Proteomic analysis of rat plasma by two-dimensional liquid chromatography and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

The proteomic analysis of plasma and serum samples represents a formidable challenge due to the presence of a few highly abundant proteins such as albumin and immunoglobulins. Detection of low abundance protein biomarkers therefore requires either the specific depletion of high abundance proteins using immunoaffinity columns and/or optimized protein fractionation methods based on charge, size or hydrophobicity. Here we describe a two-dimensional (2D) liquid chromatography separation method for the fractionation of rat plasma. In the first dimension proteins were separated by chromatofocusing according to their isoelectric point (pI). In the second dimension, proteins were further fractionated by non-porous, reversed-phase chromatography according to their hydrophobicity. The data from both separations was displayed as a 2D protein expression map of pI versus retention time (relative hydrophobicity). Both separations were carried out on the ProteomeLab PF 2D system (Beckman Coulter), an instrument platform that provides a high degree of automation and real-time monitoring of the separation process. The reproducibility of the first-dimension separation was evaluated in terms of pH gradient formation. The second-dimension separation was evaluated in terms of peak retention times on the reversed-phase column. We found in four consecutive chromatofocusing separations that the pH gradient differed by less than 0.2 pH units at any time during the elution step. Second dimension retention times of peaks from identical pI fractions differed by less than 7 s in six consecutive separations. Each 2D separation generated a total of 540 fractions which were analyzed by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). We detected approximately 275 peptides and proteins with molecular masses ranging from 3 to 225 kDa. Most fractions were found to contain multiple low and high molecular weight proteins. Differential display of 2D protein expression maps from retinol-sufficient and -deficient rat plasma samples identified a fraction with several proteins that appeared to be down-regulated in the vitamin A-deficient animal. Quantitative proteomic analysis of complex samples such as plasma is still a difficult task. We discuss the potential of this approach for biomarker discovery and address the experimental challenges that remain.     

Use of polymeric reversed-phase columns for the characterization of polypeptides extracted from human pancreata. II. Effect of the stationary phase

The potential value of eight commercial available polymer-based reversed-phase (RP) columns for peptide and protein separations was evaluated using crude acetic acid extracts of normal and diabetic human pancreata and mixtures of pure polypeptides as samples. All columns were characterized with acetic acid gradients in water as mobile phase, and different chromatographic profiles were obtained depending on the type of polymer column (bare or derivatized) and the type of ligand. Some of the columns were virtually free from effects related to the polymer skeleton whereas in others the separation was influenced by both the ligand and the polymeric backbone. Two selected polymeric RP columns were, together with a silica-based C4 column, further characterized with acetonitrile gradients in trifluoroacetic acid (TFA), and the separation temperature was found to have a drastic effect on the separation efficiency for proteins with mol. wt. greater than 6000 dalton. No such effect was seen for polypeptides with mol. wt. less than 6000 dalton. Mixtures of pure peptides and proteins were separated using acetic acid gradients in water, acetonitrile or isopropanol, and normally the highest efficiency was found with the use of acetonitrile as mobile phase modifier. Isopropanol was less suitable as an organic modifier. The separation of the beta-lactoglobulin A- and B-chains may be used to give a rapid estimate of the chromatographic usability of polymer-based RP-columns for peptide and protein separations in acetic acid gradients in water and in acetonitrile gradients. Recoveries for insulin, proinsulin, growth hormone, ovalbumin and human serum albumin were measured for several polymer-based RP columns eluted with acetic acid gradients in water and with acetonitrile-based mobile phases. The highest recoveries of serum albumin and ovalbumin were found after elution with acetic acid gradients in water.     

Combining restricted access material (RAM) and turbulent flow for the rapid on-line extraction of the cyclooxygenase-2 inhibitor rofecoxib in plasma samples

Restricted access material (RAM) has been used in the packing of a solid-phase extraction (SPE) column for on-line extractions under turbulent flow conditions. The bio-compatible RAM material works by the principle of size exclusion in addition to conventional reversed-phase chromatography, thereby allowing the extraction and preconcentration of small analyte molecules from biological samples such as plasma. Using small column dimensions (0.76 mm x 50 mm) and a consequently high linear velocity, turbulent flow was achieved during online sample extractions. The improved mass-transfer rate characteristic of turbulent flow allows fast sample cleanup without decreased extraction efficiency. The novel use of the RAM column, connected upstream to a C18 monolithic column, allowed the direct injection, extraction, separation, and MS/MS detection of plasma samples spiked with rofecoxib in a span of 5 min. Calibration curves obtained using this RAM turbulent flow coupled column method showed good linearity (R2 > 0.99) and reproducibility (%RSD < or = 7%). The lower limit of quantitation of rofecoxib in plasma samples was found to be 40 ng/ml. The extraction method showed good recovery of rofecoxib from a plasma matrix with minimal signal loss and robustness after more than 200 plasma injections.     

Non-particulate (continuous bed or monolithic) restricted-access reversed-phase media for sample clean-up and separation by capillary-format liquid chromatography

Restricted-access reversed-phase non-particulate (continuous bed or monolithic) stationary phases of different hydrophobicity synthesized in 100 m i.d. fused silica capillaries have been evaluated. A specific property of restricted-access media (RAM) is that they interact with small analytes and exclude big molecules, e.g. proteins, from access to the active sites and adsorption on the surface. This dual property facilitates direct injection of biological fluids for drug or drug-metabolite analysis. Different RAM and RAM-precursor capillary columns were tested to assess the influence of chromatographic bed morphology on loadability. Inverse size-exclusion chromatography was used for investigation of pore structural properties of the capillary-format continuous beds. The data obtained were used to discuss the mechanism of separation of the biological samples using capillary columns and to propose a model for the topochemical architecture of the RAM investigated. Different morphology of the non-particulate reversed-phase precursors resulted in two types of RAM material shielded with hydrophilic polymer, classified as homogeneous or heterogeneous topochemistry stationary phases. Capillary columns were applied for chromatography of biological fluids. High resolution was obtained, without the need for column switching, when capillary columns operated in gradient conditions. Extensive evaluation of the chromatographic properties (hydrophobicity, efficiency, separation impedance, and loadability) of the non-particulate reversed-phase materials was performed before and after shielding with hydrophilic polymer to generate restricted-access properties. Minor changes of hydrophobicity, efficiency, or separation impedance were observed after the shielding.     

Capillary scale monolithic trap column for desalting and preconcentration of peptides and proteins in one- and two-dimensional separations

Monolithic columns based on poly-(styrene-divinylbenzene) (PS-DVB) were utilized both for preconcentration (in 10 mm x 0.20 mm I.D. format) and analytical separation (in 60 mm x 0.20 and 0.10 mm I.D. format) of peptides and proteins in column switching micro-scale high-performance liquid chromatography. A special holder for short monolithic preconcentration columns was designed and pressure durability tests approved long-term stability up to 400 bar. An 11-20% decrease in the average peak widths of nine peptides was obtained upon combining a preconcentration column with an analytical column as compared with a setup using an analytical column only. Trapping efficiency, especially for small and hydrophilic peptides, was optimized by using 0.10% heptafluorobutyric acid instead of 0.050% trifluoroacetic acid as solvent additive during sample loading. Using a 10 mm x 0.20 mm I.D. preconcentration column, loadabilities between 0.5 and 1.6 microg were determined by frontal analysis of proteins and bioactive peptides, respectively. A 100-fold concentration followed by direct on-line intact mass determination is demonstrated for diluted (3 micromolL(-1)) protein solutions. The applicability of the monolithic preconcentration column for multidimensional chromatography was tested by off-line two-dimensional separation, combining strong cation-exchange chromatography and ion-pair reversed-phase chromatography. Peptide identification data from digested protein mixtures demonstrated reproducibilities of 46-75% in triplicate analyses, and confident peptide identifications of low abundant peptides even in the presence of a 650-fold molar excess of high abundant peptides.     

An improved method for tracking and reducing the void volume in nano HPLC–MS with micro trapping columns

Tandem mass spectrometry coupled to HPLC is the state of the art technique in proteomic research. Here we describe a highly sensitive nano liquid chromatography system (nano HPLC) for analysis of protein digests. Using preconcentration in a column-switching set-up, we were able to inject large sample volumes (250 µL) without significant loss of sensitivity. The major problem with this type of preconcentration is usually the occurrence of void volumes. In order to diagnose void volumes a simple and easy test was developed by which the UV trace and the pressure profile in the separation column were monitored. Part by part replacement of connection tubing restored a void volume-free system. A major pre-requisite for handling samples in the femtomol range was found to be the use of protein/peptide-saturated columns tryptic digests of cytochrome C were injected directly onto the reversed-phase nano separation column (75 µm inner diameter) and the separation results were compared with chromatograms obtained from separations using column switching. By using column switching we were able to inject large sample volumes in a short time period without losing resolution.     

Analysis of native carotenoid composition of sweet bell peppers by serially coupled C30 columns

Serial coupled columns reversed-phase separations in high-performance liquid chromatography can be a useful tool for the analysis of complex real samples. The great difficulties found when analyzing complex carotenoid samples, due to the high natural variability of these compounds, as well as to the presence of carotenoid esters, are well documented. In the present contribution, the applicability of connecting two C30 columns to increase significantly the separation power, resolution and peak capacity for the analysis of carotenoids in a complex carotenoid sample, like sweet bell peppers, has been shown for the first time. By using LC coupled to PDA/APCI-MS detectors, 56 different carotenoids have been detected in red sweet bell peppers. By using two serial coupled C30 columns a peak capacity of 95.4 was obtained, compared with 73 achieved using a single column. Moreover, resolution greatly improved between different critical peaks when using two serial coupled C30 columns, compared with a single column. Interestingly, free carotenoids, mono-esters and diesters were quantitatively equally represented (around 33% for each different class) in red sweet bell pepper, showing, therefore, a value for the ratio of mono-esters/diesters of around 1, which could be considered a parameter of typicality. Free beta-carotene (12.6%), capsanthin-C14:0 (8.4%), and capsanthin-C12:0-C14:0 (8.9%) were the most abundant carotenoids in the three different classes of red sweet bell pepper. No carotenoid esters were detected in either yellow or green sweet bell peppers. The application of such methodology in the analysis of other complex carotenoid matrices could be a future objective of research.     

Elevated temperature-extended column length conventional liquid chromatography to increase peak capacity for the analysis of tryptic digests

High efficiency separations (200 000 plates) were obtained on conventional LC equipment by coupling 8 x 25 cm x 2.1 (or 4.6) mm id x 5 microm d(p) ODS columns (total length 2 m) and operation at 60 degrees C using a dedicated LC oven. The peak capacity in this 1-D set-up was 900 for the separation of human serum tryptic peptides analyzed after depletion of six highly abundant proteins. The chromatographic performance of an elevated temperature-extended column length conventional LC is highlighted.     

Comparison of the performance of conventional microparticulates and monolithic reversed-phase columns for liquid chromatography separation of eleven pollutant phenols

The performance of isocratic separations of 11 pollutant phenols (PP) using monolithic (Chromolith RP-18e) and conventional reversed-phase 5 microm (Luna and Purospher C18) and 4 microm (Synergi C12) particulate size columns, selected from high purity silica materials, has been compared. The separations have been optimized based on a previously optimized separation in which a reversed-phase C18 Luna column and acetonitrile as organic modifier were used, allowing the separation of all phenols tested in 23 min. The optimization process was carried out for each column by studying the effect of the mobile phase (acetonitrile as organic modifier, pH, flow-rate) on phenols separation. Under the optimized separation conditions, all phenols were separated in less than 23 min for all columns tested. Asymmetry factors were further evaluated and used to estimate column efficiency using the Dorsey-Foley equation. The efficiency and asymmetry factors were lower for Chromolith than for Purospher and Luna columns respectively. The Chromolith column was finally selected, due to its lower flow resistance, analysis time and good efficiency and asymmetry factors. The PPs separation was achieved in 3 min. The asymmetry factors were in the range 0.9-1.5 using 50mM acetate buffer (pH = 5.25)-ACN (64:36, v/v) as mobile phase, T=45 degrees C and 4.0 ml min(-1) flow-rate.     

Multidimensional on-line solid-phase extraction (SPE) using restricted access materials (RAM) in combination with molecular imprinted polymers (MIP)

A novel, multidimensional SPE sample-processing platform for complex fluids, which relies on the combination of small LC columns packed with restricted access materials (RAM) and molecular imprinted polymers (MIP) is described. It is called the Six-S ProcEdure (Six-SPE). Six-SPE involves a size-selective sample-separation step followed by a solvent-switch. Six-SPE efficiently removes interfering matrix components of complex aqueous samples and creates optimal conditions for selective recognition, i.e. binding of the imprinted target analyte(s). A Six-SPE analysis cycle consists of four distinct steps: 1. separation of a given sample (e.g. plasma, urine, saliva, milk, etc.) by adsorptive extraction (e.g. reversed-phase partitioning) of low molecular weight components on to the stationary phase of a RAM column and simultaneous size-exclusion, i.e. quantitative disposal of macromolecular matrix constituents to waste; 2. desorption and transfer of the extract from the RAM column on to a series-connected MIP column using a pure organic mobile phase (e.g. acetonitrile) [solvent switch]; 3. molecular recognition, i.e. selective binding of the target analyte(s) by a tailor-made MIP column; and 4. desorption and transfer of the analyte fraction on to a series-connected separation (e.g. HPLC) and/or detection system (e.g. UV, FD, MS). As a first application we coupled the Six-SPE platform to a conventional HPLC system for on-line analysis of the analgesic drug Tramadol in human plasma using LiChrospher ADS RP-18 as a RAM precolumn for the fractionation step in the first and second chromatographic dimension and a Tramadol imprinted polymer for the molecular recognition step, i.e. third chromatographic dimension.     

Application of micropellicular poly-styrene/divinylbenzene stationary phases for high-performance reversed-phase liquid chromatography electrospray-mass spectrometry of proteins and peptides

Summary Short columns packed with highly crosslinked 2.3 μm poly-styrene/divinylbenzene (PS/DVB) particles were used for rapid and efficient separation of proteins and peptides by reversed-phase high-performance liquid chromatography at elevated temperatures. Enhancement of the diffusivities of the sample components at elevated temperatures together with the short diffusion pathlength with the micropellicular polymeric stationary phases were responsible for high efficiency, high speed of analysis, and short column regeneration times. Underivatized PS/DVB beads as well as PS/DVB microspheres which have been modified with polyvinylalcohol or octadecyl chains on the surface were synthesized, employed, and compared to HY-TACH-C18, a commercially available micropellicular octadecyl-silica stationary phase, for the separation of proteins, octapeptides and tryptic protein digests. Highest performance was obtained with the silica- and PS/DVB-based octadecyl stationary phases, which exhibited similar column efficiencies but different selectivities for proteins and peptides. The minimum detectability at 214 nm and the maximum loading capacity for ribonuclease A using analytical 30×4.6 mm I.D. columns were 10 ng (0.6 pmol) and 1 μg, respectively. Finally, reversed-phase HPLC with a 60×2 mm I.D. narrow-bore column packed with micropellicular octadecyl PS/DVB was coupled successfully to electrospray mass spectrometry at a flow-rate of 0.15 mL min⁻¹ and on-line full-scan mass spectra for molecular mass determination and identification of proteins in the lower picomol range were obtained.     

Development of an on-line immobilized-enzyme reversed-phase HPLC method for protein digestion and peptide separation

This paper describes use of a novel glass bead-based immobilized-enzyme micro column for simple and swift on-line protein digestion then peptide separation by reversed-phase HPLC. The inexpensive and easily made immobilized-enzyme micro column was prepared from aminopropyl controlled-pore glass that was reacted first with glutaraldehyde then with trypsin in the presence of phosphate buffer. Tryptic digestion of bovine serum albumin (BSA) was achieved simply by passing pretreated protein solution through the laboratory made immobilized-trypsin column; the tryptic fragments were then separated by reversed-phase HPLC. The peptide separation was found to be identical to separation of a sample which had undergone conventional enzymatic protein digestion in solution. Digestion of BSA by the immobilized-trypsin column decreased with increasing flow rate of the solution through the column, and 1.0 μL min⁻¹ was found to be the optimum flow rate for on-line protein digestion with our system. It was also found that the sample required pretreatment with urea before injection, because of a change in the properties of the protein in the presence of urea, and the immobilized-trypsin column lost its function in the presence of acetonitrile. This on-line proteomics system enables simple and rapid protein digestion and was successfully applied to partially micro two-dimensional (2D) chromatographic separation of proteins.     

Preparation of a butyl–silica hybrid monolithic column with a “one-pot” process for bioseparation by capillary liquid chromatography

A butyl–silica hybrid monolithic column for bioseparation by capillary liquid chromatography (cLC) was prepared with butyl methacrylate and alkoxysilanes through a “one-pot” process. The effects of polycondensation temperature, volume percentage of N,N′-dimethylformamide, and content of cetyltrimethylammonium bromide and butyl methacrylate on the morphologies of the hybrid monolithic columns prepared were investigated in detail. Baseline separations of proteins and small peptides on the hybrid monolithic column were achieved by cLC with gradient elution. In addition, the resulting hybrid column was also applied for analysis of tryptic digests of bovine serum albumin by cLC coupled with tandem mass spectrometry. The results demonstrate its potential application in separation of complex biological samples.     

Factors affecting the separation and loading capacity of proteins in preparative gradient elution high-performance liquid chromatography.

The optimum conditions for the purification of proteins by gradient elution in reversed-phase liquid chromatography were studied, with emphasis on the column length. Because of the strong dependence of the retention of proteins on the mobile phase composition, very short columns can be used successfully to perform analytical separations. A similar conclusion is extended to preparative separations. Columns with different lengths and diameters were used. The dependence of the loading capacity for touching band separation on the column length, diameter and volume was studied, in addition to the regeneration time between successive runs, the starting mobile phase composition and the necessary column efficiency.     

Micropreparative separation of peptides derived from sodium dodecyl sulphate-solubilized proteins

A systematic investigation of the influence of the detergent sodium dodecyl sulphate (SDS) on micropreparative peptide separations on microbore reversed-phase high-performance liquid chromatographic columns is reported. A tryptic digest of bovine serum albumin and a mixture of synthetic peptides were used to monitor the separation behaviour of a 1.6 mm I.D. Nucleosil C18 column in the presence of various amounts of SDS. The data demonstrate that even traces of SDS in the sample reduce the separation efficiency and peptide recovery. An extraction method is presented which reduces the SDS content in peptide mixtures below the critical concentration without affecting significantly the recovery of individual peptides. After acidification of the sample, the detergent is extracted into heptane-isoamyl alcohol (4:1, v/v). In combination with chemical or enzymatic fragmentation techniques, this extraction method facilitates the sequence analysis of minute amounts of SDS-solubilized hydrophobic proteins. The applicability of the method is demonstrated on the example of the integral membrane protein bacteriorhodopsin.     

Micellar electrokinetic chromatography - From theoretical concepts to real samples (Review)

Micellar electrokinetic chromatography (MEKC) is an alternative to liquid chromatographic separations. It is a highly efficient separation technique that is performed with the same experimental set-up as is used for capillary electrophoresis (CE), thus extending the applicability of CE to neutral solutes. MEKC can be regarded as a separation technique with a similar scope to that of reversed-phase high-performance liquid chromatography (RP-HPLC), having advantages over HPLC with regard to the efficiency of the separation system, separation speed, cost, and tolerance to matrix constituents. This paper discusses the applicability of MEKC to real samples and also addresses developments widening the scope of this emerging technique: on-line concentration by stacking or sweeping and sensitive detection schemes.     

Anion chromatography with a crown ether-based stationary phase and an organic modifier in the eluent

The unique ability of macrocyclic ligands, such as the crown ethers and cryptands, to selectively complex alkali metal cations can be used as the basis for chromatographic separations of anions. Specifically, macrocycles which are adsorbed onto a reversed-phase column, form positively charged anion-exchange sites when they combine with eluent cations. Previously we have demonstrated gradient anion separations based on changing the column capacity during the course of the separation by altering the eluent cation, temperature, or organic modifier content using cryptand-based columns. Herein we report that excellent separations can also be achieved using 18-crown-6 based columns. In this column, anion retention increases with increasing eluent strength and organic modifier content. This observation is in keeping with the relatively moderate affinity of crown ethers for alkali metals when compared to cryptands. The separation of anions achieved by optimizing mobile phase variables shows that isocratic separations of anions on the crown-based column are almost as good as separations achieved only under gradient conditions on cryptand-based columns. Cation gradients provide additional improvements on the separations using the crown-based column.     

Superficially porous silica microspheres for fast high-performance liquid chromatography of macromolecules

Very fast reversed-phase separations of biomacromolecules are performed using columns made with superficially porous silica microsphere column packings ("Poroshell"). These column packings consist of ultra-pure "biofriendly' silica microspheres composed of solid cores and thin outer shells with uniform pores. The excellent kinetic properties of these new column packings allow stable, high-resolution gradient chromatography of polypeptides, proteins, nucleic acids, DNA fragments, etc. in a fraction of the time required for conventional separations. Contrasted with <2-microm non-porous particles, Poroshell packings can be used optimally with existing equipment and greater sample loading capacities, while retaining kinetic (and separation speed) advantages over conventional totally porous particles.     

Column-friendly reversed-phase high-performance liquid chromatography of peptides and proteins using formic acid with sodium chloride and dynamic column coating with crown ethers.

Reversed-phase high-performance liquid chromatography of proteins, traditionally carried out with strong acids like trifluoroacetic acid or phosphoric acid, which can damage reversed-phase columns, can be performed with excellent results using the far milder formic acid in the presence of salt. For certain separations, dynamic coating of the column with crown ethers can bring added resolution. Examples given are for peptides from a digest of methionine growth hormone, protein separations from whey proteins containing alpha-lactalbumin and the beta-lactoglobulins A and B, and bovine and porcine insulins. The separation of methionine-growth hormone from growth hormone is also described.     

Protein mapping by two-dimensional high performance liquid chromatography

Current developments in drug discovery in the pharmaceutical industry require highly efficient analytical systems for protein mapping providing high resolution, robustness, sensitivity, reproducibility and a high throughput of samples. The potential of two-dimensional (2D) HPLC as a complementary method to 2D-gel electrophoresis is investigated, especially in view of speed and repeatability. The method will be applied for proteins of a molecular mass <20 000 which are not well resolved in 2D-gel electrophoresis. The 2D-HPLC system described in this work consisted of anion- or cation-exchange chromatography in the first dimension and reversed-phase chromatography in the second dimension. We used a comprehensive two-dimensional approach based on different separation speeds. In the first dimension 2.5 microm polymeric beads bonded with diethylaminoethyl and sulfonic acid groups, respectively, were applied as ion exchangers and operated at a flow-rate of 1 ml/min. To achieve very high-speed and high-resolution separations in the second dimension, short columns of 14 x 4.6 mm I.D. with 1.5 microm n-octadecyl bonded, non-porous silica packings were chosen and operated at a flow-rate of 2.5 ml/min. Two reversed-phase columns were used in parallel in the second dimension. The analyte fractions from the ion-exchange column were transferred alternatively to one of the two reversed-phase columns using a 10-port switching valve. The analytes were deposited in an on-column focusing mode on top of one column while the analytes on the second column were eluted. Proteins, which were not completely resolved in the first dimension can, in most cases, be baseline-separated in the second dimension. The total value of peak capacity was calculated to 600. Fully unattended overnight runs for repeatability studies proved the applicability of the system. The values for the relative standard deviation (RSD) of the retention times of proteins were less than 1% (n = 15), while the RSDs of the peak areas were less than 15% (n = 15) on average. The limit of detection was 300 ng of protein on average and decreased to 50 ng for ovalbumin. The 2D-HPLC system offered high-resolution protein separations with a total analysis time of less than 20 min, equivalent to the run time of the first dimension.