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Analytical and Bioanalytical Chemistry (v.404, #4)
Andreas Römpp and Sabine Guenther win the ABC Best Paper Award
by Nicola Oberbeckmann-Winter; Andrea Pfeifer (pp. 923-925).
Student-driven independent research projects: developing a framework for success in analytical chemistry by Heather A. Bullen (pp. 927-930).
is an Associate Professor of Chemistry at Northern Kentucky University. She is committed to the education of students in the STEM (Science technology Engineering and Mathematics) disciplines and inspiring young girls to consider pursuing a degree in science; she has received several research and programmatic grants to support STEM students at NKU. Heather Bullen has an active undergraduate research program in bioanalytical and materials science, evaluating biofilm formation and the toxicity of nanoparticles for drug delivery applications. She is noted for her development of inquiry and problem based approaches to teaching analytical chemistry and is an associate editor of the Analytical Sciences Digital Library.
Quantitative mass spectrometry in proteomics by Marcus Bantscheff; Bernhard Kuster (pp. 937-938).
graduated in Chemistry from the University of Konstanz and obtained his PhD degree from the University of Rostock, working with Prof. Glocker on structure–function correlation of bacterial response regulator proteins utilizing mass spectrometric and protein chemistry methods. As a postdoctoral fellow at the Proteome Center in Rostock, Marcus was involved in setting up a proteomics unit and focused on the analysis of synovial fluids and tissue samples derived from rheumathoid arthritis patients and CIA mice. At Cellzome since 2002, Dr. Bantscheff’s research interests have focused on quantitative proteomics and chemoproteomic technologies. Marcus is an inventor on several patent applications including Cellzome’s Kinobeads™ and Episphere™ technologies, author of more than 30 publications in scientific journals including Nature Biotechnology, Nature, and Nature Chemical Biology. He is the editor of a chemoproteomics methods compendium and reviewer for a number of scientific journals. is a chemist by training and obtained an MSc in 1994 from the University of Cologne. He received his PhD in Biochemistry from the University of Oxford in 1997 and spent his PostDoc years with Matthias Mann at the European Molecular Biology Laboratory in Heidelberg and at the University of Southern Denmark in Odense, Denmark. Between 2000 and 2007, Professor Kuster held several positions at the biotech firm Cellzome, most recently that of VP Analytical Sciences and Informatics. In 2007, he was appointed Full Professor and Chair of Proteomics and Bioanalytics at the Technische Universität München, TUM where he is currently also the Head of the Department for Biosciences, an executive of the TUM graduate school Experimental Biomedicine and a member of the Excellence Cluster CIPSM. Professor Kuster is an inventor of several patent applications including Cellzome’s Kinobeads™ and has published more than 70 scientific articles in highly reputed journals. He also serves on the editorial and scientific advisory boards of several journals and university institutes. His current research interests include functional proteomics, chemical biology and cancer drug and biomarker discovery.
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present by Marcus Bantscheff; Simone Lemeer; Mikhail M. Savitski; Bernhard Kuster (pp. 939-965).
Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.
Keywords: Quantitative proteomics; Liquid chromatography; Mass spectrometry; Bioinformatics
The expanding field of SILAC by Shao-En Ong (pp. 967-976).
Stable isotope labeling by amino acids (SILAC) metabolically encodes cell populations for protein quantification by mass spectrometry. SILAC was introduced in 2002 and the field of mass spectrometry based proteomics has changed dramatically over the last decade. Increased sensitivity and speed of mass spectrometry instruments coupled with significantly improved mass resolution and precision have led to much higher rates of peptide identification and deeper coverage of proteomic samples. Several proteomics approaches are now available for quantifying proteins and their post-translational modifications, each with their strengths and weaknesses. The simplicity and robustness of SILAC have led to its widespread adoption and new applications have emerged that play to its particular strengths as a metabolic labeling approach.
Keywords: SILAC; Quantification; Proteomics; Mass spectrometry; Stable isotopes
QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification by Deborah M. Simpson; Robert J. Beynon (pp. 977-989).
Systems biology requires knowledge of the absolute amounts of proteins in order to model biological processes and simulate the effects of changes in specific model parameters. Quantification concatamers (QconCATs) are established as a method to provide multiplexed absolute peptide standards for a set of target proteins in isotope dilution standard experiments. Two or more quantotypic peptides representing each of the target proteins are concatenated into a designer gene that is metabolically labelled with stable isotopes in Escherichia coli or other cellular or cell-free systems. Co-digestion of a known amount of QconCAT with the target proteins generates a set of labelled reference peptide standards for the unlabelled analyte counterparts, and by using an appropriate mass spectrometry platform, comparison of the intensities of the peptide ratios delivers absolute quantification of the encoded peptides and in turn the target proteins for which they are surrogates. In this review, we discuss the criteria and difficulties associated with surrogate peptide selection and provide examples in the design of QconCATs for quantification of the proteins of the nuclear factor κB pathway. Figure Workflow for QconCAT mediated protein quatification
Keywords: Quantification concatamer; Multiplexed quantification; Absolute quantification; Nuclear factor κB
Applications of stable isotope dimethyl labeling in quantitative proteomics by Duangnapa Kovanich; Salvatore Cappadona; Reinout Raijmakers; Shabaz Mohammed; Arjen Scholten; Albert J. R. Heck (pp. 991-1009).
Mass spectrometry has proven to be an indispensable tool for protein identification, characterization, and quantification. Among the possible methods in quantitative proteomics, stable isotope labeling by using reductive dimethylation has emerged as a cost-effective, simple, but powerful method able to compete at any level with the present alternatives. In this review, we briefly introduce experimental and software methods for proteome analysis using dimethyl labeling and provide a comprehensive overview of reported applications in the analysis of (1) differential protein expression, (2) posttranslational modifications, and (3) protein interactions.
Keywords: Dimethyl labeling; Stable isotope labeling; Quantitative proteomics
An insight into iTRAQ: where do we stand now? by Caroline Evans; Josselin Noirel; Saw Yen Ow; Malinda Salim; Ana G. Pereira-Medrano; Narciso Couto; Jagroop Pandhal; Duncan Smith; Trong Khoa Pham; Esther Karunakaran; Xin Zou; Catherine A. Biggs; Phillip C. Wright (pp. 1011-1027).
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ’s attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground. Figure
Keywords: Shotgun proteomics; iTRAQ; Ratio underestimation; Relative quantification; MS/MS instrumentation; Isotopic impurities; Statistical validation; Modelling; PTMs; Label-free
Isobaric tagging approaches in quantitative proteomics: the ups and downs by Andy L. Christoforou; Kathryn S. Lilley (pp. 1029-1037).
Isobaric tagging has proven to be a popular quantitative proteomics tool and has been rapidly adopted to study a wide range of biological questions in the few years since its commercialization. While the flexibility and multiplexing capacity afforded by this technology are clear attractions, it is not without its shortcomings. As the speed and sensitivity of mass spectrometers have improved and the application of isobaric tags to all manner of biological systems has increased, significant issues with quantitative accuracy and precision have come to light. Here we review the issues associated with the use of isobaric tagging methods and discuss the possible solutions which have been proposed to improve their precision and accuracy to approach the levels required within quantitative proteomics.
Keywords: iTRAQ; Tandem mass tags; TMT; Isobaric tagging; Quantitative proteomics
Label-free quantification using MALDI mass spectrometry: considerations and perspectives by Amelie S. Benk; Christoph Roesli (pp. 1039-1056).
Profound knowledge of protein abundances in healthy tissues and their changes in disease is crucial for understanding biological processes in basic science and for the development of novel diagnostics and therapeutics. Mass spectrometrybased label-free protein quantification is used increasingly often to gain insights into physiological changes observed in perturbed systems. Although the soft ionization techniques electrospray ionization and matrix-assisted laser desorption/ionization have both been used for protein quantification, this article focuses on instrumental setups with a MALDI ion source. Beside reviewing current bioinformatic data-processing tools for label-free quantification and elaborating on the technical benefits of combining UHPLC and MALDI–MS, we outline the potential of state-of-the-art instruments by reporting unpublished results obtained from twenty-four complex biological samples. This review points out that the capabilities of LC–MALDI MS systems have not yet been fully utilized because of a lack of suitable software tools. Online Abstract Figure Graphical representation of the LC–MALDI–MS procedure for label-free protein quantification. Tryptic peptides are separated by reversed-phase ultra-high performance liquid chromatography and eluting fractions are mixed with matrix before robotic deposition on a MALDI target plate. Subsequent to analysis of each spot by MS1 and MS2, bioinformatic tools are used for the label-free protein quantification
Keywords: Proteomics; Ultra-high performance liquid chromatography (UHPLC); Mass spectrometry; Matrix-assisted laser desorption/ionization (MALDI); Protein quantification; Label-free
Advancing formaldehyde cross-linking towards quantitative proteomic applications by Cordula Klockenbusch; Jane E. O’Hara; Juergen Kast (pp. 1057-1067).
Formaldehyde is a key fixation reagent. This review explores its application in combination with qualitative and quantitative mass spectrometry (MS). Formalin-fixed and paraffin-embedded (FFPE) tissues form a large reservoir of biologically valuable samples and their investigation by MS has only recently started. Furthermore, formaldehyde can be used to stabilise protein–protein interactions in living cells. Because formaldehyde is able to modify proteins, performing MS analysis on these samples can pose a challenge. Here we discuss the chemistry of formaldehyde cross-linking, describe the problems of and progress in these two applications and their common aspects, and evaluate the potential of these methods for the future.
Keywords: FFPE; Formaldehyde cross-linking; Protein–protein interactions; Mass spectrometry
Towards a human proteomics atlas by Giulia Gonnelli; Niels Hulstaert; Sven Degroeve; Lennart Martens (pp. 1069-1077).
Proteomics research has taken up an increasingly important role in life sciences over the past few years. Due to a strong push from publishers and funders alike, the community has also started to freely share its data in earnest, making use of public repositories such as the highly popular PRIDE database at EMBL-EBI. Reuse of these publicly available data has so far been confined to rather specific, targeted reanalyses, but this limited reuse is set to expand dramatically as repositories continue to grow exponentially. Examples of large-scale reuse are readily found in other omics disciplines, where more comprehensive public data have already accumulated over longer periods. Here, a typical example of integrative data reuse is provided by the construction of so-called expression atlases. We here therefore investigate the issues involved in using the human data currently stored in the PRIDE database to construct a robust, tissue-specific protein expression atlas from tandem-MS based label-free quantification.
Keywords: Proteomics; Bioinformatics; Mass spectrometry; Quantification
Improving the precision of quantitative bottom-up proteomics based on stable isotope-labeled proteins by Anna Konopka; Martin E. Boehm; Marion Rohmer; Dominic Baeumlisberger; Michael Karas; Wolf D. Lehmann (pp. 1079-1087).
Stable isotope dilution-based quantitative proteomics with intact labeled proteins as internal standards in combination with a bottom-up approach, i.e., with quantification on the peptide level, is an established method. To explore the technical precision of this approach, calmodulin-like protein 3 was prepared in non-labeled (light) and SILAC-type labeled (heavy) form by cell-free synthesis, mixed, digested with trypsin, and analyzed by UPLC-ESI-MS. In total, 16 light/heavy peptide pair ratios were determined. Pair-wise comparison of ratios of 12 peptides selected according to S/N ratios >50 revealed that the majority exhibited ratios, which were different at a high level of statistical significance (p < 0.001). HPLC-MALDI-MS ratio data confirmed this observation, thus excluding the ionization method as a source of the observed ratio differences. Variation of the digestion time from 0.25 to 4 h showed that the light/heavy ratios of most peptides decrease with time, indicating a kinetic isotope effect leading to preferred cleavage of light calmodulin-like protein 3. The subset of peptides with statistically identical ratios resulted in an average ratio with a RSD of 1.0 %. The light/heavy ratio calculated on the basis of these peptides probably provides the most accurate molar protein ratio.
Keywords: Peptides; Quantitative proteomics; Kinetic isotope effects; Stable isotope dilution
Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins by Andrew J. Percy; Andrew G. Chambers; Juncong Yang; Dominik Domanski; Christoph H. Borchers (pp. 1089-1101).
The analytical performance of a standard-flow ultra-high-performance liquid chromatography (UHPLC) and a nano-flow high-performance liquid chromatography (HPLC) system, interfaced to the same state-of-the-art triple-quadrupole mass spectrometer, were compared for the multiple reaction monitoring (MRM)-mass spectrometry (MS)-based quantitation of a panel of 48 high-to-moderate-abundance cardiovascular disease-related plasma proteins. After optimization of the MRM transitions for sensitivity and testing for chemical interference, the optimum sensitivity, loading capacity, gradient, and retention-time reproducibilities were determined. We previously demonstrated the increased robustness of the standard-flow platform, but we expected that the standard-flow platform would have an overall lower sensitivity. This study was designed to determine if this decreased sensitivity could be compensated for by increased sample loading. Significantly fewer interferences with the MRM transitions were found for the standard-flow platform than for the nano-flow platform (2 out of 103 transitions compared with 42 out of 103 transitions, respectively), which demonstrates the importance of interference-testing when nano-flow systems are used. Using only interference-free transitions, 36 replicate LC/MRM-MS analyses resulted in equal signal reproducibilities between the two platforms (9.3 % coefficient of variation (CV) for 88 peptide targets), with superior retention-time precision for the standard-flow platform (0.13 vs. 6.1 % CV). Surprisingly, for 41 of the 81 proteotypic peptides in the final assay, the standard-flow platform was more sensitive while for 9 of 81 the nano-flow platform was more sensitive. For these 81 peptides, there was a good correlation between the two sets of results (R 2 = 0.98, slope = 0.97). Overall, the standard-flow platform had superior performance metrics for most peptides, and is a good choice if sufficient sample is available. Figure Optimization of sample loading on a standard- and b nano-flow systems; c comparison of plasma protein concentrations determined by both systems
Keywords: Nano-flow; Standard-flow; Plasma; Stable isotope labeling; Multiple reaction monitoring; Quantitative proteomics
Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL) by Christian J. Koehler; Magnus Ø. Arntzen; Achim Treumann; Bernd Thiede (pp. 1103-1114).
Isobaric peptide termini labeling (IPTL) is a quantification method which permits relative quantification using quantification points distributed throughout the whole tandem mass spectrometry (MS/MS) spectrum. It is based on the complementary derivatization of peptide termini with different isotopes resulting in isobaric peptides. Here, we use our recently developed software package IsobariQ to investigate how processing and data analysis parameters can improve IPTL data. Deisotoping provided cleaner MS/MS spectra and improved protein identification and quantification. Denoising should be used with caution because it may remove highly regulated ion pairs. An outlier detection algorithm on the ratios within every individual MS/MS spectrum was beneficial in removing false-positive quantification points. MS/MS spectra using IPTL typically contain two peptide series with complementary labels resulting in lower Mascot ion scores than non-labeled equivalent peptides. To avoid this penalty, the two chemical modifications for IPTL were specified as variables including satellite neutral losses of tetradeuterium with positive loss for the heavy isotopes and negative loss for the light isotopes. Thus, the less dominant complementary ion series were not considered for the scoring, which improved the ion scores significantly. In addition, we showed that IPTL was suitable for fragmentation by electron transfer dissociation (ETD) and higher energy collisionally activated dissociation (HCD) besides the already reported collision-induced dissociation (CID). Notably, ETD and HCD data can be identified and quantified using IsobariQ. ETD outperformed CID and HCD only for charge states ≥4+ but yielded in total fewer protein identifications and quantifications. In contrast, the high-resolution information of HCD fragmented peptides provided most identification and quantification results using the same scan speed.
Keywords: CID; ETD; HCD; Isobaric labeling; IPTL; IsobariQ; MS/MS; Quantitative proteomics
Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines by Yao-Yi Chen; Surendra Dasari; Ze-Qiang Ma; Lorenzo J. Vega-Montoto; Ming Li; David L. Tabb (pp. 1115-1125).
Spectral counting has become a widely used approach for measuring and comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly affects the assessment of peptide and protein inventories, differentiation, and quantification. Meanwhile, the configuration of database searching algorithms that assign peptides to MS/MS spectra may produce different results in comparative proteomic analysis. Here, we present three strategies to improve comparative proteomics through spectral counting. We show that comparing spectral counts for peptide groups rather than for protein groups forestalls problems introduced by shared peptides. We demonstrate the advantage and flexibility of this new method in two datasets. We present four models to combine four popular search engines that lead to significant gains in spectral counting differentiation. Among these models, we demonstrate a powerful vote counting model that scales well for multiple search engines. We also show that semi-tryptic searching outperforms tryptic searching for comparative proteomics. Overall, these techniques considerably improve protein differentiation on the basis of spectral count tables.
Keywords: Label-free comparative proteomics; Spectral counting; Combining database search engines
Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples by Scott J. Geromanos; Chris Hughes; Steven Ciavarini; Johannes P. C. Vissers; James I. Langridge (pp. 1127-1139).
To accurately determine the quantitative change of peptides and proteins in complex proteomics samples requires knowledge of how well each ion has been measured. The precision of each ions’ calculated area is predicated on how uniquely it occupies its own space in m/z and elution time. Given an initial assumption that prior to the addition of the “heavy” label, all other ion detections are unique, which is arguably untrue, an initial attempt at quantifying the pervasiveness of ion interference events in a representative binary SILAC experiment was made by comparing the centered m/z and retention time of the ion detections from the “light” variant to its “heavy” companion. Ion interference rates were determined for LC-MS data acquired at mass resolving powers of 20 and 40 K with and without ion mobility separation activated. An ion interference event was recorded, if present in the companion dataset was an ion within ± its Δ mass at half-height, ±15 s of its apex retention time and if utilized by ±1 drift bin. Data are presented illustrating a definitive decrease in the frequency of ion interference events with each additional increase in selectivity of the analytical workflow. Regardless of whether the quantitative experiment is a composite of labeled samples or label free, how well each ion is measured can be determined given knowledge of the instruments mass resolving power across the entire m/z scale and the ion detection algorithm reporting both the centered m/z and Δ mass at half-height for each detected ion. Given these measurements, an effective resolution can be calculated and compared with the expected instrument performance value providing a purity score for the calculated ions’ area based on mass resolution. Similarly, chromatographic and drift purity scores can be calculated. In these instances, the error associated to an ions’ calculated peak area is estimated by examining the variation in each measured width to that of their respective experimental median. Detail will be disclosed as to how a final ion purity score was established, providing a first measure of how accurately each ions’ area was determined as well as how precise the calculated quantitative change between labeled or unlabelled pairs were determined. Presented is how common ion interference events are in quantitative proteomics LC-MS experiments and how ion purity filters can be utilized to overcome and address them, providing ultimately more accurate and precise quantification results across a wider dynamic range. Fig In-line ion mobility increases peak capacity and spatial resolution. Ion purity scoring provides a measure of uniqueness. Together they enhance the precision and accuracy of quantitative change across a wider dynamic range.
Keywords: LC-MS; Proteomics; Label free; SILAC; Ion mobility; Ion purity scoring
Glycoprotein analysis using mass spectrometry: unraveling the layers of complexity by John E. Schiel (pp. 1141-1149).
A glycoprotein exists as a heterogeneous mixture of forms due to differential glycosylation, each of which may confer different functionality and/or serve as a biochemical marker for disease. The complex structure of glycans make them a bioanalytical challenge requiring multiple mass spectrometry based approaches to gain different types of information. The following article will briefly describe recently utilized mass spectrometry methods to identify glycosylation sites and measure glycan composition, sequence, branching, and relative quantities. Potential metrological developments are discussed in light of current trends toward complete, reliable glycoanalytical characterization in a high-throughput manner.
Keywords: Glycoprotein; Glycan; Mass spectrometry; Standards; Reference material
Advances in field-flow fractionation for the analysis of biomolecules: instrument design and hyphenation by Samantha Schachermeyer; Jonathan Ashby; Wenwan Zhong (pp. 1151-1158).
Field-flow fractionation (FFF) separates analytes by use of an axial channel-flow and a cross-field. Its soft separation capability makes it an ideal tool for initial fractionation of complex mixtures, but large elution volumes and high flow rates have limited its applicability without significant user handling. Recent advances in instrumentation and miniaturization have successfully reduced channel size and elution speed, and thus the volume of each fraction, making it possible to conveniently couple FFF with orthogonal separation techniques for improved resolution. More detailed analysis can also be performed on the fractions generated by FFF by use of diverse analytical techniques, including MS, NMR, and even X-ray scattering. These developmental trends have given FFF more power in the analysis of different types of molecule, and will be the direction of choice for further advances in FFF technology.
Keywords: Field-flow fractionation; Instrument design; Hyphenation; Miniaturization
Accurate mass measurements and their appropriate use for reliable analyte identification by A. Ruth Godfrey; A. Gareth Brenton (pp. 1159-1164).
Accurate mass instrumentation is becoming increasingly available to non-expert users. This data can be mis-used, particularly for analyte identification. Current best practice in assigning potential elemental formula for reliable analyte identification has been described with modern informatic approaches to analyte elucidation, including chemometric characterisation, data processing and searching using facilities such as the Chemical Abstracts Service (CAS) Registry and Chemspider. Figure Enhancement of peak (mass) resolution for data acquired using a double focussing magnetic sector mass spectrometer.
Keywords: Accurate mass measurement; Mass accuracy and precision; Statistics for mass measurement; Fragmentation map/tree; High resolution; Database searching
Quantitative NMR for bioanalysis and metabolomics by Gregory A. Barding Jr.; Ryan Salditos; Cynthia K. Larive (pp. 1165-1179).
Over the last several decades, significant technical and experimental advances have made quantitative nuclear magnetic resonance (qNMR) a valuable analytical tool for quantitative measurements on a wide variety of samples. In particular, qNMR has emerged as an important method for metabolomics studies where it is used for interrogation of large sets of biological samples and the resulting spectra are treated with multivariate statistical analysis methods. In this review, recent developments in instrumentation and pulse sequences will be discussed as well as the practical considerations necessary for acquisition of quantitative NMR experiments with an emphasis on their use for bioanalysis. Recent examples of the application of qNMR for metabolomics/metabonomics studies, the characterization of biologicals such as heparin, antibodies, and vaccines, and the analysis of botanical natural products will be presented and the future directions of qNMR discussed.
Keywords: qNMR; Bioanalysis; Isotope enrichment; Metabonomics; Metabolomics; Natural products; Biofluids; Tissues; HR-MAS
Affinity and enzyme-based biosensors: recent advances and emerging applications in cell analysis and point-of-care testing by Ying Liu; Zimple Matharu; Michael C. Howland; Alexander Revzin; Aleksandr L. Simonian (pp. 1181-1196).
The applications of biosensors range from environmental testing and biowarfare agent detection to clinical testing and cell analysis. In recent years, biosensors have become increasingly prevalent in clinical testing and point-of-care testing. This is driven in part by the desire to decrease the cost of health care, to shift some of the analytical tests from centralized facilities to “frontline” physicians and nurses, and to obtain more precise information more quickly about the health status of a patient. This article gives an overview of recent advances in the field of biosensors, focusing on biosensors based on enzymes, aptamers, antibodies, and phages. In addition, this article attempts to describe efforts to apply these biosensors to clinical testing and cell analysis. Figure Biosensor for Point of care
Keywords: Biosensor; Enzyme; Aptamers; Phage; Point of care
Monitoring automotive oil degradation: analytical tools and onboard sensing technologies by Adnan Mujahid; Franz L. Dickert (pp. 1197-1209).
Engine oil experiences a number of thermal and oxidative phases that yield acidic products in the matrix consequently leading to degradation of the base oil. Generally, oil oxidation is a complex process and difficult to elucidate; however, the degradation pathways can be defined for almost every type of oil because they mainly depend on the mechanical status and operating conditions. The exact time of oil change is nonetheless difficult to predict, but it is of great interest from an economic and ecological point of view. In order to make a quick and accurate decision about oil changes, onboard assessment of oil quality is highly desirable. For this purpose, a variety of physical and chemical sensors have been proposed along with spectroscopic strategies. We present a critical review of all these approaches and of recent developments to analyze the exact lifetime of automotive engine oil. Apart from their potential for degradation monitoring, their limitations and future perspectives have also been investigated. Figure Onboard assessment of oil quality: the sensors and spectroscopic strategies proposed for this are reviewed
Keywords: Engine oil degradation; Onboard sensing; Acidic products; Automotive sensors
Bioreactor monitoring with spectroscopy and chemometrics: a review by N. D. Lourenço; J. A. Lopes; C. F. Almeida; M. C. Sarraguça; H. M. Pinheiro (pp. 1211-1237).
Biotechnological processes are crucial to the development of any economy striving to ensure a relevant position in future markets. The cultivation of microorganisms in bioreactors is one of the most important unit operations of biotechnological processes, and real-time monitoring of bioreactors is essential for effective bioprocess control. In this review, published material on the potential application of different spectroscopic techniques for bioreactor monitoring is critically discussed, with particular emphasis on optical fiber technology, reported for in situ bioprocess monitoring. Application examples are presented by spectroscopy type, specifically focusing on ultraviolet–visible, near-infrared, mid-infrared, Raman, and fluorescence spectroscopy. The spectra acquisition devices available and the major advantages and disadvantages of each spectroscopy are discussed. The type of information contained in the spectra and the available chemometric methods for extracting that information are also addressed, including wavelength selection, spectra pre-processing, principal component analysis, and partial least-squares. Sample handling techniques (flow and sequential injection analysis) that include transport to spectroscopic sensors for ex-situ on-line monitoring are not covered in this review.
Keywords: In situ monitoring; Bioreactors; Spectroscopy; Chemometrics
Serum metabolomics as a novel diagnostic approach for disease: a systematic review by Aihua Zhang; Hui Sun; Xijun Wang (pp. 1239-1245).
Metabolomics is a promising “omics” field in systems biology; its objective is comprehensive analysis of low-molecular-weight endogenous metabolites in a biological sample. It could enable mapping of perturbations of early biochemical changes in diseases and hence provide an opportunity to develop predictive biomarkers that could result in earlier intervention and provide valuable insights into the mechanisms of diseases. Because of the possible discovery of clinically relevant biomarkers, metabolomics has potential advantages that routine approaches to clinical diagnosis do not. Monitoring specific metabolite levels in serum, the most commonly used biofluid in metabolomics, has become an important way of detecting the early stages of a disease. Serum is a readily accessible and informative biofluid, making it ideal for early detection of a wide range of diseases, and analysis of serum has several advantages over analysis of other biofluids. Metabolite profiles of serum can be regarded as important indicators of physiological and pathological states and may aid understanding of the mechanism of disease occurrence and progression on the metabolic level, and provide information enabling identification of early and differential metabolic markers of disease. Analysis of these crucial metabolites in serum has become important in monitoring the state of biological organisms and is widely used for diagnosis of disease. Emerging metabolomics will drive serum analysis, facilitate and improve the development of disease treatments, and provide great benefits for public health in the long-term.
Keywords: Metabolomics; System biology; Serum analysis; Metabolites; Biomarkers; Disease diagnostics
Potential of MALDI-TOF mass spectrometry as a rapid detection technique in plant pathology: identification of plant-associated microorganisms by Faheem Ahmad; Olubukola O. Babalola; Hamid I. Tak (pp. 1247-1255).
Plant diseases caused by plant pathogens substantially reduce crop production every year, resulting in massive economic losses throughout the world. Accurate detection and identification of plant pathogens is fundamental to plant pathogen diagnostics and, thus, plant disease management. Diagnostics and disease-management strategies require techniques to enable simultaneous detection and quantification of a wide range of pathogenic and non-pathogenic microorganisms. Over the past decade, rapid development of matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for characterization of microorganisms has enabled substantially improved detection and identification of microorganisms. In the biological sciences, MALDI-TOF MS is used to analyze specific peptides or proteins directly desorbed from intact bacteria, fungal spores, nematodes, and other microorganisms. The ability to record biomarker ions, in a broad m/z range, which are unique to and representative of individual microorganisms, forms the basis of taxonomic identification of microorganisms by MALDI-TOF MS. Recent advances in mass spectrometry have initiated new research, i.e. analysis of more complex microbial communities. Such studies are just beginning but have great potential for elucidation not only of the interactions between microorganisms and their host plants but also those among different microbial taxa living in association with plants. There has been a recent effort by the mass spectrometry community to make data from large scale mass spectrometry experiments publicly available in the form of a centralized repository. Such a resource could enable the use of MALDI-TOF MS as a universal technique for detection of plant pathogens and non-pathogens. The effects of experimental conditions are sufficiently understood, reproducible spectra can be obtained from computational database search, and microorganisms can be rapidly characterized by genus, species, or strain. Figure Schematic representation showing the MALDI-TOF mass spectrometry as detection technique in plant pathology. Recent advances in mass spectrometry have provided ways to characterize different plant-associated microorganisms. This technique is easy and rapid.
Keywords: Plant-associated microorganisms; Mass spectrometry; Protein biomarker; Identification
Magnetic techniques for the detection and determination of xenobiotics and cells in water by Ivo Safarik; Katerina Horska; Kristyna Pospiskova; Mirka Safarikova (pp. 1257-1273).
Magnetic techniques based on the application of magnetic nanoparticles and microparticles and films have been successfully used for the determination and detection of different types of xenobiotics (e.g. herbicides, insecticides, fungicides, aromatic and polyaromatic hydrocarbons, pentachlorophenol and heavy metal ions) as well as viruses, microbial pathogens and protozoan parasites in water samples. Preconcentration of xenobiotics from large volumes of samples can be performed using magnetic solid-phase extraction, stir-bar sorptive extraction and related procedures. This review provides basic information about these techniques. Published examples of successful applications document the importance of these simple and efficient procedures employing magnetic materials.
Keywords: Bioanalytical methods; Enzymes; Immunoassays/ELISA; Organic compounds; Water; Preconcentration