Recent advances in capillary separations for proteomics

The sequencing of several organisms' genomes, including the human's one, has opened the way for the so-called postgenomic era, which is now routinely coined as "proteomics". The most basic task in proteomics remains the detection and identification of proteins from a biological sample, and the most traditional way to achieve this goal consists of protein separations performed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Still, the 2-D PAGE-mass spectrometry (MS) approach remains lacking in proteome coverage (for proteins having extreme isoelectric points or molecular masses as well as for membrane proteins), dynamic range, sensitivity, and throughput. Consequently, considerable efforts have been devoted to the development of non-gel-based proteome separation technologies in an effort to alleviate the shortcomings in 2-D PAGE while reserving the ability to resolve complex protein and peptide mixtures prior to MS analysis. This review focuses on the most recent advances in capillary-based separation techniques, including capillary liquid chromatography, capillary electrophoresis, and capillary electrokinetic chromatography, and combinations of multiples of these mechanisms, along with the coupling of these techniques to MS. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state-of-the-art integrated proteome effort. Miniaturized and integrated multidimensional peptide/protein separations using microfluidics are further summarized for their potential applications in high-throughput protein profiling toward biomarker discovery and clinical diagnosis.     

Determination of pesticide transformation products: A review of extraction and detection methods

Pesticides are widely applied and they can produce a variety of transformation products (TPs), through different pathways and mechanisms. Nowadays there is a growing interest related to the determination of pesticide TPs in several matrices (environmental, food and biological samples), due to these compounds can be more toxic and persistent than parent compounds, and some of them can be used as markers of exposure to different pesticides. Although solid-phase extraction (SPE) is mainly used for the extraction of TPs, alternative techniques such as solid-phase microextraction (SPME) and liquid-phase extraction (LPE) can be used. These TPs are mainly determined by liquid chromatography (LC) due to the recent developments in this technique, especially when it is coupled to mass spectrometry (MS) detectors, allowing the determination of known and/or unknown TPs. Furthermore, MS is a very valuable tool for the structural elucidation of unknown TPs. This review discusses all phases of analytical procedure, including sample treatment and analysis, indicating the main problems related to the extraction of TPs from several matrices due to their high polarity, as well as the different alternatives found for the simultaneous determination of parent compounds and TPs, using chromatographic techniques coupled to MS detection.     

Electron ionization mass spectrometry: Quo vadis?

Mass spectrometry (MS) is a fundamental technique to identify compounds by their mass-to-charge ratio. It is known that MS can only detect target compounds when they are converted to ions in the gas phase. The ionization procedure is considered one of the most critical steps, and there are distinct techniques for it. One of them is electron ionization (EI), a widely used hard-ionization technique capable of generating several ions due to the excess energy employed. The existence of distinct ionization mechanisms turns EI capable of producing a fingerprint-like spectrum for each molecule. So, it is an essential technique for obtaining structural information. EI is often combined with chromatography to obtain a practical introduction of pretreated samples despite its excellent performance. EI–MS has been applied coupled with gas chromatography (GC) since the 1960s as both are very compatible. Currently, analytes of interest are more suitable for liquid chromatography (LC) analysis, so there are researchers dedicated to developing suitable interfaces for coupling LC and EI–MS. EI excels, as a reliable technique to fill the gap between GC and LC, possibly allowing them to coexist in a single instrument. In this work, the authors will present the fundamentals of EI–MS, emphasizing the development over the years, coupling with gas and LC, and future trends.     

The use of tandem mass spectrometry for the differentiation of bile acid isomers and for the identification of bile acids in biological extracts

Tandem mass spectrometric (MS/MS) techniques hae been widely used for the differentiation of isomeric compounds, since their spectra may show differences sufficient to distinguish between them. There are several different ways by which the MS/MS data can be obtained depending on the energies of the ions and the collisions. In this paper MS/MS spectra have been obtained for a group of isomeric bile acids using: 1, low-energy ions and low-energy collisions in a triple quadrupole mass spectrometer by liquid chromatography/MS/MS; 2, high-energy ions and low-energy collisions in a hybrid mass spectrometer by fast-atom bombardment MS/MS. Liquid chromatography combined with tandem mass spectrometry (LC/MS/MS) has also been used to identify the bile acids present in biological matrices such as bile extracts.     

Rapid and high resolution capillary supercritical fluid chromatography (SFC) and SFC/MS of trichothecene mycotoxins

The potential application of capillary column supercritical fluid chromatography (SFC) and SFC/mass spectrometry (SFC/MS) for the separation and analysis of mycotoxins of the trichothecene group was examined. Trichothecenes present significant analytical problems for both gas and liquid chromatography with a major difficulty for the latter being the lack of sufficiently sensitive and selective detectors. Supercritical carbon dioxide mobile phases at temperatures up to 100 degrees C were used with deactivated fused silica columns coated with crosslinked stationary phases. Separations were obtained under pressure ramped conditions using long (15 m) 50-micron i.d. columns for several trichothecenes (diacetoxyscirpenol, deoxynivalenol, and T-2 toxin) and related higher molecular weight macrocyclic (roridin and verrucarin) trichothecenes. In addition, new rapid pressure programming techniques with short (less than 2m) 25- to 50-micron i.d. capillary columns were used to obtain fast separations in as little as 1 min. SFC/MS with ammonia chemical ionization provided high selectivity and sensitive detection (with approximately 1-pg detection limits) for trichothecene mixtures. The extension to complex sample matrices is discussed and the application of selective MS/MS detection is demonstrated.     

On the use of different mass spectrometric techniques for characterization of sequence variability in genomic DNA

After completion of the human genome sequence the search for differences among individual genomes has become the centre of focus for geneticists. Two different types of polymorphism—single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs)—are major sources of genetic diversity and are of widespread use in genetic analysis. A plethora of genotyping techniques have been developed, and mass spectrometry (MS) is among the most widely used analytical platforms. The most striking advantage of mass spectrometric genotyping assays over others is the use of the measured molecular mass information for allele calling. The molecular mass is less error-prone than other sequence-specific parameters, including migration times, retention times, or hybridization yields, as it represents an intrinsic property of a nucleic acid molecule that is directly related to its nucleotide composition. Mass spectrometric assays can roughly be divided into two major groups—matrix-assisted laser desorption/ionization (MALDI)-based and electrospray ionization (ESI)-based assays. An important subdivision of ESI-based genotyping methods are approaches that originate from the hyphenation of liquid chromatography (LC) to MS. The principles of these three classes of mass spectrometric genotyping techniques are summarized in this review. Possibilities and limitations are critically discussed to assist scientists, especially non-experts in MS, in choosing the appropriate mass spectrometric assay for genotyping a genetic marker of interest. Figure Comparison of the principle workflows applied for the characterization of genetic markers by MALDI–MS, ESI–MS, and LC–MS     

Determination of paramethoxyamphetamine and other amphetamine-related designer drugs by liquid chromatography/sonic spray ionization mass spectrometry

Paramethoxyamphetamine (PMA) is an amphetamine-like designer drug that has emerged recently on the European illicit drug market. This drug has a wicked reputation, as a number of lethal intoxications have occurred. A method using high-performance liquid chromatography coupled to ion trap based mass spectrometry (LC/MS) is described for the determination of this compound together with 3,4-methylenedioxymethamphetamine (XTC or MDMA), amphetamine and 3,4-methylenedioxyamphetamine (MDA) in human matrices. A liquid/liquid extraction (LLE) was applied to whole blood, urine and postmortem tissues. Reversed-phase liquid chromatography was performed on a narrow-bore phenyl-type column at a flow rate of 0.3 mL/min. A switch box allowed disposal of early-eluting irrelevant material to waste, protecting the mass spectrometer from contamination. The column effluent was directed into an ion trap mass spectrometer by a sonic spray ionization (SSI) interface. The method was validated for all three matrices, proving the applicability of SSI even when dealing with complex biological matrices. The within-and between-day precisions were less than 17.5% and accuracy was below 16.2%. Weighted (1/x) quadratic calibration curves were generated ranging from 10 to 1000 ng/mL (blood and urine) or 20 to 2000 ng/g (tissue) and correlation coefficients (r(2)) always exceeded 0.995. In addition, the mass spectrum of PMA is given together with a proposed fragmentation pattern for the obtained LC/MS spectrum. This information can be useful for future identification of PMA with LC/MS in biological matrices as well as in confiscated powders or tablets.     

Hyphenated mass spectrometric techniques-indispensable tools in clinical and forensic toxicology and in doping control

Hyphenated mass spectrometric techniques, particularly gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS), are indispensable tools in clinical and forensic toxicology and in doping control owing to their high sensitivity and specificity. They are used for screening, library-assisted identification and quantification of drugs, poisons and their metabolites, prerequisites for competent expertise in these fields. In addition, they allow the study of metabolism of new drugs or poisons as a basis for developing screening procedures in biological matrices, most notably in urine, or toxicological risk assessment. Concepts and procedures using GC/MS and LC/MS techniques in the areas of analytical toxicology and the role of mass spectral libraries are presented and discussed in this feature article. Finally, perspectives of their future position are discussed.     

Review of the QuEChERS method for the analysis of organic pollutants: Persistent organic pollutants,polycyclic aromatic hydrocarbons,and pharmaceuticals

In multi-residue pesticide analysis, the quick, easy, cheap, effective, rugged, and safe (QuEChERS) extraction method has replaced less efficient traditional extraction methods due to its many advantages. In addition to pesticide analysis, this method has been widely used for the detection and analysis of pharmaceuticals, polycyclic aromatic hydrocarbons (PAHs), and several persistent organic pollutants (POPs), including dioxins, polychlorinated biphenyls, perfluoroalkyl substances, and brominated flame retardants in food, biological, and environmental matrices. The analysis of PAHs and POPs is challenging due to the properties of the target compounds and their low concentrations in complex matrices. This review summarizes previously reported the QuEChERS extraction approaches to the analysis of a wide range of analytes. The QuEChERS approaches, which include dispersive solid phase extraction (d-SPE), have generally been combined with either gas chromatography–mass spectrometry (GC–MS) or liquid chromatography–mass spectrometry (LC–MS) analysis. Further on, in recent years, GC and LC-tandem mass spectrometry has been utilized with the QuEChERS extraction due to its high selectivity, sensitivity, and specificity. This enables the extraction methods for target analytes to be modified through the selection of different extraction solvents, salt formulations, and buffers for salting-out partitioning and the selection of different d-SPE and SPE sorbents for the clean-up process. The most significant advantage of this method is that concentration steps are not required. This review aims to provide an up-to-date overview of information regarding the modification of extraction techniques based on target compounds and sample matrices.     

Building an empirical mass spectra library for screening of organic pollutants by ultra-high-pressure liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry

Hybrid quadrupole time-of-flight mass spectrometry (QTOF MS) has gained wide acceptance in many fields of chemistry, for example, proteomics, metabolomics and small molecule analysis. This has been due to the numerous technological advances made to this mass analyser in recent years. In the environmental field, the instrument has proven to be one of the most powerful approaches for the screening of organic pollutants in different matrices due to its high sensitivity in full acquisition mode and mass accuracy measurements. In the work presented here, the optimum experimental conditions for the creation of an empirical TOF MS spectra library have been evaluated. For this model we have used a QTOF Premier mass spectrometer and investigated its functionalities to obtain the best MS data, mainly in terms of mass accuracy, dynamic range and sensitivity. Different parameters that can affect mass accuracy, such as lock mass, ion abundance, spectral resolution, instrument calibration or matrix effect, have also been carefully evaluated using test compounds (mainly pesticides and antibiotics). The role of ultra-high-pressure liquid chromatography (UHPLC), especially when dealing with complex matrices, has also been tested. In addition to the mass accuracy measurements, this analyser allows the simultaneous acquisition of low and high collision energy spectra. This acquisition mode greatly enhances the reliable identification of detected compounds due to the useful (de)protonated molecule and fragment ion accurate mass information obtained when working in this mode. An in-house empirical spectral library was built for approximately 230 organic pollutants making use of QTOF MS in MS(E) mode. All the information reported in this paper is made available to the readers to facilitate screening and identification of relevant organic pollutants by QTOF MS.     

Composite sequence proteomic analysis of protein biomarkers of Campylobacter coli, C. lari and C. concisus for bacterial identification

Protein biomarkers observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF-MS) of cell lysates of three strains of Campylobacter coli, two strains of C. lari and one strain of C. concisus have been identified by 'bottom-up' proteomic techniques. The significant findings are as follows. First, the protein biomarkers identified were: PhnA-related protein, 4-oxalocrotonate tautomerase (DmpI)-related protein, NifU-like protein, cytochrome c, DNA-binding protein HU, 10 kDa chaperonin, thioredoxin, as well as several conserved hypothetical and ribosomal proteins. Second, variations in the biomarker ion m/z in MALDI-TOF-MS spectra across species and strains are the result of variations in the amino acid sequence of the protein due to non-synonymous mutations of the biomarker gene. Third, the most common post-translational modifications (PTMs) were the removal of the N-terminal methionine and N-terminal signal peptides. However, in the case of the NifU protein (an iron-sulfur cluster transport protein), post-translational cleavage occurred from the C-terminus. Fourth, only the genomes of the C. coli strain RM2228 and C. lari strain RM2100 have been sequenced; thus, proteomic identification of the proteins of the other strains in this study relied upon sequence homology to the genomic sequence of these strains as well as the genomes of sequences of other Campylobacter strains. In some cases, the determination of the full amino acid sequence of a protein biomarker from a genomically non-sequenced strain was accomplished by combining non-overlapping partial sequences from proteomic identifications of genomically-sequenced strains that were of the same species (or of a different species) to that of the non-sequenced strain. The accuracy of this composite sequence was confirmed by both MS and MS/MS. It was necessary, in some cases, to perform de novo sequencing on 'gaps' in the composite sequence that were not homologous to any genomically-sequenced strain. In order to validate the composite sequence approach, composite sequences were further confirmed by subsequent DNA sequencing of the biomarker gene. Thus, using the composite sequence approach, it was possible to determine the full amino acid sequence of an unknown protein from a genomically non-sequenced bacterial strain without the necessity of either sequencing the biomarker gene or performing full de novo MS/MS sequencing. The sequence obtained could then be used as a strain-specific biomarker for analysis by 'top-down' proteomics techniques.     

Novel contribution of chromatography in the development and analyses of metformin hydrochloride in biological and environmental samples

Globally, metformin hydrochloride (HCl) is the most commonly used antidiabetic drug and provides safe medication because of low risk of the side effects (lactic acidosis). Therefore, various researches have been established in pharmacodynamics and pharmacokinetic studies using various analytical applications such as calorimetry, spectrophotometry, and chromatography. But the chromatographic techniques are most widely used methods for the analysis of metformin HCl. This review discussed the different chromatographic methods used for the analysis of metformin HCl and its sample preparation for the isolation in different biological and environmental samples. Moreover, the mechanism for the fragmentation of ion products in LC–MS/MS is indicated for high throughput of the methods involved in the determination of metformin HCl in various sample matrices. The advancement in the chromatographic modalities provides the wide range of assays discussed herein.     

Distribution study of atorvastatin and its metabolites in rat tissues using combined information from UHPLC/MS and MALDI-Orbitrap-MS imaging

The combination of ultrahigh-resolution mass spectrometry imaging (UHRMSI) and ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC/MS/MS) was used for the identification and the spatial localization of atorvastatin (AT) and its metabolites in rat tissues. Ultrahigh-resolution and high mass accuracy measurements on a matrix-assisted laser desorption/ionization (MALDI)-Orbitrap mass spectrometer allowed better detection of desired analytes in the background of matrix and endogenous compounds. Tandem mass spectra were also used to confirm the identification of detected metabolites in complex matrices. The optimization of sample preparation before imaging experiments included the tissue cryogenic sectioning (thickness 20 μm), the transfer to stainless steel or glass slide, and the selection of suitable matrix and its homogenous deposition on the tissue slice. Thirteen matrices typically used for small molecule analysis, e.g., 2,5-dihydroxybenzoic acid (DHB), 1,5-diaminonaphthalene (DAN), 9-aminoacridine (AA), etc., were investigated for the studied drug and its metabolite detection efficiency in both polarity modes. Particular matrices were scored based on the strength of extracted ion current (EIC), relative ratio of AT molecular adducts, and fragment ions. The matrix deposition on the tissue for the most suitable matrices was done by sublimation to obtain the small crystal size and to avoid local variations in the ionization efficiency. UHPLC/MS profiling of drug metabolites in adjacent tissue slices with the previously optimized extraction was performed in parallel to mass spectrometry imaging (MSI) measurements to obtain more detailed information on metabolites in addition to the spatial information from MSI. The quantitation of atorvastatin in rat liver, serum, and feces was also performed.

Recently developed GC/MS and LC/MS methods for determining NSAIDs in water samples

Pharmaceuticals have become major targets in environmental chemistry due to their presence in aquatic environments (following incomplete removal in wastewater treatment or point-source contaminations), threat to drinking water sources and concern about their possible effects to wildlife and humans. Recently several methods have been developed for the determination of drugs and their metabolites in the lower nanogram per litre range, most of them using solid-phase extraction (SPE) or solid-phase microextraction (SPME), derivatisation and finally gas chromatography mass spectrometry (GC-MS), gas chromatography tandem mass spectrometry (GC-MS/MS) and liquid chromatography electrospray tandem mass spectrometry (LC-ES/MS/MS). Due to the elevated polarity of non-steroidal anti-inflamatory drugs (NSAIDs), analytical techniques based on either liquid chromatography coupled to mass spectrometry (LC-MS) and gas chromatography coupled to mass spectrometry (GC-MS) after a previous derivatisation step are essential. The most advanced aspects of current GC-MS, GC-MS/MS and LC-MS/MS methodologies for NSAID analysis are presented.     

Peptidomics: the integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis

MS is currently one of the most important analytical techniques in biological and medical research. ESI and MALDI launched the field of MS into biology. The performance of mass spectrometers increased tremendously over the past decades. Other technological advances increased the analytical power of biological MS even more. First, the advent of the genome projects allowed an automated analysis of mass spectrometric data. Second, improved separation techniques, like nanoscale HPLC, are essential for MS analysis of biomolecules. The recent progress in bioinformatics is the third factor that accelerated the biochemical analysis of macromolecules. The first part of this review will introduce the basics of these techniques. The field that integrates all these techniques to identify endogenous peptides is called peptidomics and will be discussed in the last section. This integrated approach aims at identifying all the present peptides in a cell, organ or organism (the peptidome). Today, peptidomics is used by several fields of research. Special emphasis will be given to the identification of neuropeptides, a class of short proteins that fulfil several important intercellular signalling functions in every animal. MS imaging techniques and biomarker discovery will also be discussed briefly.     

Chromatographic analysis of unsaponifiable compounds of olive oils and fat-containing foods

The analysis of the "minor components" present in food lipids is usually hampered by the large diversity of compounds found in this fraction. High-purity degree reagents and solvents, good collection techniques and highly sensitive analysis are required in order to accurately identify and quantify these components. Chromatographic techniques have proven to be particularly suitable for these determinations, especially capillary gas chromatography. This study reports several analytical cases of the main classes of components of the unsaponifiable matter obtained from olive oils or food matrices.     

Applications of single-drop microextraction in analytical chemistry: A review

Single-drop microextraction (SDME) has been recognized as one of the simple miniaturized sample preparation tools for the isolation and preconcentration of several analytes from a complex sample matrix. In this review, we explored the applications of SDME coupled with various analytical techniques (spectroscopy, chromatography, and mass spectrometry) for the analysis of organic molecules, inorganic ions, and biomolecules from various sample matrices including food, environmental, clinical, pharmaceutical, and industrial samples. Also, it summarizes the use of nanoparticles in SDME combined with various analytical tools for the rapid analysis of several trace-level target analytes. An overview of ionic liquids, deep eutectic solvents, and SUPRAS, which improved the selectivity and sensitivity of various analytical techniques toward several analytes, as promising extracting solvent systems in SDME is also included. Finally, discussed the impressive analytical features and future perspectives of SDME in this review article.     

The assay of pterostilbene in spiked matrices by liquid chromatography tandem mass spectrometry and isotope dilution method

Pterostilbene (trans‐3,5‐dimethoxy‐4‐hydroxystilbene) is an active component found in several plant species, exhibiting important pharmacological properties. A new and reliable method of assaying this phyto compound in various matrices is presented; the assay is based on (1) the selectivity of liquid chromatography (LC) hyphenated with electrospray ionisation (ESI), (2) the specificity of a two‐step mass spectrometric analysis (MS/MS) and (3) the accuracy of the isotope dilution method. The labelled analogue may be conveniently synthesised in a few steps. The sensitivity of the method is confirmed by the very low limit of detection (LOD) and limit of quantitation (LOQ) values achieved in the assay of pterostilbene in two distinct fortified matrices, and is further supported by the observed accuracy values. Copyright © 2010 John Wiley & Sons, Ltd.     

On-line microdialysis of proteins with high-salt buffers for direct coupling of electrospray ionization mass spectrometry and liquid chromatography

Mass spectrometry (MS) is one of the most powerful instrumental techniques for protein analysis. The electrospray ionization (ESI) approach is known to be very gentle and at the same time compatible with liquid separation techniques such as HPLC and CE. However, ESI is known to be susceptible to salts and impurities, which often cause a dramatic decrease in sensitivity due to the suppression of the ionization of the product of interest. For this reason, LC-ESI-MS coupling has so far been largely limited to reversed-phase chromatography with its hydro-organic mobile phases. Other chromatographic techniques are typically "linked" to ESI-MS by time consuming, off-line desalting steps. On-line microdialysis has been proposed as a solution to this dilemma. In this paper, we introduce an improved microdialysis system, which enlarges the number of putative applications, thus allowing chromatographic separations of biological compounds to be directly coupled to MS detection with little to no loss in time or chromatographic resolution. Examples include separations by affinity, ion-exchange and size-exclusion chromatography, all of which were connected successfully to the ESI-MS detector via the on-line microdialyzer. We propose that, using this system, any kind of chromatography technique can be coupled to ESI-MS, thus enabling for example application in quality control or process monitoring of many bioproduction and downstream processes.