On-line coupling of aptamer affinity solid-phase extraction and immobilized enzyme microreactor capillary electrophoresis-mass spectrometry for the sensitive targeted bottom-up analysis of protein biomarkers

In this paper, we present a fully integrated valve-free method for the sensitive targeted bottom-up analysis of proteins through on-line aptamer affinity solid-phase extraction and immobilized enzyme microreactor capillary electrophoresis-mass spectrometry (AA-SPE-IMER-CE-MS). The method was developed analyzing α-synuclein (α-syn), which is a protein biomarker related to different neurodegenerative disorders, including Parkinson's disease. Under optimized conditions, on-line purification and preconcentration of α-syn, enzymatic digestion, electrophoretic separation, and identification of the tryptic peptides by mass spectrometry was achieved in less than 35 min. The limit of detection was 0.02 μg mL-1 of digested protein (66.7% of coverage, i.e., 8 out of 12 expected tryptic peptides were detected). This value was 125 and 10 times lower than for independent on-line digestion by IMER-CE-MS (2.5 μg mL-1) and on-line preconcentration by AA-SPE-CE-MS (0.2 μg mL-1). The repeatability of AA-SPE-IMER-CE-MS was adequate (at 0.5 μg mL-1,% RSD ranged from 3.7 to 16.9% for peak areas and 3.5 to 7.7% for migration times of the tryptic peptides), and the modified capillary could be reused up to 10 analyses with optimum performance, similarly to IMER-CE-MS. The method was subsequently applied to the analysis of endogenous α-syn from red blood cell lysates. Ten α-syn tryptic peptides were detected (83.3% of coverage), enabling the characterization and localization of post-translational modifications of blood α-syn (i.e., N-terminal acetylation)

Evaluation of on-line solid-phase extraction capillary electrophoresis-mass spectrometry with a nanoliter valve for the analysis of peptide biomarkers

On-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS) is a powerful technique for high throughput sample clean-up and analyte preconcentration, separation, detection, and characterization. The most typical design due to its simplicity and low cost is unidirectional SPE-CE-MS. However, in this configuration, the sample volumes introduced by pressure depend on the dimensions of the separation capillary and some matrix components could be irreversibly adsorbed in its inner walls. Furthermore, in many cases, the requirements of on-line preconcentration are incompatible with the background electrolyte necessary for an efficient separation and sensitive MS detection. Here, we present SPE-CE-MS with a nanoliter valve (nvSPE-CE-MS) to overcome these drawbacks while keeping the design simple. The nvSPE-CE-MS system is operated with a single CE instrument and two capillaries for independent and orthogonal SPE preconcentration and CE separation, which are interfaced through an external and electrically isolated valve with a 20 nL sample loop. The instrumental setup is proved for the analysis of opioid and amyloid beta peptide biomarkers in standards and plasma samples. NvSPE-CE-MS allowed decreasing the limits of detection (LODs) 200 times with regard to CE-MS. Compared to unidirectional SPE-CE-MS, peak efficiencies were better and repeatabilities similar, but total analysis times longer and LODs for standards slightly higher due to the heart-cut operation and the limited volume of the valve loop. This small difference on the LODs for standards was compensated for plasma samples by the improved tolerance of nvSPE-CE-MS to complex sample matrices. In view of these results, the presented setup can be regarded as a promising versatile alternative to avoid complicated matrix samples entering the separation capillary in SPE-CE-MS

Determination of acidity constants and prediction of electrophoretic separation of amyloid beta peptides

In this paper we describe a strategy to estimate by CE the acidity constants (pKa) of complex polyprotic peptides from their building peptide fragments. CE has been used for the determination of the pKas of five short polyprotic peptides that cover all the sequence of amyloid beta (Aβ) peptides 1-40 and 1-42 (Aβ fragments 1-15, 10-20, 20-29, 25-35 and 33-42). First, the electrophoretic mobility (me) was measured as a function of pH of the background electrolyte (BGE) in the pH range 2-12 (bare fused silica capillary, I=25mM and T=25ºC). Second, the mes were fitted to equations modelling the ionisable behaviour of the different fragments as a function of pH to determine their pKas. The accuracy of the pKas was demonstrated predicting the electrophoretic behaviour of the studied fragments using the classical semiempirical relationships between me and peptide charge-to-mass ratio (me vs. q/Mr1/2, classical polymer model, q=charge and Mr=relative molecular mass). Separation selectivity in a mixture of the fragments as a function of pH was evaluated, taking into account the influence of the EOF at each pH value, and a method for the simple and rapid simulation of the electropherograms at the optimum separation pH was described. Finally, the pKas of the fragments were used to estimate the pKas of the Aβ peptides 1-40 and 1-42 (tC and D 3.1, E 4.6 and Y 10.8 for acidic amino acids and tN-D 8.6, H 6.0, K 10.6 and R 12.5 for basic amino acids), which were used to predict their behaviour and simulate their electropherograms with excellent results. However, as expected due to the very small differences on q/Mr1/2 values, separation resolution of their mixtures was poor over the whole pH range. The use of poly(vinyl alcohol) (PVA) coated capillaries allowed reducing the electroosmotic flow (EOF) and a slight improvement of resolution

Analysis of circulating microRNAs and their post-transcriptional modifications in cancer serum by on-line solid-phase extraction-capillary electrophoresis-mass spectrometry

In this paper, an on-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS) method is described for the purification, preconcentration, separation, and characterization of endogenous microRNA (miRNA) and their post-transcriptional modifications in serum. First, analysis by CE-MS was optimized using a standard mixture of hsa-miR-21-5p (miR-21-5p) and hsa-let-7g-5p (let-7g-5p). For SPE-CE-MS, a commercial silicon carbide (SiC) resin was used to prepare the microcartridges. Under the optimized conditions with standards, the microcartridge lifetime (>25 analyses) and repeatability (2.8% RSD for the migration times; 4.4 and 6.4% RSD for the miR-21-5p and let-7g-5p peak areas, respectively) were good, the method was linear between 25 and 100 nmol·L-1, and the limit of detection (LOD) was around 10 nmol·L-1 (50 times lower than by CE-MS). In order to analyze human serum samples, an off-line sample pretreatment based on phenol/chloroform/isoamyl alcohol (PCA) extraction was necessary prior to SPE-CE-MS. The potential of the SPE-CE-MS method to screen for B-cell chronic lymphocytic leukemia (CLL) was demonstrated by an analysis of serum samples from healthy controls and patients. MicroRNAs, specifically miR-21-5p and a 23 nucleotide long 5'-phosphorylated miRNA with 3'-uridylation (iso-miR-16-5p), were only detected in the CLL patients

A review of sample preparation for purification of microRNAs and analysis by mass spectrometry methods

MicroRNAs (miRNAs) play an important role in regulation of different bioprocesses, including multiple diseases, such as cancer, neurodegenerative and immune-related disorders. Analysis of miRNA biomarkers in biological fluids requires accurate, sensitive, reproducible, and multiplexed methods. This review covers miRNA purification and measurement, which are the core of these analytical methods, and critically affect the output of biomarker research studies. With regard to miRNA measurement, the typical bioanalytical methods (e.g. reverse transcription polymerase chain reaction, RT-PCR), which have been extensively reviewed elsewhere, have been excluded to focus on less conventional methods based on mass spectrometry (MS). This review provides a broad overview of liquid-phase and solid-phase extraction purification methods for miRNA clean-up and enrichment and a critical insight into direct and indirect MS-based methods to disclose the true potential of MS in the field

Analysis of serum transthyretin by on-line immunoaffinity solid-phase extraction capillary electrophoresis mass spectrometry using magnetic beads

In this paper, an on-line immunoaffinity solid-phase extraction capillary electrophoresis mass spectrometry (IA-SPE-CE-MS) method using magnetic beads (MBs) is described for the analysis of serum transthyretin (TTR), which is a protein related to different types of amyloidosis. First, purification of TTR from serum was investigated by off-line immunoprecipitation and CE-MS. The suitability of three Protein A (ProA) MBs (Protein A Ultrarapid AgaroseTM (UAPA), Dynabeads® Protein A (DyPA) and SiMAG-Protein A (SiPA)) and AffiAmino Ultrarapid AgaroseTM (UAAF) MBs to prepare an IA sorbent with a polyclonal antibody (Ab) against TTR, was studied. In all cases results were repeatable and it was possible the identification and the quantitation of the relative abundance of the 6 most abundant TTR proteoforms. Although recoveries were the best with UAPA MBs, UAAF MBs were preferred for on-line immunopurification because Ab was not eluted from the MBs. Under the optimised conditions with standards in IA-SPE-CE-MS, microcartridge lifetime (>20 analyses/day) and repeatability (2.9 and 4.3 % RSD for migration times and peak areas) were good, the method was linear between 5- 25 µg·mL-1 and limit of detection (LOD) was around 1 µg·mL-1 (25 times lower than by CE-MS, 25 µg·mL-1). A simple off-line sample pretreatment based on precipitation of the most abundant proteins with 5% (v/v) of phenol was necessary to clean-up serum samples. The potential of the on-line method to screen for familial amyloidotic polyneuropathy type I (FAP-I), which is the most common hereditary systemic amyloidosis, was demonstrated analysing serum samples from healthy controls and FAP-I patients

Analytical performance of an on-line preconcentration system to determine mercury speciation in water

Treballs Finals de Grau de Química, Facultat de Química, Universitat de Barcelona, Any: 2014, Tutora: Àngels SahuquilloEl mercuri i els seus compostos estan considerats contaminants pràcticament omnipresents en l’ambient a causa de la seva mobilitat en el medi. La seva determinació en una àmplia varietat de mostres ha esdevingut un tema molt important per la seva elevada toxicitat així com el seu caràcter acumulatiu i persistent. D’altra banda, el mercuri està present en diverses formes, que determinen la seva distribució i toxicitat. La determinació del mercuri en aigua és particularment important ja que l’aigua potable és essencial per als éssers humans i la seva contaminació té un gran impacte en la seva salut. És per això que la Directiva 2008/105/EC del Parlament Europeu i del Consell sobre normes de qualitat ambiental en l'àmbit de la política d'aigües identifica el mercuri i els seus compostos com a substàncies perilloses prioritàries..

Nuevas estrategias para la mejora de la sensibilidad y la selectividad en el análisis de biomarcadores proteómicos y miRNómicos en fluidos biológicos mediante CE-MS

[spa] En las últimas décadas, el análisis de compuestos biomarcadores en muestras biológicas se ha convertido en una herramienta esencial para el diagnóstico, seguimiento y pronóstico de diversas enfermedades. Las principales dificultades en muchos casos son la baja concentración de los biomarcadores, la complejidad de la matriz de la muestra y la limitada disponibilidad de muestra. En esta tesis doctoral, se presentan nuevas estrategias basadas en electroforesis capilar- espectrometría de masas (CE-MS) para la separación, detección, caracterización y cuantificación de péptidos, proteínas y microARNs (miRNAs) biomarcadores en fluidos biológicos. La CE-MS es una técnica excelente para la separación de biomoléculas cargadas y su identificación inequívoca. En esta tesis, se han desarrollado estrategias novedosas para la predicción y optimización de las separaciones de mezclas complejas de péptidos en CE. Para evaluar estas estrategias, se han estudiado los péptidos beta amiloides. Una limitación importante de la CE es su baja sensibilidad en términos de concentración para la mayoría de analitos a causa del pequeño volumen de inyección de muestra. La extracción en fase sólida en línea con la electroforesis capilar (SPE-CE) es una excelente estrategia para disminuir los límites de detección. En esta tesis se han investigado diferentes metodologías de SPE-CE-MS unidireccional empleando sorbentes selectivos, como los sorbentes de inmunoafinidad, afinidad a aptámero, afinidad a metal inmovilizado y el carburo de silicio, para el análisis de proteínas intactas (transtiretina y α-sinucleína), digestos de proteínas y miRNAs en fluidos biológicos. También se ha investigado el potencial de la SPE-CE-MS con una nanoválvula (nvSPE-CE-MS) para el análisis de péptidos en fluidos biológicos. Se ha desarrollado un método de nvSPE-CE-MS empleando un sorbente C18 para el análisis de péptidos opioides y péptidos beta amiloides y se han comparado las ventajas e inconvenientes de la nvSPE-CE-MS respecto a la SPE-CE-MS unidireccional. Finalmente, se han investigado nuevas estrategias para el análisis rápido y eficiente de digestos de proteínas. La tripsina es la enzima proteolítica más comúnmente utilizada y la digestión se realiza habitualmente en disolución, requiriéndose largos tiempos de digestión. Con el objetivo de disminuir el volumen de muestra, su manipulación y el tiempo total de análisis, en esta tesis se ha desarrollado una metodología de análisis de proteínas empleando microrreactores empaquetados con partículas con tripsina inmovilizada en línea con la CE-MS (IMER-CE-MS).[eng] In recent years, an increased emphasis has been placed on the analysis of biomarker compounds in biological samples for the diagnosis, follow-up and prognosis of numerous diseases. The leading difficulties in many of these analyses are the low concentration of the biomarkers, their structural complexity, the sample matrix effects and the limited availability of sample. In this doctoral thesis, we present novel strategies based on capillary electrophoresis- mass spectrometry (CE-MS) for the separation, detection, characterization and quantification of peptide, protein and microRNA (miRNA) biomarkers in biological fluids. MS is a powerful technique for the unequivocal identification of biomolecules due to its potential with regard to the detailed structural characterization of unknown compounds. However, due to the complexity of most biological fluids, the hyphenation of high-performance separation techniques is essential prior to MS analysis. In this regard, CE is a microscale technique that is very suitable for the separation of charged biomolecules. Nevertheless, electrophoretic separation methods must be properly optimized to achieve rapid, efficient, sensitive and high-resolution separations. In this thesis, we have investigated novel strategies to predict and optimize the separation of complex mixtures of peptides in CE. To assess these strategies, amyloid beta peptides, which are biomarkers of Alzheimer’s disease, were studied. A major limitation of CE is the relatively poor concentration sensitivity for most analytes due to the small sample volume that can be injected in the separation capillary. On-line solid- phase extraction capillary electrophoresis (SPE-CE) is a powerful approach for sample clean-up and reduction of the limits of detection. In SPE-CE, analytes from a large volume of sample are retained on a sorbent contained in a microcartridge. In unidirectional SPE-CE, the most typical configuration, the microcartridge is mounted in series to the separation capillary, inserted near the capillary inlet. After sample loading, the microcartridge is washed to remove non-selectively retained molecules. Then, the retained analytes are desorbed in a small volume of eluent, resulting in sample clean-up and concentration enhancement before electrophoretic separation and detection. In the present thesis, selective sorbents, such as immunoaffinity, aptamer affinity, immobilized metal affinity and silicon carbide sorbents have been explored in unidirectional SPE-CE-MS for the analysis of intact proteins, such as transthyretin, which is a biomarker of familial amyloidotic polyneuropathy type I, and α-synuclein, which is related to Parkinson’s disease, protein digests and miRNAs, which are related to cancer, in biological fluids. Unidirectional SPE-CE-MS is straightforward to implement. However, this simple setup has some inherent limitations. On the one hand, the sample volumes introduced using pressure depend on the dimensions of the separation capillary. On the other hand, sample loading is conducted in the same direction as the subsequent separation. Therefore, some of the matrix components could be irreversibly adsorbed in the inner wall of the separation capillary. Furthermore, in many cases, the requirements of on-line preconcentration are incompatible with the BGE necessary for an efficient separation or sensitive MS detection. In order to overcome these drawbacks, some new configurations where the sample is introduced in an orthogonal direction to the separation have been proposed, requiring the use of valves. We have investigated SPE-CE-MS with a nanoliter valve (nvSPE-CE-MS). A nvSPE-CE-MS method with a C18 sorbent for the analysis of opioid peptides and amyloid beta peptide fragments has been developed and the advantages and disadvantages compared to the unidirectional SPE-CE- MS have been discussed. New strategies for high-throughput bottom-up analysis of proteins have also been investigated. Tryptic digestion has been traditionally conducted in solution and requires long digestion times. In contrast, immobilized enzymes allow decreasing the sample volume and the total digestion times, minimize the sample handling, improve the digestion yields, as well as to stabilize the enzyme, avoid its autoproteolysis and simplify its recovery making it reusable. In this thesis, we have investigated on-line immobilized enzyme microreactor capillary electrophoresis-mass spectrometry (IMER-CE-MS) using microreactors packed with immobilized trypsin particles