Group-selective prefractionation and analysis of nucleosides and catecholamines by high-performance liquid chromatographic techniques

Conclusions The use of borate as ligand in conventional affinity chromatography has found numerous applications in biochemical research [6], as for example for the clean-up of ribonucleosides and catecholamines in physiological fluids, the separation of DNA and RNA, the isolation of glycosidated hemoglobins, separation of aminoacylated RNA from free RNA, ligand mediated (piggyback) chromatographic enrichment of enzymes or the separation of base Q containing tRNA from base Q free tRNA. With the development of borate functionalized silica borate affinity chromatography has also been turned out to work under HPLAC conditions.By use of a column switching technique we could introduce a combined HPLAC/HPLC method particularly suitable for the on-line clean-up and analysis of ribonucleosides in complex matrices. We now have expanded the application of our on-line system for the clean-up and analysis of the adrenergic amines from spiked physiological matrix which means a powerful improvement compared to the system introduced by [7] for the on-line analysis just of one of the dopamine catabolites. The method described should be the method of choice for the majority of applications mentioned above as it greatly decreases the analysis time, is suitable for automation and in conjunction with a data-processing system, is applicable to routine clinical analysis.

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Gruppenselektive Vortrennung und Analyse von Nucleosiden und Catecholaminen mittels hochleistungs-chromatographischer Techniken

     

Improved gas chromatographic analysis of naturally occurring oxygen-containing monoterpenes following prefractionation by liquid-solid chromatography

Summary A liquid-solid column chromatographic method for separation of mixtures of naturally occurring oxygen-containing monoterpenes has been developed. The LSC was carried out on a column of silica gel applying a 2.5%–50% gradient elution of ethyl ether in pentane and collecting a number of fractions. The enrichment of the various components in the fractions led to a better gas chromatographic separation and identification. The elution sequence during LSC gave extra information about the functional group of the compounds. Isomerization processes could be avoided by using purified and deactivated silica gel.     

A turning point in proteome analysis: sample prefractionation via multicompartment electrolyzers with isoelectric membranes

Sample prefractionation, as obtained via multicompartment electrolyzers with isoelectric membranes, greatly enhanced the load ability, resolution and detection sensitivity of two-dimensional (2-D) maps in proteome analysis. This was demonstrated with different samples. In an Escherichia coli total cell extract, analysis by a 2-D map run in a pH 4-5 gradient showed many more spots when prefractionated, as compared with standard maps available in databases such as SWISS-2DPAGE. Analysis of human plasma in the pH 3-6 range showed an increase in the number of highly acidic proteins in the fractionated sample compared to whole plasma. With both samples no protein precipitation or smears occurred and much larger sample amounts could be loaded upon prefractionation, so that a large number of spots could be visualized by Coomassie staining, which is fully compatible with subsequent matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis.     

Gel-free IEF in a membrane-sealed multicompartment cell for proteome prefractionation

A minidevice for performing gel-free proteome prefractionation via conventional IEF in soluble carrier ampholyte buffers is reported here. It consists of a compact block of polyoxymethylene in which eight samples and two electrode chambers are machined. Each of the eight sample chambers can be filled with up to 120 microL of sample and has the following size: 7 mm width, 3 mm depth and 10 mm height. The anodic and cathodic compartments have the same width and height as the sample chambers, but with a depth of 6 mm, thus accepting up to 250 microL of electrodic solutions. Focusing is in general accomplished in 2 h with a voltage gradient of up to 1000 V (7 cm electrode distance). Easy fractionation and collection of the content of the eight chambers is achieved by simply pressing a rubber diaphragm against the edges of the thin walls separating each well, this automatically breaking liquid continuity. The performance of this device has been tested by subfractionating total cell lysates of a human cancer cell line (U2Os) and of Escherichia coli bacterial cells, and by analysing the content of each chamber by mono-dimensional SDS-PAGE and 2-D maps.     

Comprehensive proteome analysis of mouse liver by ampholyte-free liquid-phase isoelectric focusing

In this study, ampholyte-free liquid-phase IEF (LIEF) was combined with narrow pH range 2-DE and SDS-PAGE RP-HPLC for comprehensive analysis of mouse liver proteome. Because LIEF prefractionation was able to reduce the complexity of the sample and enhance the loading capacity of IEF strips, the number of visible protein spots on subsequent 2-DE gels was significantly increased. A total of 6271 protein spots were detected after integrating five narrow pH range 2-DE gels following LIEF prefractionation into a single virtual 2-DE gel. Furthermore, the pH 3-5 LIEF fraction and the unfractionated sample were separated by pH 3-6 2-DE and identified by MALDI-TOF/TOF MS, respectively. In parallel, the pH 3-5 LIEF fraction was also analyzed by SDS-PAGE RP-HPLC MS/MS. LIEF-2-DE and LIEF-HPLC could obviously improve the separation efficiency and the confidence of protein identification, which identified a higher number of low-abundance proteins and proteins with extreme physicochemical characteristics or post-translational modifications compared to conventional 2-DE method. Furthermore, there were 207 proteins newly identified in mouse liver in comparison with previously reported large-scale datasets. It was observed that the combination of LIEF-2-DE and LIEF-HPLC was effective in promoting MS-based liver proteome profiling and could be applied on similar complex tissue samples.     

Comprehensive analysis of chromatographic data by using PARAFAC2 and principal components analysis

The most straightforward method to analyze an obtained GC–MS dataset is to integrate those peaks that can be identified by their MS profile and to perform a Principal Component Analysis (PCA). This procedure has some important drawbacks, like baseline drifts being scarcely considered or the fact that integration boundaries are not always well defined (long tails, co-eluted peaks, etc.). To improve the methodology, and therefore, the chromatographic data analysis, this work proposes the modeling of the raw dataset by using PARAFAC2 algorithm in selected areas of the GC profile and using the obtained well-resolved chromatographic profiles to develop a further PCA model. With this working method, not only the problems arising from instrumental artifacts are overcome, but also the detection of new analytes is achieved as well as better understanding of the studied dataset is obtained. As a positive consequence of using the proposed working method human time and work are saved. To exemplify this methodology the aroma profile of 36 apples being ripened were studied. The benefits of the proposed methodology (PARAFAC2 + PCA) are shown in a practitioner perspective, being able to extrapolate the conclusions obtained here to other hyphenated chromatographic datasets.     

Group-selective prefractionation and analysis of urinary catecholamines by on-line HPLAC-HPLC Chromatography

Summary An on-line-method for the direct, rapid and convenient quantitation of the catecholamines norepinephrine, epinephrine and dopamine in human urine samples by a boronic-acid substituted silica HPLAC/cation exchange-HPLC with electrochemical detection is described. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

A comprehensive and non‐prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine

Increasing attention has been paid to the urinary proteome because it holds the promise of discovering various disease biomarkers. However, most of the urine proteomics studies routinely relied on protein pre‐fractionation and so far did not present characterization on phosphorylation status. Two robust approaches, integrated multidimensional liquid chromatography (IMDL) and Yin‐yang multidimensional liquid chromatography (MDLC) tandem mass spectrometry, were recently developed in our laboratory, with high‐coverage identification of peptide mixtures. In this study, we adopted a strategy without pre‐fractionation on the protein level for urinary proteome identification, using both the IMDL and the Yin‐yang MDLC methods for peptide fractionation followed by identification using a linear ion trap‐orbitrap (LTQ‐Orbitrap) mass spectrometer with high resolution and mass accuracy. A total of 1310 non‐redundant proteins were highly confidently identified from two experiments, significantly including 59 phosphorylation sites. More than half the annotated identifications were membrane‐related proteins. In addition, the lysosomal as well as kidney‐associated proteins were detected. Compared with the six largest datasets of urinary proteins published previously, we found our data included most of the reported proteins. Our study developed a robust approach for exploring the human urinary proteome, which would provide a catalogue of urine proteins on a global scale. It is the first report, to our best knowledge, to profile the urinary phosphoproteome. This work significantly extends current comprehension of urinary protein modification and its potential biological significance. Moreover, the strategy could further serve as a reference for biomarker discovery. Copyright © 2010 John Wiley & Sons, Ltd.     

Comprehensive two-dimensional gas chromatographic analysis of commercial lemon-flavored beverages

Fresh lemon juice and lemon-flavored beverages were analyzed by using comprehensive 2-D GC (GC x GC) with flame-ionization detection, with a nonpolar-polar column combination. A low-alcohol, ready-to-drink (RTD) beverage was also analyzed as fresh, and after deterioration for 12 days at 50 degrees C. Identification of some of the components in the 2-D plots was performed by comparison of peak positions of authentic standards and comparison with 1-D GC. However, without the aid of GC x GC-mass spectral data, only 24 components were identified; a large number of components remained unassigned. In some soft drinks obtained in the market, components indicative of deterioration, such as p-methylacetophenone and p-cymen-8-ol were already present in the products. In contrast, even upon heat challenge, a low-alcohol RTD beverage did not generate deterioration products of citral, such as p-methylacetophenone and the intermediates, p-menth-2-ene-1,8-diols. This was apparently related to the fact that the original formulation contained only a minute amount of the citral ingredient.     

Toward chromatographic analysis of interacting protein networks

Protein complexes, collectively referred to as the cellular interactome, appear to play a major role in cellular regulation. At present it is thought that the interactome could be composed of hundreds of protein assemblies. The objective of the work described here was to examine the prospect that chromatographic methods widely used in the preparative isolation of native proteins could be incorporated into global proteomics methods in such a way that the primary structure of protein complexes of sufficient stability to survive chromatography could be recognized along with their participation in protein complexes. Because wide differences in sizes are a unique feature of protein complexes, size-exclusion chromatography (SEC) was incorporated into all the fractionation strategies examined. Anion-exchange chromatography (AEC) and hydrophobic-interaction chromatography (HIC) were also examined because of the broad utility that these methods have shown in the preparation of proteins with native structure. Slightly more than a third of all proteins identified in yeast lysates were found to elute from SEC, AEC, and HIC columns with an apparent molecular weight much higher than that predicted from their parent gene. These results were interpreted to mean that these proteins were migrating through columns as components of protein complexes. Based on studies with multidimensional SEC-->RPLC (reversed-phase liquid chromatography), AEC-->SEC, and HIC-->SEC systems, it was concluded that recognition of proteins in complexes could be easily incorporated into multidimensional chromatographic methods for global proteomics when at least one of the fractionation dimensions included SEC of native proteins.     

Comprehensive headspace gas chromatographic analysis of denaturants in denatured ethanol

To discourage consumption, ethanol is often denatured using both volatile (e.g., methyl ethyl ketone and isopropanol) and nonvolatile (e.g., denatonium benzoate) chemical substances. As a result, the analysis of denatured ethanol samples is usually performed by multiple techniques such as gas chromatography for the volatile denaturants and liquid chromatography for the nonvolatile ones. However, the need for multiple techniques increases the cost of analysis and forms a severe obstruction for on‐site product control. Using the full evaporation technique combined with gas chromatography and flame ionization detection, only one analytical methodology has to be used here to determine both volatile and nonvolatile denaturants in denatured ethanol. Denatonium benzoate is determined as benzyl chloride following an in‐vial reaction. Compared to conventional techniques, the novel method performs equally well, but it is simpler to apply. At the same time, drawbacks of alternative methods are circumvented such as equilibration issues and alterations to the stationary phase when using liquid chromatography with ion pairing agents or matrix effects when applying static headspace gas chromatography. The developed method showed good linearity, repeatability, and recovery toward all analytes and was applied to the analysis of commercial denatured ethanol for disinfection and ethanol‐based windscreen washer fluids.     

New method for prefractionation of plasma for proteomic analysis

The depth of proteome analysis is severely limited in complex samples with a wide dynamic range of protein abundance such as plasma. Removal of high‐abundance proteins should reveal the signal of lower abundance plasma proteins. However, smaller proteins may be part of larger protein complexes and hence the removal of proteins involved in complexes with high‐abundance proteins such as albumin may inhibit the search for disease biomarkers. Prefractionation of a sample divides it into fractions of reduced complexity, allowing improved detection of lower abundance proteins. Using a prefractionation device, which employs Gradiflow? technology, we were able to separate small volume plasma samples into multiple fractions based on the molecular weight and/or charge. The resulting samples of reduced complexity were directly compatible with 2‐DE. The use of this prefractionation machine may therefore be useful in the hunt for disease biomarkers.     

Carrier ampholyte-free solution isoelectric focusing as a prefractionation method for the proteomic analysis of complex protein mixtures

The field of proteomics requires methods that offer high sensitivity and wide dynamic range. One of the strategies used to improve the dynamic range is sample prefractionation, such as microsolution isoelectric focusing (IEF). We have modified a commercial solution IEF instrument, the Rotofor, to prefractionate protein mixtures by carrier ampholyte-free solution IEF. The focusing chamber of the Rotofor was divided into several compartments by polyacrylamide membranes with imbedded Immobiline mixtures of specific pH values. When an electric field is applied, each protein migrates to the compartment confined by membranes with pH values flanking its isoelectric point. The approach was demonstrated for the focusing of myoglobin into a predicted compartment, as well as the separation of a complex soluble yeast protein mixture into several distinct fractions. The proteins were dissolved in water or 30% isopropanol. The method is applicable to both gel-based and solution-phase protein identification methods, without the need for further sample preparation.     

Column chromatographic prefractionation leads to the detection of 543 different gene products in human fetal brain

In a previous publication a large series of proteins were identified in fetal human brain by the use of two-dimensional electrophoresis (2-DE) with subsequent matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and MALDI-tandem time-of-flight (TOF/TOF) analysis. Further identification of many more different spots by traditional 2-DE without additional step such as narrow immobilized ph gradient (IPG) strips or prefractionation seems unlikely and we therefore decided to separate extracted brain proteins by ion-exchange chromatography using a TSK gel DEAE-5PW column followed by 2-DE of individual fractions and analysis by MALDI-TOF/TOF with LIFT technology in fetal brain of the early second trimester. About 1880 protein spots corresponding to 543 different gene products were identified. These proteins included housekeeping, signaling, cytoskeletal, metabolic, antioxidant, and neuron/synaptosomal specific proteins. Among these, 314 gene products (314/543, 57.8%), which have never been detected in traditional 2-DE of human fetal brain, were observed by this method. This updated map of fetal brain proteins may serve as data base and reference map for fetal brain proteins, and the methodology applied may be used as a valuable analytical tool for the basis of protein expressional studies in health and disease.     

A combinatorial approach to studying protein complex composition by employing size-exclusion chromatography and proteome analysis

The genome sequences of numerous organisms are available now, but gene sequences alone do not provide sufficient information to accurately deduce protein functions. Protein function is largely dependent on the association of multiple polypeptide chains into large structures with interacting subunits that regulate and support each other. Therefore, the mapping of protein interaction networks in a physiological context is conducive to deciphering protein functions, including those of hypothetical proteins. Although several high-throughput methods to globally identify protein interactions have been reported in recent years, these approaches often have a high rate of nonspecific or artificial interactions detected. For instance, the fraction of false positives of the protein interactions identified by yeast two-hybrid assay has been predicted to be of the order of 50%. We have developed a strategy to globally map Bacillus subtilis protein-protein interactions in a physiological context by fractionating the cell lysates using size-exclusion chromatography (SEC), followed by proteome analysis. Components of both known and unknown protein complexes, multisubunits and multiproteins, have been identified using this strategy. In one case, the partners of the B. subtilis protein complex have been coexpressed in Escherichia coli, and the formation of the overexpressed protein complex has been further confirmed by a pull-down assay.     

Comprehensive chromatographic separations in proteomics

In such a complicated field as proteomic analysis, scientists are more and more challenged in implementing separation systems capable to provide enhanced separation power, as well as sensitivity of detection for adequate identification and, to a lesser extent, quantification of the separated compounds. To address such issues, several combinations of different separation modes have been investigated in comprehensive liquid chromatographic platforms, in which the entire sample eluted from the first dimension is subjected to a secondary chromatographic separation. The different applications exploited for comprehensive LC analysis of intact or digested proteins are the focus of this review, in which advantages and disadvantages of the different columns combinations, interfaces, and operating modes are pointed out. The combination with mass spectrometry as part of the total system is stressed, and illustrated in more detail. Theoretical concerns and practical requirements will be briefly discussed, as well.     

Chromosome protein framework from proteome analysis of isolated human metaphase chromosomes

We have presented a structural model of the chromosome based on its constituent proteins. Development of a method of mass isolation for intact human metaphase chromosomes and proteome analysis by mass spectrometry of the isolated chromosomal proteins enabled us to develop a four-layer structural model of human metaphase chromosomes. The model consists of four layers, each with different chromosomal protein sets, i.e., chromosome coating proteins (CCPs), chromosome peripheral proteins (CPPs), chromosome structural proteins (CSPs), and chromosome fibrous proteins (CFPs). More than 200 identified proteins have been classified and assigned to the four layers with each layer occupying a distinct region of the chromosome. CCPs are localized at the most outer regions of the chromosomes and they attach to the regions tentatively and occasionally. CCPs include mostly mitochondrial and cytoplasmic proteins, e.g., 70 kDa heat shock protein 9B and Hsp60. CPPs are also localized at the peripheral regions of the chromosomes, but as the essential part of the chromosomes. CPPs include nucleolin, lamin A/C, fibrillarin, etc. CSPs are the primary chromosomal structure proteins, and include topoisomerase IIalpha, condensin subunits, histones, etc. CFPs have a fibrous nature, e.g., beta-actin, vimentin, myosin II, tublin, etc. A data set of these proteins, which we developed, contains essential chromosome proteins with classified information based on this four-layer model and presents useful leads for further studies on chromosomal structure and function.     

Comprehensive two-dimensional liquid chromatographic analysis of rooibos (Aspalathus linearis) phenolics

Rooibos tea is an unique beverage prepared from unfermented and fermented plant material of the endemic Cape fynbos plant, Aspalathus linearis. The well-known health-promoting benefits of rooibos are partly attributed to its phenolic composition. Detailed investigation of the minor phenolic constituents of rooibos is, however, hampered by the limitations associated with conventional HPLC methods used for its analysis. In this study, the applicability of comprehensive two-dimensional liquid chromatographic methods for the in-depth analysis of rooibos phenolics was investigated. Phenolic compounds were separated according to polarity by hydrophilic interaction chromatography (HILIC) in the first dimension, whilst reversed-phase liquid chromatography (RP-LC) provided separation according to hydrophobicity in the second dimension. Ultraviolet photodiode array and electrospray ionisation mass spectrometry were used to identify phenolic compounds. Comprehensive HILIC × RP-LC demonstrated its applicability for the analysis of a diverse range of phenolic compounds in unfermented and fermented rooibos samples, in which large qualitative differences in the phenolic composition were established. The combination of these orthogonal separations provided a significant improvement in resolution, as exemplified by practical peak capacities in excess of 2000 and 500 for off-line and on-line methods, respectively.     

Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography

We describe an approach for fractionating complex protein samples prior to two-dimensional gel electrophoresis using reversed-phase high-performance liquid chromatography. Whole lysates of cells and tissue were prefractionated by reversed-phase chromatography and elution with a five-step gradient of increasing acetonitrile concentrations. The proteins obtained at each step were subsequently separated by high-resolution two-dimensional gel electrophoresis (2-DE). The reproducibility of this prefractionation technique proved to be optimal for comparing 2-DE gels from two different cell states. In addition, this method is suitable for enriching low-abundance proteins barely detectable by silver staining to amounts that can be detected by Coomassie blue and further analyzed by mass spectrometry.