Increased throughput and reduced carryover of mass spectrometry-based proteomics using a high-efficiency nonsplit nanoflow parallel dual-column capillary HPLC system

We report a new design of a fully automated, high-efficiency parallel nonsplit nanoflow capillary HPLC system, coupled on-line with linear ion trap (LTQ) and high performance nanoelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (nanoESI LTQ-FTICR MS). The system, intended for high-throughput proteome analysis of complex protein mixtures, notably serum and plasma, consists of two reversed-phase trap columns for large volume sample injection with high speed sample loading and desalting and two reversed-phase analytical capillary columns. Through a nanoscale two-position, 10-port switching valve, the whole system is terminated by a 10 microm i.d. of nanoemitter mounted on the nanoelectrospray source in front of the sampling cone of the LTQ-FTICR MS. Gradient elution to both nanoflow-rate capillary columns is simultaneously delivered by a single HPLC system via two independent binary gradient pump systems. The parallel capillary column approach eliminates the time delays for column regeneration/equilibration since one capillary column is used for separating the sample mixtures and delivering the separated fractions to the MS, while the other capillary column is being regenerated and equilibrated. The reproducibility of retention time and peak intensity of the present automated parallel nanoflow-rate capillary HPLC system is comparable to that obtained using a single column configuration. Replicate injections of tryptic digests indicated that this system provided good reproducibility of retention time and peak area on both columns with average CV values of less than 1.08% and 7.04%, respectively. Throughput was increased to 100% for 2-h LC-MS analysis compared to the single capillary column LC-MS pipeline. Application of this system is demonstrated in a plasma proteomic study. A total of 312 868 MSMS events were acquired and 1564 proteins identified with high confidence (Protein Prophet > or = 0.9, and peptides matched > or = 2). Comparison of a series of plasma fractions run using the single-column LC-MS versus the parallel-column LC-MS demonstrated that parallel-column LC-MS system significantly reduced the sample carryover, improved MS data quality and increased the number of MS/MS sequence scan events.     

Applications of monolithic silica capillary columns in proteomics

The use and applicability of silica based capillary monolithic reversed-phase columns in proteomic analysis has been evaluated by liquid chromatography-mass spectrometry (LC-MS). Chromatographic performance of the monolithic capillaries was evaluated with a tryptic digest of cytochrome C showing very good resolution and reproducibility in addition to the known advantages of a low pressure drop over a time period of 6 months. Monoliths were subsequently tested for their suitability to separate proteins and peptides from samples typically encountered in proteomic research such as in-gel digested tryptic peptide mixtures or fractions of proteolytically digested human serum. The monolithic capillaries also proved useful in the analysis of phospholipid species in bronchoalveolar lavage fluid. Compared to particle-filled conventional capillary columns, rapid and highly efficient separation of peptides and proteins was achieved using these bimodal pore size distribution columns, and good quality collision induced dissociation (CID) mass spectra were obtained on an ion trap mass spectrometer. These novel monolithic separation media are thus a promising addition to the methodological toolbox of proteomics research.     

Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column

An approach was developed to automate sample introduction for nanoflow LC-MS/MS (microLC-MS/MS) analysis using a strong cation exchange (SCX) trap column. The system consisted of a 100 microm id x 2 cm SCX trap column and a 75 microm id x 12 cm C18 RP analytical column. During the sample loading step, the flow passing through the SCX trap column was directed to waste for loading a large volume of sample at high flow rate. Then the peptides bound on the SCX trap column were eluted onto the RP analytical column by a high salt buffer followed by RP chromatographic separation of the peptides at nanoliter flow rate. It was observed that higher performance of separation could be achieved with the system using SCX trap column than with the system using C18 trap column. The high proteomic coverage using this approach was demonstrated in the analysis of tryptic digest of BSA and yeast cell lysate. In addition, this system was also applied to two-dimensional separation of tryptic digest of human hepatocellular carcinoma cell line SMMC-7721 for large scale proteome analysis. This system was fully automated and required minimum changes on current microLC-MS/MS system. This system represented a promising platform for routine proteome analysis.     

Array based capillary IEF with a whole column image of laser-induced fluorescence in coupling to capillary RPLC as a comprehensive 2-D separation system for proteome analysis

Based on array CIEF (ACIEF) and a novel whole column imaging detection (WCID), a comprehensive 2-D system with laser-induced fluorescence was developed for protein mapping. By coupling capillary RPLC (CRPLC) as the first dimension and ACIEF as the second dimension, a high-throughput and high-resolution proteomic expression profiling was obtained. An array of up to 60 capillaries was assembled, with electrical connections made through filling small breaks, created on each capillary at positions of buffer reservoirs, with a porous polymer. A whole column image system with laser-induced fluorescence (LIF) was devised. Spot excitation was performed with a laser converted to produce linear light, and a CCD camera was employed to take images of the protein fluorescence during line laser scanning of the capillary array. Quantitative detection of thousands of focusing protein bands in the capillary array was achieved. Details on the capillary array fabrication and scanning LIF detection system devices are discussed. The efficiency of this CRPLC-ACIEF-LIF-WCID system was further demonstrated using samples of soluble proteins extracted from liver cancer tissue. The overall peak capacity was estimated to be around 18 000 in an analysis time of less than 3 h. The reproducibility of consecutive runs and different columns were assessed as having an RSD of 1.5% and 2.2% in focusing positions, respectively.     

Palmitoylated proteins: purification and identification

This proteomic protocol purifies and identifies palmitoylated proteins (i.e., S-acylated proteins) from complex protein extracts. The method relies on an acyl-biotinyl exchange chemistry in which biotin moieties are substituted for the thioester-linked protein acyl-modifications through a sequence of three in vitro chemical steps: (i) blockade of free thiols with N-ethylmaleimide; (ii) cleavage of the Cys-palmitoyl thioester linkages with hydroxylamine; and (iii) labeling of thiols, newly exposed by the hydroxylamine, with biotin-HPDP (Biotin-HPDP-N-[6-(Biotinamido)hexyl]-3'-(2'-pyridyldithio)propionamide. The biotinylated proteins are then affinity-purified using streptavidin-agarose and identified by multi-dimensional protein identification technology (MuDPIT), a high-throughput, tandem mass spectrometry (MS/MS)-based proteomic technology. MuDPIT also affords a semi-quantitative analysis that may be used to assess the gross changes induced to the global palmitoylation profile by mutation or drugs. Typically, 2-3 weeks are required for this analysis.     

A new fast method for nanoLC-MALDI-TOF/TOF-MS analysis using monolithic columns for peptide preconcentration and separation in proteomic studies

A new fast method for identification and characterization of proteolytic digests of proteins by monolithic liquid chromatography coupled with mass spectrometry has been developed. The advantages of the monolithic columns are a high-pressure stability and low back pressure resulting in higher flow rates for capillary or nanosize columns simplifying the system handling. As was shown in several publications, such monolithic stationary phases are highly qualified for the analysis of peptides and proteins, but so far, only small volumes could be injected into the system, which might hamper the sample preparation leading to protein precipitation and partial loss of sample. To overcome the problem of small injection volumes, we established a system including a short monolithic trap column to allow preconcentration of the peptides. The injected sample is flushed at higher flow rates onto the trap column, bound to the stationary phase, and in this way concentrated in a few nanoliters before starting the separation. The expanded system was optimized and tested using different reference protein samples. Eluting peptides were detected by MALDI-TOF/TOF-MS and identified by database searching. The system is now a permanent part for proteome analysis in our lab, and as such, it was successfully applied for the detection of post-translational modifications and the analysis of membrane proteins. One example for these analyses is also included in this paper.     

Capillary array reversed-phase liquid chromatography-based multidimensional separation system coupled with MALDI-TOF-TOF-MS detection for high-throughput proteome analysis

A high-throughput on-line capillary array-based two-dimensional liquid chromatography (2D-LC) system coupled with MALDI-TOF-TOF-MS proteomics analyzer for comprehensive proteomic analyses has been developed, in which one capillary strong-cation exchange (SCX) chromatographic column was used as the first separation dimension and 18 parallel capillary reversed-phase liquid chromatographic (RPLC) columns were integrated as the second separation dimension. Peptides bound to the SCX phase were "stepped" off using multiple salt pulses followed by sequentially loading of each subset of peptides onto the corresponding precolumns. After salt fractionation, by directing identically split solvent-gradient flows into 18 channels, peptide fractions were concurrently back-flushed from the precolumns and separated simultaneously with 18 capillary RP columns. LC effluents were directly deposited onto the MALDI target plates through an array of capillary tips at a 15-s interval, and then alpha-cyano-4-hydroxycinnamic acid (CHCA) matrix solution was added to each sample spot for subsequent MALDI experiments. This new system allows an 18-fold increase in throughput compared with serial-based 2D-LC system. The high efficiency of the overall system was demonstrated by the analysis of a tryptic digest of proteins extracted from normal human liver tissue. A total of 462 proteins was identified, which proved the system's promising potential for high-throughput analysis and application in proteomics.     

Fibrous stationary phase in capillary electrochromatography

Capillary electrochromatography (CEC) using fibrous cellulose acetate (CA) stationary phase was investigated. The advantage of this fiber-packed column is relatively easy preparation process compared with other conventional CEC columns, such as particle-packed and wall-coated capillaries. CA fibers are manually packed into a capillary with two guide liners and fixed with a frit at the column inlet. The separation characteristics of this column were investigated using n-alkyl p-hydroxybenzoates (parabens) as the sample probe. It has been demonstrated that the use of a short column length and a specially designed tee-connector as the injection device should make the separation performance and efficiency much higher on the fiber-packed columns. Sufficient separation between methyl and n-butylparabens is obtained on the 5-cm-packed column and linear relationships between the injection time and the peak area are observed. Bubble formation is not encountered during the analysis.     

Application of open tubular capillary columns coated with zirconium phosphonate for enrichment of phosphopeptides

A new approach utilizing open tubular capillary columns coated with zirconium phosphonate (ZrP-OTCC) for enrichment of phosphopeptides is described. The experimental conditions: interior diameter, length of capillary and flow rate was optimized using tryptic digest of α-casein (a phosphoprotein) as a model sample. The ZrP-OTCC was demonstrated to tolerate urea, sodium dodecyl sulphate (SDS), and NaCl. Further experimental results show that the ZrP-OTCC can trap the phosphopeptides even at the concentration of α-casein as low as 10^?8 M. This column has also been successfully coupled online with nano-liquid chromatography for enrichment and then separation of phosphopeptides from a complex sample, and finally analyzed the phosphopeptides by mass spectrometry (MS).     

Integrated capillary isoelectric focusing/nano-reversed phase liquid chromatography coupled with ESI-MS for characterization of intact yeast proteins

An integrated protein concentration/separation platform, combining capillary isoelectric focusing (CIEF) with nano-reversed phase liquid chromatography (nano-RPLC), is developed to provide significant protein concentration and high resolving power for the analysis of complex protein mixtures. Upon completion of protein focusing, the proteins are sequentially and hydrodynamically loaded into individual trap columns using a group of microinjection and microselection valves. Repeated pro-tein loadings and injections into trap columns are carried out automatically until the entire CIEF cap-illary content is sampled and fractionated. Each CIEF fraction "parked" in separate trap columns is further resolved using nano-RPLC, and the eluants are analyzed using electrospray ionization-mass spectrometry.     

Gas chromatography: elution temperature, speed of analysis, and separation, efficiency as influenced by rate of temperature programming and carrier gas velocity in open tubular glass capillary columns.

The elution temperatures and degree of separation of a model system series of hydrocarbons were followed as functions of the rate of temperature programming and carrier gas velocity. Graphs are presented that permit individual assessment of these variables. Lower elution temperatures can be achieved by raising the carrier gas velocity or lowering the rate of temperature programming. In glass capillary columns of normal dimensions (0.25-mm i.d. × 50 m), the former is much less effective and results in lower column efficiency. The elution temperature of n-pentadecane varied from 139 to 309°C and the separation efficiency of the column decreased by 50% as the program rate varied from 1 to 32°C/min at constant pressure drop. A simplified glass inlet splitter and constant pressure-drop device is also described.     

Micro-scale open-tube capillary separations of functional proteins

This article describes a novel technique whereby fully functional proteins or multiprotein complexes are efficiently extracted from biological samples to chemically derivatized walls of fused-silica open-tube capillary columns. Proteins are eluted with very high yields into elution volumes that are smaller in volume than the internal volume of the open-tube capillary column itself, thereby achieving 100-fold increases in target protein concentrations from starting samples of less than 1 ml. The open-tube capillary columns are designed for single use; combined with the physical and chemical characteristics of the open-tube capillary column, this provides exceptional purity to the eluted proteins. Affinity-based open-tube capillary columns are demonstrated here to purify, enrich, and maintain functionality for a monomeric and dimeric enzyme, a low-abundance HeLa nuclear complex, and a light-harvesting octadecameric membrane protein complex. The design of the open-tube capillary column allows for facile direction of the processed protein sample to any number of final detection techniques and is capable of generating final protein concentrations required for many structural biology experiments. The open-tube capillary columns are also characterized by exceptional ease of use. Current designs allow for up to 10 open-tube capillary columns to be applied simultaneously with no fundamental impediments to even greater parallel operation.     

Efficacy of a pentaiodide resin disinfectant on Cryptosporidium parvum (Apicomplexa: Cryptosporidiidae) oocysts in vitro

The resin-I5 column developed at Kansas State University was tested for efficacy against oocysts of Cryptosporidium parvum (Apicomplexa: Cryptosporidiidae). Cesium chloride gradient-purified oocysts were passed through 1.0-cm-diameter columns with lengths of 2.5, 5.0, and 10.0 cm at 23 C. Following column passage, oocyst viability was determined both in vitro by excystation and in vivo by the ability to establish infections in suckling mice. Oocysts were found to be retained by the pentaiodide resin in a linear fashion, probably by electrostatic interactions. Linear regression analysis revealed 100% of the oocysts should be removed in such a manner using a column length of greater than or equal to 25.7 cm. When compared to untreated control oocysts, less than 12% of the oocysts that passed through the columns appeared to be affected by the resin, as assessed by excystation. Inoculation of suckling mice with these column-treated oocysts supported the excystation data and revealed the coccidian to be viable. These results indicate that oocysts of C. parvum are retained on the pentaiodide column in a 1-hit manner and that, although killing of parasites may occur within the column, the greatest effect that the column may have on the parasite is as an electrostatic retention device.     

Monoliths for microfluidic devices in proteomics

We report here on the preparation of monolithic capillary columns in view to their integration in a microsystem for on-chip sample preparation before their on-line analysis by electrospray and mass spectrometry (ESI-MS). These monolithic columns are based on polymer materials and consist of reverse phases for peptide separation and/or desalting. They were prepared using lauryl methacrylate (LMA), ethylene dimethacrylate (EDMA) as well as a suitable porogenic mixture composed of cyclohexanol and ethylene glycol. The resulting stationary phases present thus a C12-functionality. The LMA-based columns were first prepared in a capillary format using capillary tubing of 75 microm i.d. and tested in nanoLC-MS experiments for the separation of a commercial Cytochrome C digest composed of 12 peptidic fragments whose isoelectric point values and hydrophobic character cover a wide range. The LMA-based columns were capable of separating the peptidic fragments and their performances were seen to be similar as those of standard commercial columns dedicated to proteomic purposes with calculated separation efficiencies up to 145 x 10(3) plates/m. Monolithic LMA-based phases were then successfully polymerized in microchannels fabricated using the negative photoresist SU-8. After the polymerization, the systems were seen to withstand the pressures applied during the nanoLC-MS separation tests that were carried out in the same conditions as for the monolithic capillary columns. The pressure drop during these tests of the in-microchannel monoliths was as high as 50 bar; however, the separation was not as good as for a capillary format which could be accounted for by the monolith dimensions.     

Detection of a mixed-backbone oligonucleotide (GEM 231) in liver and tumor tissues by capillary electrophoresis

A simple, rapid and sensitive method has been developed and validated for the analysis of a mixed-backbone oligonucleotide (GEM 231) in tumor tissues. The analysis was performed using a capillary electrophoresis (CE) system with UV detection. An extended light path (bubble cell) capillary column of 64.5 cm (effective length 56 cm)×50 μm I.D. is used as the separation column. The optimized chromatographic conditions were background electrolyte: sodium borate buffer (60 mM, pH 9.1), electrokinetic injection: 10 s, applied voltage: 30 kV, detection at λ=210 nm. A linear relationship was observed between the peak area and the amount of GEM 231 in the range of 1.0–1000 μg/ml. The lower detection limit of the drug was 100 pg with an average recovery of about 75±5%. The inter-day and intra-day relative standard deviations were <10%. Assay validation studies revealed that CE method is reproducible and specific for the determination of GEM 231 in tissue homogenates with a run time of less than 5 min.     

花卉柱式无土栽培

于玻璃温室内的160 m2面积上,以干湿交替型盆钵组装起高200 cm, 直径15 cm的立柱77根,然后组成立柱“树林”并种花,25个科的共53种草花用同一营养系统管理,生长都良好,立柱“树林”象是花的“森林”,显示了良好的生态关系。在此基础上挑选不同种盆花组成不同情趣的家庭阳台花柱。阳台花柱具若干优点：新型盆钵具良好的水、气、肥协调关系,适合多种花卉生长;柱高任选,便手提携带;柱体能环绕中轴旋转使植物受光均匀;花柱底部是具中岛结构式底盆,起蓄水和稳定作用,还便于多根立柱串联扩大栽培量;有人工和自动浇灌两种系统,省工省时且干净卫生。     

Solute exclusion from cellulose in packed columns: process modeling and analysis

In this investigation, process modeling and analysis were used to explore the behavior of solute exclusion from cellulose in packed columns. The study focused on modeling the effects of dispersion, mass transport, and pore diffusion. Three mathematical models were used to predict the behavior of the columns: an equilibrium model, a mass transfer model, and a combined mass transfer and pore diffusion model. Computer implementations of these models were tested against experimental conditions where cellulose particle size and solution velocity were used to either amplify or minimize dispersion or skewness in the elution curves. For small cellulose particles (200-300 mesh), all three models accurately predicted the shape of the elution curve and the particle porosity. For larger particles (45-60 mesh), the mass transfer model and the combined mass and pore diffusion model best represented the behavior of the column. At high solution velocities (0.63 cm(3) min(-1)) and large particles, only the combined mass transfer and pore diffusion model accurately represent the column behavior. Sensitivity analysis revealed that the mass transfer coefficient had little effect on the elution curves for the range of values (10(-6)-10(-3) cm s(-1)) calculated from the experimental data. The combined mass transfer and pore diffusion model presented in this article can be used to design solute exclusion measurement experiments for the larger cellulose particles found in a commercial cellulose-to-ethanol plant.     

Preparation of highly efficient monolithic silica capillary columns for the separations in weak cation-exchange and HILIC modes

Weak cation-exchange (WCX) and HILIC modes columns were prepared by on-column polymerization of acrylic acid on monolithic silica capillary columns modified with N-(3-triethoxysilylpropyl)methacrylamide anchor groups. The polymer-coated columns could be used for HILIC mode separation of pyridylamino (PA)-sugars and peptides including a tryptic digest of BSA, while for weak cation-exchange mode for the separation of proteins and nucleosides even at high linear velocity. The poly(acrylic acid) coated monolithic silica capillary columns showed greater retention toward PA-sugars than a polyacrylamide coated monolithic silica capillary columns prepared in the same manner. Proteins and nucleosides were separated effectively at pH 6.9 using the same column. The column provided fair permeability after the polymer-coating step. High-speed separation of proteins at u=4.66 mm/s with high efficiency was shown to be possible, while high-speed separation of nucleosides has achieved within one minute using the column at u=8.67 mm/s, suggesting that the column will be suitable for the second dimension separation of multidimensional HPLC systems.     

Separation of microcystins by capillary electrochromatography in monolithic columns

Contribution on microcystin variant analysis by capillary electrochromatography (CEC) with easily affordable spectrophotometric detection is presented. Two types of reversed-phase capillary columns formed by inorganic or organic polymer monoliths were prepared for this purpose. The analyses were performed isocratically by means of tris(hydroxymethyl) aminomethane (TRIS) buffers of mildly alkaline pH containing 30% (v/v) acetonitrile as the mobile phases. The samples were injected electrokinetically and the analyses were done at the same separation field strength of 500 V/cm. Microcystins were detected at 238 nm. Although both column types differ not only in monolith quality (inorganic versus organic) but also in the length of the aliphatic moiety (C8 versus C12) similar results were achieved. The on-column preconcentration as the encouraging prospect of electrochromatographic technique was also tested. Consequently 5% of column volume was injected in contrast with 0.5% at standard injection scheme resulting in the six times enrichment of the low concentrated cyanobacterial extract at the top of the separation column. From these preliminary results can be seen that the CEC method is fully applicable for rapid microcystin screening.     

Evaluation of four capillary columns for the analysis of organochlorine pesticides, polychlorinated biphenyls, and polybrominated diphenyl ethers in human serum for epidemiologic studies

The separation of organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether (PBDE) congeners was evaluated on four capillary columns: 60 m x 0.25 mm i.d., 0.25 microm film thickness RTX-5MS and DB-XLB capillary columns, and 60 m x 0.18 mm i.d., 0.25 microm film thickness DB-XLB and DB-5MS capillary columns. Based on performance, capacity, and cost, the RTX-5MS (60 m x 0.25 mm i.d., 0.25 microm thickness) and the DB-XLB (60 m x 0.25 mm i.d., 0.25 microm film thickness) were selected for the analysis of human serum extracts by using gas chromatography/electron-capture detection. In contrast to previous studies, the oven temperature program affords the separation of congeners that are not separated by using other combinations of capillary columns, most notably PBDE-47 and PCB 180. In addition, the method enables determination of OCPs, PCBs, and PBDEs prevalent in a single extract of serum, which can lead to considerable time savings in the analysis of large number of samples collected for epidemiologic studies.