolome has not been extensively studied....

We describe a biochemical timer composed of three biocatalytic reactions involving three types of adenylate nucleotides: adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP). The timer is triggered by a small amount of ATP or ADP. An abrupt increase in the ATP concentration (following numerous amplification c...

Chemistry-related procedures often involve a substantial investment of manual work. Automated procedures have been developed to reduce the burden of sample processing and analysis. Here, we demonstrate an automated system for sequential sample processing and delivery to a mass spectrometer. This new platform—referred to as RAMSAY-2—incorporates two...

Studies of protein folding often involve offline experimental methods such as titrating protein samples with denaturants or equilibrating them in the presence of denaturants. Here, we demonstrate an online analytical approach in which the protein structure is perturbed by a pH ramp evoked by immobilized lipase-catalyzed ester hydrolysis. Changes in...

Conventional sensing methods report on concentrations of analytes in a single point of sampled medium or provide an average value. However, distributions of substances on surfaces of sampled objects often exhibit intricate inhomogeneities. In order to obtain snapshots of the chemical distributions on surfaces, we have developed enzyme-loaded hydrog...

Ion-mobility (IM) separations-performed in conjunction with mass spectrometry (MS)-increase selectivity of MS analyses. However, IM-MS instruments are costly, and many laboratories are only equipped with standard MS instruments without an IM separation stage. Therefore, it is appealing to upgrade the existing mass spectrometers with low-cost IM sep...

A facile and rapid skin metabolomics protocol is proposed. The liquid microjunction-surface sampling probe system has been partly automated, and used in conjunction with hydrogel probes for skin metabolite analysis. A control device was built to precisely control the segmented solvent flow and analyte re-extraction into the liquid microjunction. Th...

Skin metabolites show huge potential for use in clinical diagnostics. However, skin sampling and analysis workflows are tedious and time-consuming. Here, we demonstrate a vending-machine-style skin excretion sensing platform based on hydrogel-assisted sampling of skin metabolites. In this sensing platform, a sampling probe with hydrogel is held by...

Enzyme kinetics is normally assessed by performing individual kinetic measurements using batch-type reactors (test tubes, microtiter plates), in which enzymes are mixed with different substrates. Some drawbacks of conventional methods are the large amounts of experimental materials, long analysis times, and limitations of spectrophotometry. Therefo...

One of the main factors affecting protein structure in solution is pH. Traditionally, to study pH-dependent conformational changes in proteins, the concentration of the H+ ions is adjusted manually, complicating real-time analyses, hampering dynamic pH regulation, and consequently leading to a limited number of tested pH levels. Here, we present a...

Fizzy extraction (FE) is an extraction technique that extracts volatile organic compounds (VOCs) from liquid matrices using pressure-induced effervescence. The sudden decompression of a gas-saturated sample solution generates numerous microbubbles, which trap and transfer VOCs with different volatilities from the liquid phase into the headspace of...

Ion signals in electrospray ionization (ESI) mass spectrometry (MS) are affected by addition of acid or base. Acids or bases are typically added to samples to enhance detection of analytes in positive- or negative-ion mode, respectively. To carry out simultaneous monitoring of analytes with different ionogenic moieties by ESI-MS, a rapid acid/base...

Volatile organic compounds (VOCs) are omnipresent in daily life, industry, and science. Among many VOCs, some can affect the food quality while others are environmental pollutants. We previously developed a portable pen-probe ion-mobility spectrometry (IMS)-based analyzer for in situ detection of VOCs emanating from surfaces and wireless transmissi...

Electrospray ionization (ESI) mass spectrometry (MS) is one of the key techniques used in biomolecular analysis nowadays. It relies on formation of polydisperse microdroplets, which undergo desolvation and liberate ions to the gas phase. Here we demonstrate low-frequency-sound-modulated ESI for analysis of biomolecules. By using a low-frequency (50...

Fizzy extraction (FE) is a technique that utilizes effervescence phenomenon to extract volatile organic compounds (VOCs) from liquid matrices for subsequent analysis. To induce effervescence, a liquid sample is first pressurized (at ∼ 150 kPa) with an extractant gas (here, nitrogen), and then rapidly depressurized. In this work, we combine an in-ho...

Sweat analysis provides an alternative and noninvasive way of clinical diagnostics. However, sampling and transferring sweat-derived samples to analytical instruments is challenging. In this report, we demonstrate a method utilizing a flat disc-shaped sampling probe, and a compatible re-extraction apparatus coupled online with extractive electrospr...

Implementation of the Internet-of-Things in chemistry research has the potential to improve research methodologies. Here, we describe a cloud-integrated real-time laboratory monitoring system for: (i) monitoring reactions involving fluorescent chemical species, and (ii) monitoring laboratory environment for safety purpose. A probe-type fluorescence...

Analysis of volatile organic compounds (VOCs) is normally preceded by sample homogenization and solvent extraction. This methodology does not provide spatial resolution of the analyzed VOCs in the examined matrix. Here, we present a robotized pen-shaped probe for open-space sampling and mapping of VOCs emanating from solid specimens (dubbed "PENVOC...

The analysis of volatile organic compounds (VOCs) normally involves sample collection, sample transfer to laboratory, sample preparation, and the chromatographic separation of analytes. However, in some cases, it is impractical or impossible to collect samples prior to the analysis, while the analysis time has to be minimized. Ion mobility spectrom...

Skin retains numerous low-molecular-weight compounds (metabolites). Some of these compounds fulfill specific physiological roles, while others are by-products of metabolism. The skin surface can be sampled to detect and quantify skin metabolites related to diseases. Miniature probes have been developed to detect selected high-abundance metabolites...

Sample flow rate is one of the parameters that influence sensitivity of electrospray ionization (ESI) mass spectrometry. By varying sample flow rate, initial droplets of different size can be generated. Protein molecules in small droplets form gas-phase ions earlier than the ones in large droplets. Here, we have systematically studied the influence...

With the rapid development of high technology, chemical science is not as it used to be a century ago. Many chemists acquire and utilize skills that are well beyond the traditional definition of chemistry. The digital age has transformed chemistry laboratories. One aspect of this transformation is the progressing implementation of electronics and c...

This perspective highlights a malpractice in handling calibration datasets. It refers to relating analytical response with logarithm of concentration, fitting such a dataset with linear function, and deriving method characteristics from the slope of that function. A distinction is made between this malpractice and the proper use of logarithmic plot...

Background: Psoriasis is an inflammatory skin disease causing multisystem effects. Introduction of biologic drugs has led to promising results in treatment of this disease. Here, we carry out time-dependent profiling of psoriasis-related putative metabolic biomarkers. Methods: Skin excretion specimens were collected from 17 patients with psorias...

Discovery of new protein biomarker candidates has become a major research goal in the areas of clinical chemistry, analytical chemistry, and biomedicine. These important species constitute the molecular target when it comes to diagnosis, prognosis, and further monitoring of disease. However, their analysis requires powerful, selective and high-thro...

Since the advent of modern science, researchers have had to rely on their technical skills or the support of specialized workshops to construct analytical instruments. The notion of the ‘fourth industrial revolution’ promotes construction of customized systems by individuals using widely available, inexpensive electronic modules. This protocol show...

Extraction of volatile compounds from complex liquid matrices is a critical step in volatile compound analysis workflows. Recently, green chemistry principles are increasingly implemented in extraction processes. Some of the available approaches are solvent-free but still require concentration or trapping of analytes. Here, we propose effervescent...

Fizzy extraction (FE) facilitates analysis of volatile solutes by promoting their transfer from the liquid to the gas phase. A carrier gas is dissolved in the sample under moderate pressure (Δ p ≈ 150 kPa), followed by an abrupt decompression, what leads to effervescence. The released gaseous analytes are directed to an on-line detector due to a sm...

Simultaneous distillation-extraction (SDE) using Likens-Nickerson apparatus is a convenient technique used to isolate volatile organic compounds (VOCs) from complex liquid matrices. The technique combines steam distillation with solvent extraction. While analytical extractions are normally followed by off-line separation/detection, it is advantageo...

Sampling and extraction of chemical residues present on flat or curved surfaces as well as touch-sensitive objects are challenging. Hydrogels are characterized by high mechanical flexibility and water content. Thus, they are an ideal medium for transferring water-soluble analytes from a sampled surface to the next stage of an analytical workflow. H...

An acoustic wave-assisted microscale assay platform is demonstrated. Liquid droplets containing samples and reagents are dispensed and pinned onto a hydrophobic thread, and actuated by sound waves. The transport of droplets is achieved by modulating sound emitted by two sources. The resulting sound intensity gradient pushes the droplets in one dire...

The developments in mass spectrometry (MS) in the past few decades reveal the power and versatility of this technology. MS methods are utilized in routine analyses as well as research activities involving a broad range of analytes (elements and molecules) and countless matrices. However, manual MS analysis is gradually becoming a thing of the past....

We demonstrate an analytical approach to monitor the effect of pH on protein tertiary structure. An autocatalytic enzyme reaction is used to stimulate refolding of proteins during real-time analysis. The method takes advantage of a non-linear pH ramp generated by urea-urease clock reaction. In this study, alterations to the structures of model prot...

The implementation of most instrumental analysis methods requires a considerable amount of human effort at every step, including sample preparation, detection, and data processing. Automated analytical workflows decrease the amount of required work. However, commercial automated platforms are mainly available for well-established sample processing...

Fizzy extraction (FE) is carried out by first dissolving a carrier gas (typically, carbon dioxide) in a liquid sample at a moderate pressure (typically, 150 kPa) and then rapidly depressurizing the sample. The depressurization leads to instant release of numerous microbubbles in the liquid matrix. The abruptly released gas extracts the volatile sol...

Experimentation in chemistry normally involves manual handling of hazardous chemicals, and observing chemical transformations that occur within minutes, hours, or days. Nowadays, acquisition, exchange, and analysis of digital datasets are facilitated by the emerging technology called the Internet-of-Things (IoT). Chemists are also empowered to impl...

In order to expedite characterization of on-line detection systems, we have developed a flow rate scanner comprising a pump, an inexpensive single-board computer, and an associated Python program. The program controls the pump, triggers the detector, acquires raw data, filters/smooths the data, calculates the first derivative of the temporal signal...

Extraction of volatile organic compounds (VOCs) into a condensed phase requires maximizing the surface-to-volume ratio of the extracting medium. In the case of the solid-phase extracting media, the surface-to-volume ratio can be increased by implementing porous monoliths or particles with different size. In the case of the liquid-phase extracting m...

Growth of microorganisms is often accompanied by the release of volatile organic compounds (VOCs). The released VOCs may qualitatively or quantitatively reflect the physiological states of microbial cultures. A number of VOCs are produced during microbial degradation of organic matter accompanying food spoilage. In order to characterize the dynamic...

Kinetic optimization of continuous liquid-liquid extraction (CLLE) can shorten sample preparation times and reduce losses of labile or volatile analytes. Here, we coupled a downscaled CLLE apparatus with atmospheric pressure chemical ionization interface of triple quadrupole mass spectrometer. Real-time sampling was guided by an Arduino-based progr...

Most analytical methods are based on “analogue” inputs from sensors of light, electric potentials, or currents. The signals obtained by such sensors are processed using certain calibration functions to determine concentrations of the target analytes. The signal readouts are normally done after an optimised and fixed time period, during which an ass...

Open‐source electronics and programming can augment chemical and biomedical research. Currently, chemists can choose from a broad range of low‐cost universal electronic modules (microcontroller boards and single‐board computers) and use them to assemble working prototypes of scientific tools to address specific experimental problems and to support...

Open‐source electronics and programming can augment chemical and biomedical research. Currently, chemists can choose from a broad range of low‐cost universal electronic modules (microcontroller boards and single‐board computers) and use them to assemble working prototypes of scientific tools to address specific experimental problems and to support...

The purpose of analytical extractions is to simplify sample matrix without losing analyte molecules. Here we present a technique of extracting volatile compounds by scavenging gas-phase molecules with tiny liquid droplets (<10 μm). A cool mist of the extracting solvent is generated by an ultrasonic transducer, transferred to the headspace of the sa...

The temporal effects of luciferase reaction luminescence have only been discussed in the context of light intensity (flash vs. glow). However, alterations in the color of the light emitted over the course of the luciferase reaction have not been reported. Here, we show a temporal change in the light color emitted during the reaction catalyzed by un...

Chemical analysis of volatile and semivolatile compounds dissolved in liquid samples can be challenging. The dissolved components need to be brought to the gas phase, and efficiently transferred to a detection system. Fizzy extraction takes advantage of the effervescence phenomenon. First, a carrier gas (here, carbon dioxide) is dissolved in the sa...

Chemical analysis of complex matrices—containing hundreds of compounds—is challenging. Two-dimensional separation techniques provide an efficient way to reduce complexity of mixtures analyzed by mass spectrometry (MS). For example, gasoline is a mixture of numerous compounds, which can be fractionated by distillation techniques. However, coupling c...

Sampling the skin surface is a convenient way to obtain biological specimens bearing clinically relevant information. Hydrogel micropatches enable non-invasive collection of skin excretion specimens, which can subsequently be subjected to rapid mass spectrometric analysis providing insights into the skin metabolome.

The twentieth century has brought enormous developments in instrumentation for chemical analysis. However, most of the state-of-the-art analytical instruments still require a substantial investment of human labor. In the twenty first century, some laboratories need to analyze thousands of samples every day, at the same time maintaining high repeata...

Dilution is one of the common chemical procedures, which are carried out in all chemistry laboratories - to prepare standard solutions with different concentrations for assay calibration, and to reduce matrix effects while handling complex samples. Yet dilution is mostly performed manually using large-volume manual liquid-handling tools (volumetric...

Gasometric assays involve measurements of the amounts of gases that are released during physical or chemical processes. The available instrumentation for gasometric analysis is generally difficult to use, and requires large sample volumes. In some cases, toxic materials (mercury) are involved in the analysis process. Here we propose a microscale ga...

The development of sensitive and versatile mass spectrometric methodology has fuelled interest in the analysis of metabolites and drugs in unconventional biological specimens. Here, we discuss the analysis of eight human matrices—hair, nail, breath, saliva, tears, meibum, nasal mucus and skin excretions (including sweat)—by mass spectrometry (MS)....

Mass spectrometry (MS) is a mainstream chemical analysis technique in the twenty-first century. It has contributed to numerous discoveries in chemistry, physics and biochemistry. Hundreds of research laboratories scattered all over the world use MS every day to investigate fundamental phenomena on the molecular level. MS is also widely used by indu...

Extraction of volatile and semi-volatile compounds from liquid matrices with high yields, and transferring the extracts to detectors in real time, is challenging. Common extraction procedures involve heating the samples to release the analytes to the gas phase, and – in some cases – trapping the gas-phase analytes into sorbents or containers. Here,...

Biocatalytic reactions often require supplying chemical energy and phosphate groups in the form of adenosine triphosphate (ATP). Auxiliary enzymes can be used to convert a reaction by-product-adenosine diphosphate (ADP)-back to ATP. By employing real-time mass spectrometry (RTMS), one can gain an insight into inter-conversions of reactants in multi...

Liposomes and cells have high lipid contents, which are the main components of the external and internal membranes. Mass spectrometry (MS) is widely used in the analysis of the lipids present in the biological matrices. However, MS analysis of liposome and cell suspensions is challenging due to the presence of other high-abundance matrix components...

This commentary discusses differences between the so-called “mass sensitivity” and “concentration sensitivity”. These terms are freely used in analytical chemistry literature to characterize operation of analytical techniques and methods. The type of sensitivity in an analytical method delimits the method’s applications (e.g., in analysis of volume...

Microbial cells are known to form aggregates. Such aggregates can be found in various matrices; for example, functional drinks. Capillary hydrodynamic chromatography (HDC) enables separation of particles by size using nanoliter-scale volumes of samples. Here we propose an approach based on HDC for characterisation of real samples containing aggrega...

This chapter discusses the development of interfaces used to introduce dynamic samples to mass spectrometers for analysis with temporal resolutions that are adequate for the processes. Interfacing is vital for the operation of time-resolved mass spectrometry (TRMS), and it influences the quality of analysis output. The chapter provides examples of...

This chapter introduces the underlying principles behind frequently used mass analyzers and ion detectors. It also summarizes different hybrid instruments, which combine the advantages of different mass analysis techniques. Four types of individual mass analyzer are introduced in the order of increasing spectrum acquisition time (SAT). These are ti...

This chapter addresses the basic aspects of time-resolved mass spectrometry (TRMS) in physical chemistry studies. It presents a few important representative examples, which highlight the usefulness of TRMS in solving various physical chemistry problems. Based on timescales, physical chemistry problems can be grouped qualitatively into two categorie...

The main goal of data treatment in conventional mass spectrometry (MS) is to facilitate identification and quantification of analytes. The focus of time-resolved mass spectrometry (TRMS) is to track variations of identities and quantities of analytes and products over time. This chapter first introduces definitions of various technical terms of mas...

Mass spectrometry (MS) is a prime tool for chemical characterization of various matrices. Therefore, it is appealing to extend the current mass spectrometric toolkit to enable analysis of temporal properties of dynamic samples without losing chemical information. Various mass spectrometric techniques facilitate time-resolved mass spectrometry (TRMS...

The color illustrations for Chapters 2, 6, 12 and 13 are included, as follows: Figures 2.15, 2.8, 2.18 Figure 6.4 Figures 12.3, 12.5 Figures 13.1, 13.8 Figures 2.15, 2.8, 2.18 Figure 6.4 Figures 12.3, 12.5 Figures 13.1, 13.8

A vast number of conventional physicochemical methods are suitable for the analysis of homogeneous samples. However, in various cases, the samples exhibit intrinsic heterogeneity. Tomography allows one to record approximate distributions of chemical species in the three-dimensional space. Here we develop a simple optical tomography system which ena...

Micropatch-arrayed pads (MAPAs) are presented as a facile and sensitive sampling method for spatial profiling of topical agents adsorbed on the surface of skin. MAPAs are 28 × 28 mm sized pieces of polytetrafluoroethylene containing plurality of cavities filled with agarose hydrogel. They are affixed onto skin for 10 min with the purpose to collect...

Most real samples cannot directly be infused to mass spectrometers because they could contaminate delicate parts of ion source and guides, or cause ion suppression. Conventional sample preparation procedures limit temporal resolution of analysis. We have developed an automated liquid-liquid extraction system that enables unsupervised repetitive tre...

A simple format for microscale chemical assays is proposed. It does not require the use of test tubes, microchips or microtiter plates. Microlitre-range (ca. 0.7 – 5.0 μL) aqueous droplets are generated by commercial micropipette in a non-polar matrix inside a Petri dish. When two droplets are pipetted nearby, they spontaneously coalesce within sec...

Soxhlet extraction is a popular sample preparation technique used in chemical analysis. It enables liberation of molecules embedded in complex matrices (for example, plant tissues, foodstuffs). In most protocols, samples are analyzed after the extraction process is complete. However, in order to optimize extraction conditions and enable comparisons...

In order to ascertain optimum conditions for biocatalytic processes carried out in vitro, we have designed a bio-opto-electronic system which ensures real-time compensation for depletion of adenosine triphosphate (ATP) in reactions involving transfer of phosphate groups. The system covers ATP concentration range of 2-48 μM. The report demonstrates...

Digital microfluidics (DMF) based on the electrowetting-on-dielectric phenomenon is a convenient way of handling microlitre-volume aliquots of solutions prior to analysis. Although it was shown to be compatible with on-line mass spectrometric detection, due to numerous technical obstacles, the implementation of DMF in conjunction with MS is still b...

This minireview discusses universal electronic modules (generic programmable units) and their use by analytical chemists to construct inexpensive, miniature or automated devices. Recently, open-source platforms have gained considerable popularity among tech-savvy chemists because their implementation often does not require expert knowledge and inve...

This commentary presents an unconventional view of analytical chemistry as seen through the prism of “name concepts”. First, I provide examples of various analytical methods and phenomena that are referred to by the names of their inventors/discoverers. Second, I suggest that emphasizing name concepts in the analytical chemistry course syllabus can...

Mass spectrometry (MS) is an important analytical technique with numerous applications in clinical analysis, biochemistry, environmental analysis, geology and physics. Its success builds on the ability of MS to determine molecular weights of analytes, and elucidate their structures. However, sample handling prior to MS requires a lot of attention a...

The origin of life on Earth has been the subject of inquiry since the early days of philosophical thought. The main questions are centred around the formation of protocells capable of metabolism and replication. Research studies have been carried out to simulate the conditions on early Earth. They led to a proposal that the first cells could have e...

Various processes in chemistry lead to formation of spatial gradients, and cannot be directly studied using conventional spectroscopic techniques. Here we aimed to develop a simple method for the monitoring of light absorption at three wavelengths in two dimensions. The experimental setup consists of a commercial liquid crystal display (LCD) comput...

Probiotic drinks constitute an important component of the daily diet in the modern society. They contain active microbial strains, which contribute to the chemical composition of these dairy products. The metabolic activity of microbes can affect the flavor and smell of probiotic drinks at room temperature. “Kefir” is an example of fermented milk,...

Gas chromatography (GC) is frequently used in qualitative and quantitative analysis of volatile organic molecules. In its most common embodiment, samples are prepared in the laboratory, and injected into the capillary column using an autosampler. Analytes are separated, and detected by one of several available detection systems, including mass spec...

This technology report discusses the possibility of using open-source electronic platforms to enhance technology-oriented training of chemistry students at the undergraduate and graduate level. It is anticipated that the increasing availability of open-source microcontrollers and programming tools can be helpful while teaching students the principl...

Adequate sample treatment is critical when employing mass spectrometry (MS) in the analyses of complex biological matrices. Despite various improvements, it is generally difficult to automate the process of preparing solid biological samples for MS analysis. Here we demonstrate a facile approach for automation of the whole analysis (from an untreat...

It is of great economical and practical significance to distinguish between different classes, brands, and places of origin of commercial tea. Herein, an analytical method has been developed to characterize samples of oriental teas (with an emphasis on Taiwanese teas). It is based on the implementation of liquid chromatography coupled with mass spe...

Mass spectrometry has been implemented as an on-line detection tool to monitor transmission of chemical signals due to natural processes such as diffusion and convection as well as a bienzymatic autocatalytic process. It was found that the enzyme-accelerated chemical wave propagates faster than the chemical wave propelled by other processes. The tw...

Interrogating three-dimensional structures of biomolecules is instrumental to the fields of biochemistry and biophysics. Mass spectrometry is a technique that can provide important data on the molecular weight of protein molecules in the gas phase. However, the relationship between the structure of biomolecules in the native water-rich environment...

In order to investigate metabolic properties of single cells of freshwater algae (Haematococcus pluvialis), we implement matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) in combination with microspectroscopic mapping. Straightforward coupling of these two detection platforms was possible thanks to the self-aliquoting propert...