Two-dimensional Liquid Chromatography Separation Research Articles

Blind column selection protocol for two-dimensional high performance liquid chromatography

The selection of two orthogonal columns for two-dimensional high performance liquid chromatography (LC×LC) separation of natural product extracts can be a labour intensive and time consuming process and in many cases is an entirely trial-and-error approach. This paper introduces a blind optimisation method for column selection of a black box of constituent components. A data processing pipeline, created in the open source application OpenMS®, was developed to map the components within the mixture of equal mass across a library of HPLC columns; LC×LC separation space utilisation was compared by measuring the fractional surface coverage, fcoverage. It was found that for a test mixture from an opium poppy (Papaver somniferum) extract, the combination of diphenyl and C18 stationary phases provided a predicted fcoverage of 0.48 and was matched with an actual usage of 0.43. OpenMS®, in conjunction with algorithms designed in house, have allowed for a significantly quicker selection of two orthogonal columns, which have been optimised for a LC×LC separation of crude extractions of plant material.

A comparison of one-dimensional and microscale two-dimensional liquid chromatographic approaches coupled to high resolution mass spectrometry for the analysis of complex samples

The interest in two-dimensional liquid chromatography separations is growing every year together with the number of open questions on the benefits.

Determination of neurotransmitters and their metabolites using one- and two-dimensional liquid chromatography with acidic potassium permanganate chemiluminescence detection

High-performance liquid chromatography with chemiluminescence detection based on the reaction with acidic potassium permanganate and formaldehyde was explored for the determination of neurotransmitters and their metabolites. The neurotransmitters norepinephrine and dopamine were quantified in the left and right hemispheres of rat hippocampus, nucleus accumbens and prefrontal cortex, and the metabolites vanillylmandelic acid, 3,4-dihydrophenylacetic acid, 5-hydroxyindole-3-acetic acid and homovanillic acid were identified in human urine. Under optimised chemiluminescence reagent conditions, the limits of detection for these analytes ranged from 2.5 × 10(-8) to 2.5 × 10(-7)M. For the determination of neurotransmitter metabolites in urine, a two-dimensional high-performance liquid chromatography (2D-HPLC) separation operated in heart-cutting mode was developed to overcome the peak capacity limitations of the one-dimensional separation. This approach provided the greater separation power of 2D-HPLC with analysis times comparable to conventional one-dimensional separations.

Modified MuDPIT Separation Identified 4488 Proteins in a System-wide Analysis of Quiescence in Yeast

A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near-complete yeast proteome from a whole cell tryptic digest. This modified online two-dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4269 protein identifications were made from 4189 distinguishable protein families from yeast during log phase growth. The "Micro" MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days' time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations "oxidation reduction", "catabolic processing" and "cellular response to oxidative stress" was seen in the quiescent cellular fraction, consistent with their long-lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of "Ribosome" and "Proteasome", further defining the complex nature of yeast populations present during stationary phase growth. In total, 4488 distinguishable protein families were identified in all cellular conditions tested.

Chromatographic evaluation of multi-mode retention behavior of thiol-ene click chemistry based β-cyclodextrin stationary phase

A native beta-cyclodextrin (beta-CD) stationary phase was prepared by covalent bonding of beta-CD on silica particles via thiol-ene click chemistry. The resulting beta-CD bonded silica (Click TE-CD) was characterized by elemental analysis, which proved the successful immobilization of beta-CD on the silica support with thiol-ene click chemistry. Click TE-CD was chromatographically evaluated with a set of flavone glycosides under hydrophilic interaction chromatography (HILIC) mode, reversed-phase chromatography (RPLC) mode and supercritical fluid chromatography (SFC) mode. The acetonitrile content dependent "U" retention curves indicated its HILIC/RPLC mixed-mode retention behavior. The difference of the separation selectivity between HILIC, RPLC and SFC was described as orthogonality by using geometric approach. The orthogonalities between HILIC/RPLC, HILIC/SFC, and RPLC/SFC reached 69. 8%, 50. 8% and 50. 8%, respectively. The separation of Chinese traditional medicine Lignum Dalbergia Odorifera extract under HILIC, RPLC and SFC modes indicated the potential of Click TE-CD stationary phase in the analysis of complex samples. The mixed-mode HPLC properties and excellent orthogonality demon strated its flexibility in HPLC method development and its great potential in two-dimensional liquid chromatography separation on one HPLC column by different separation modes.

Limitation of predictive 2‐D liquid chromatography in reducing the database search space in shotgun proteomics: In silico studies

A two-dimensional (2-D) liquid chromatography (LC) separation of complex peptide mixtures that combines a normal phase utilizing hydrophilic interactions and a reversed phase offers reportedly the highest level of 2-D LC orthogonality by providing an even spread of peptides across multiple LC fractions. Matching experimental peptide retention times to those predicted by empirical models describing chromatographic separation in each LC dimension leads to a significant reduction in a database search space. In this work, we calculated the retention times of tryptic peptides separated in the C18 reversed phase at different separation conditions (pH 2 and pH 10) and in TSK gel Amide-80 normal phase. We show that retention times calculated for different 2-D LC separation schemes utilizing these phases start to correlate once the mass range of peptides under analysis becomes progressively narrow. This effect is explained by high degree of correlation between retention coefficients in the considered phases.

Two-dimensional high performance liquid chromatography separation and tandem mass spectrometry detection of atrazine and its metabolic and hydrolysis products in urine

Atrazine [6-chloro-N-ethyl-N′-(1-methylethyl)-1,3,5-triazine-2,4-diamine] is the most widely used herbicide in the United States. In recent years, there has been controversy about atrazine's potential endocrine/reproductive and neurological adverse effects in wildlife and humans. The controversy triggered several environmental and epidemiologic studies, and it generated needs for sensitive and selective analytical methods for the quantification of atrazine, atrazine metabolites, and degradation or hydrolysis products. We developed a two-dimensional high performance liquid chromatography (2D-HPLC) method with isotope dilution tandem mass spectrometry detection to measure atrazine in urine, along with 11 atrazine metabolites and hydrolysis products, including 6-chloro (Cl), 6-mercapto (Mer) and 6-hydroxy (OH) derivatives, and their desethyl, desisopropyl and diamino atrazine analogs (DEA, DIA and DAA, respectively). The 2D-HPLC system incorporated strong cation exchange and reversed phase separation modes. This versatile approach can be used for the quantitative determination of all 12 compounds in experimental animals for toxicological studies. The method requires only 10μL of urine, and the limits of detection (LODs) range from 10 to 50μg/L. The method can also be applied to assess atrazine exposure in occupational settings by measurement of 6-Cl and 6-Mer analogs, which requires only 100μL of urine with LODs of 1–5μg/L. Finally, in combination with automated off-line solid phase extraction before 2D-HPLC, the method can also be applied in non-occupational environmental exposure studies for the determination of −6-Cl and 6-Mer metabolites, using 500μL of urine and LODs of 0.1–0.5μg/L.

Proteomic analysis of early response lymph node proteins in mice treated with titanium dioxide nanoparticles.

Human exposure to nanoparticles is inevitable from natural and anthropogenic sources. Titanium dioxide (TiO2) nanoparticles are increasingly being used in pharmaceutical and cosmetic products. Previous studies revealed that TiO2 levels were significantly increased in tissues (e.g., lymph nodes) after mice were injected with nanosized TiO2. To identify early response lymph node proteins to TiO2 nanoparticles, groups of mice were intradermally injected with a low dose of DeGussa P25 TiO2 nanoparticles or vehicle alone. The proteomes of lymph nodes at 24 h were quantitatively analyzed using trypsin-catalyzed 16O/18O labeling in conjunction with two-dimensional liquid chromatography separation and tandem mass spectrometry (2DLC-MS/MS). A total of 33 proteins were significantly changed (over 1.3-fold, p<0.05) in the mice treated with TiO2 nanoparticles, which accounted for approximately 1% of the total proteins identified. The differentially expressed proteins mainly involve the immune response (e.g., inflammation), lipid and fatty acid metabolism, mRNA processing, and nucleosome assembly. Regulation of functionally distinct classes of proteins could be mediated by estrogen receptor (ESR1), PPARγ, and c-Myc signalings, etc. The differentially expressed proteins identified in this experiment could represent early response proteins to TiO2 nanoparticle treatment in mouse lymph nodes.

Two-dimensional liquid chromatography separation of peptides using reversed-phase/weak cation-exchange mixed-mode column in first dimension

Selection of a first-dimensional separation method is very important in proteomic studies performed with two-dimensional liquid chromatography (2D-LC), since reversed-phase chromatography (RPLC) is usually chosen as the second-dimensional separation method in most studies. In this paper, we assess the potential use of mixed-mode reversed-phase/weak cation-exchange (RP/WCX) chromatography in 2D-LC proteomic studies. First, a new RP/WCX mixed-mode stationary phase (named C18WCX) was synthesized based on the polar-copolymerized approach, and a C18WCX column with separation efficiency comparative to conventional C18 columns was developed. This new mixed-mode column primarily provides hydrophobic interactions under acidic condition, but can offer hydrophobic and cation-exchange interactions under neutral and weak basic conditions. An off-line 2D-RP/WCX–RPLC system was established using the C18WCX column with a mobile phase of pH 6.5 in the first dimension and a C18 column with a mobile phase of pH 3.0 in the second dimension. The orthogonality of this two-dimensional system, evaluated through the separation of 123 tryptic peptides, was shown to be higher than that of the conventional 2D-RP–RPLC approach. Applying this 2D-LC method to rat brain samples, we identified 1031 proteins and 4397 unique peptides. In addition, this new two-dimensional method improved the identification of basic peptides. Therefore, we propose that this novel 2D-RP/WCX–RPLC system can be used as an alternative approach for the two-dimensional separation of peptides.

Simultaneous quantification of four native estrogen hormones at trace levels in human cerebrospinal fluid using liquid chromatography–tandem mass spectrometry

Estrogens are known to exhibit neuroprotective effects on the brain. Their importance in this regard and in others has been emphasized in many recent studies, which increases the need to develop reliable analytical methods for the measurement of estrogen hormones. A heart-cutting two-dimensional liquid chromatography separation method coupled with electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been developed for simultaneous measurement of four estrogens, including estriol (E3), estrone (E1), 17β-estradiol (17β-E2), and 17α-estradiol (17α-E2), in human cerebrospinal fluid (CSF). The method was based on liquid–liquid extraction and derivatization of estrogens with dansyl chloride to enhance the sensitivity of ESI-based detection in conjunction with tandem mass spectrometry. Dansylated estriol and estrone were separated in the first dimension by an amide-C18 column, while dansylated 17β- and 17α-estradiol were resolved on the second dimension by two C18 columns (175mm total length) connected in series. This is the first report of a method for simultaneous quantification of all four endogenous estrogen compounds in their dansylated form. The detection limits for E1, 17α-E2, 17β-E2, and E3 were 19, 35, 26, and 61pg/mL, respectively. Due to matrix effects, validation and calibration was carried out in charcoal-stripped CSF. The precision and accuracy were more than 86% for the two E2 compounds and 79% for E1 and E3 while the extraction recovery ranged from 91% to 104%. The method was applied to measure estrogens obtained in a clinical setting, from the CSF of ischemic trauma patients. While 17β-estradiol was present at a significant level in the CSF of some samples, other estrogens were present at lower levels or were undetectable.

Differential liver proteome mapping of control and cadmium-fed rats

A comparative study of proteome maps from control and Cd-exposed rat liver was performed using a new technology of two-dimensional liquid chromatography separation method (PF-2D system, Beckman Coulter). Rats were fed for one month 0 or 100 μg Cd g −1. The between-replicate and between-sample variations showed good repeatability and suitable reproducibility for the two dimensions of separation of proteins. In this complex mixture, PF-2D led to the separation of two major peaks which differed between control and Cd-exposed rat livers, one being identified by mass spectrometry as Cu/Zn superoxide dismutase (SOD), a well-known biomarker of Cd exposure, the other as phosphatidylethanolamine binding protein (PEBP). SOD content was decreased in Cd-exposed rat liver, compared to the control group which was corroborated by a significant decrease of SOD activity. PEBP content also tended to be decreased after Cd exposure. Present results demonstrate interest but also limitations of proteomic approach using PF-2D system to analyze effects of chemicals on organisms.

Quantification of unbound prednisolone, prednisone, cortisol and cortisone in human plasma by ultrafiltration and direct injection into liquid chromatrography tandem mass spectrometry

The existing methods for quantitative analysis of free corticosteroids require high volume of plasma and laborious extraction processes. Development of ultrafiltration followed by the liquid chromatrography tandem mass spectrometry (LC-MS/MS) method that requires 300 microL of plasma, does not entail any offline extraction and achieves good sensitivity was described. Unbound corticosteroids were separated by the ultrafiltration of plasma using Microcon centrifugal filter devices (10,000 Dal nominal molecular weight limit). A 30 microL aliquot of the ultrafiltrate was directly injected into a two-dimensional high-performance liquid chromatography clean-up and separation system coupled with API-4000 mass spectrometer. The clean-up was performed on a Strata-X on-line extraction cartridge. A Zorbax-SB Phenyl, Rapid Resolution HT (2.1 x 100 mm) column was employed to chromatographically resolve cortisol and prednisolone from each other, from cortisone and prednisone as well as from interferences found in plasma from stable kidney transplant recipients. Intra- and inter-run imprecision and inaccuracy within +/-15% were achieved during a three-batch validation for quality control samples at six concentrations in ultrafiltrate from charcoal-stripped plasma and three concentrations from normal plasma, over a 2000-fold dynamic range. The lower limit of quantification was 0.100 ng/mL for all four corticosteroids. A highly selective, sensitive, simple and robust LC-MS/MS method was developed for the simultaneous quantification of free cortisol, cortisone, prednisolone and prednisone. The performance of the Strata-X on-line extraction cartridge was maintained for over 700 injections. The assay was successfully applied for the analysis of the analytes in over 500 plasma samples from stable kidney transplant recipients.

Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses

Analysis of shotgun proteomics datasets requires techniques to distinguish correct peptide identifications from incorrect identifications, such as linear discriminant functions and target/decoy protein databases. We report an efficient, flexible proteomic analysis workflow pipeline that implements these techniques to control both peptide and protein false discovery rates. We demonstrate its performance by analyzing two-dimensional liquid chromatography separations of lens proteins from human, mouse, bovine, and chicken lenses. We compared the use of International Protein Index databases to UniProt databases and no-enzyme SEQUEST searches to tryptic searches. Sequences present in the International Protein Index databases allowed detection of several novel crystallins. An alternate start codon isoform of βA4 was found in human lens. The minor crystallin γN was detected for the first time in bovine and chicken lenses. Chicken γS was identified and is the first member of the γ-crystallin family observed in avian lenses.Electronic supplementary materialThe online version of this article (doi:10.1007/s12177-009-9042-6) contains supplementary material, which is available to authorized users.

Targeted Quantitative Mass Spectrometric Identification of Differentially Expressed Proteins between Bax-Expressing and Deficient Colorectal Carcinoma Cells

Bax, a Bcl-2 interacting protein, plays a central role in several stimuli-induced apoptosis pathways through its functional and physical interactions with various biologically important proteins. Identification of the Bax-modulating protein network should be useful to further our understanding of Bax-mediated apoptosis. For the first time, we performed proteome-wide quantification and identification of differentially expressed proteins between Bax+/- and Bax-/- HCT116 clones using a newly developed quantitative mass spectrometric analysis strategy. This strategy is based on forward and reverse differential isotope labeling of the proteome digests of two comparative cells, followed by two-dimensional liquid chromatography separation and automated peptide deposition to matrix-assisted laser desorption ionization sample plates for MS quantification and MS/MS peptide sequence identification. We quantified and identified 200 differentially expressed proteins involved in various cellular processes. Through bioinformatic analysis, four groups of differentially expressed proteins were highlighted for the association with Bax: mitochondria permeability transition channel proteins, Bax regulator proteins, heat shock protein family members, and oxidative stress-triggered proteins. These results indicate the functional diversity of Bax and provide new research directions to study the biology of Bax-regulated apoptosis.

Optimization strategies for off-line two-dimensional liquid chromatography

A step by step strategy of optimization of comprehensive off-line two-dimensional liquid chromatography (2D-LC) separations is proposed. The goal of an optimization process in the separation sciences is either to achieve a given resolution (a target peak capacity in 2D-LC) within as short a time as possible or to reach the highest possible resolution in a given analysis time. The proposed method takes into account the characteristics of the columns used in the first and the second dimension and the number of fractions of the first dimension eluent that should be collected. The effect of the time spent during the analysis on the second dimension column to carry out necessary tasks that are not the separation itself (called the additional time) on the maximum peak capacity that is achievable was carefully investigated. It was shown that (1) an increase in the peak capacity of the first dimension column combined with the collection of larger volume fractions permits a significant reduction of the time needed to achieve the desired peak capacity; and (2) there is an optimum fraction collection ratio (or number of collected fractions per peak) which yields the target peak capacity in the minimum time. The proposed strategy was used for the optimization of the separation of samples of BSA tryptic digest by an off-line 2D-LC using an SCX ⊗ RP -HPLC method. As a result of this optimization, a peak capacity of 4000 could be achieved in about 5 h with the two columns available. The time needed for the optimized analysis was less than two thirds of the analysis time that would have been needed had the conventional rule of thumb of sample collection in comprehensive on-line 2D-LC (4 samples/peak) been followed.

Comprehensive two-dimensional liquid chromatography separations of pharmaceutical samples using dual Fused-Core columns in the 2nd dimension

This paper focuses on the application of RPLC×RPLC to pharmaceutical analysis and addresses the specific problem of separating co-eluting impurities/degradation products that maybe “hidden” within the peak envelope of the active pharmaceutical ingredient (API) and thus may escape detection by conventional methods. A comprehensive two-dimensional liquid chromatograph (LC×LC) was constructed from commercially available HPLC equipment. This system utilizes two independently configurable 2nd dimension binary pumping systems to deliver independent flow rates, gradient profiles and mobile phase compositions to dual Fused-Core secondary columns. Very fast gradient separations (30s total cycle time) were achieved at ambient temperature without excessive backpressure and without compromising optimal 1st dimension sampling rates. The operation of the interface is demonstrated for the analysis of a 1mg/ml standard mixture containing 0.05% of a minor component. The practicality of using RPLC×RPLC for the analysis of actual co-eluting pharmaceutical degradation products, by exploiting pH-induced changes in selectivity, is also demonstrated using a three component mixture. This mixture (an API, an oxidation product of the API at 1.0%, w/w, and a photo degradant of the API at 0.5%, w/w) was used to assess the stability indicating nature of an established LC method for analysis of the API.

Synthesis, chromatographic evaluation and hydrophilic interaction/reversed-phase mixed-mode behavior of a “Click β-cyclodextrin” stationary phase

A native β-cyclodextrin (β-CD) stationary phase was prepared by covalently bonding β-CD on silica particles via Huisgen [3 + 2] dipolar cycloaddition between the organic azide and terminal alkyne, the so-called Click chemistry. The resulting β-CD bonded silica (Click β-CD) was characterized by FT-IR, solid state 13C cross polarization/magic-angle spinning (CP/MAS) NMR and elemental analyses, which proved the successful immobilization of β-CD on the silica support with Click chemistry. The retentive properties of Click β-CD were investigated under hydrophilic interaction liquid chromatography (HILIC) mode in different mobile phase conditions with a set of polar compounds including nucleosides, organic acids and alkaloids. The effects of water content, concentration of the salt and pH of the buffer solution on the retention time were studied and the results demonstrated the typical retention behavior of HILIC on Click β-CD. Separation of very polar components, such as nucleosides and oligosaccharides, and chiral separation under HILIC mode were successfully achieved. In addition, Click β-CD was chromatographically evaluated with a set of flavone glycosides. The retention curves depending on the mobile phase of acetonitrile content were “U” curves, which is an indication of HILIC/RPLC mixed-mode retention behavior. The difference of the separation selectivity between HILIC and RPLC was described as orthogonality by using geometric approach and the orthogonality reached 69.4%. The mixed-mode HPLC properties and excellent orthogonality demonstrated the flexibility in HPLC methods development and great potential in two-dimensional liquid chromatography separation.

Optimization of two-dimensional gradient liquid chromatography separations

An almost orthogonal comprehensive two-dimensional liquid chromatography was developed for the separation of phenolic and flavone natural antioxidants by using combinations of a polyethylene glycol silica micro-column in the first dimension and a porous-shell fused-core C18 column in the second dimension, both in the reversed-phase mode. System orthogonality was improved using parallel gradients of acetonitrile in buffered mobile phase. A new approach was proposed to optimize matching segmented gradient profiles in the two dimensions. An algorithm was developed for automatic corrections of the shifts in retention in the second dimension induced by the parallel two-dimensional gradient operation technique. Using the porous-shell C18 column in the second dimension at elevated temperature (60 °C) and high pressure (480 bar) with optimized segmented profiles of the parallel gradients in the two dimensions, the overall separation time for comprehensive LC × LC was reduced to 30 min.

Proteome Profile of Cytosolic Component of Zebrafish Liver Generated by LC−ESI MS/MS Combined with Trypsin Digestion and Microwave-Assisted Acid Hydrolysis

The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the cytosolic component of a zebrafish liver tissue sample. Our methods involve cell-compartment fractionation of liver tissue samples, four levels of protein digestion, and off-line two-dimensional liquid chromatography (2-D LC) separations of resultant peptides. Proteins are identified using an electrospray ionization quadrupole time-of-flight tandem mass spectrometer (ESI-QTOF MS/MS), which provides high-resolution and high-accuracy mass measurement of peptide ions and their fragment ions. We demonstrate that greater proteome coverage can be achieved by combining the results obtained from four methods of protein digestion: three tryptic digests (one in buffer, one in methanol, and another in SDS), and a microwave-assisted acid hydrolysate of the protein extracts. Identified proteins--which included several groups of established protein biomarkers--were functionally classified. We discuss the functions and implications of these biomarkers within the context of zebrafish toxicology.

Multidimensional capillary array liquid chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for high-throughput proteomic analysis

A two-dimensional capillary array liquid chromatography system coupled with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) was developed for high-throughput comprehensive proteomic analysis, in which one strong cation-exchange (SCX) capillary chromatographic column was used as the first separation dimension and 10 parallel reversed-phase liquid chromatographic (RPLC) capillary columns were used as the second separation dimension. A novel multi-channel interface was designed and fabricated for on-line coupling of the SCX to RPLC column array system. Besides the high resolution based on the combination of SCX and RPLC separation, the developed new system provided the most rapid two-dimensional liquid chromatography (2D-LC) separation. Ten three-way micro-splitter valves used as stop-and-flow switches in transferring SCX fractions onto RPLC columns. In addition, the three-way valves also acted as mixing chambers of RPLC effluent with matrix. The system enables on-line mixing of the LC array effluents with matrix solution during the elution and directly depositing the analyte/matrix mixtures on MALDI plates from the tenplexed channels in parallel through an array of capillary tips. With the novel system, thousands of peptides were well separated and deposited on MALDI plates only in 150 min for a complex proteome sample. Compared with common 2D-LC system, the parallel 2D-LC system showed about 10-times faster analytical procedure. In combination with a high throughput tandem time of flight mass spectrometry, the system was proven to be very effective for proteome analysis by analyzing a complicated sample, soluble proteins extracted from a liver cancer tissue, in which over 1202 proteins were identified.