Impulse-driven heated-droplet deposition interface for capillary and microbore LC-MALDI MS and MS/MS

An automated off-line liquid chromatography-matrix-assisted laser desorption ionization (LC-MALDI) interface capable of coupling both capillary and microbore LC separations with MALDI mass spectrometry (MS) and tandem mass spectrometry (MS/MS) has been developed. The interface is a combination of two concepts: analyte concentration from heated hanging droplets and impulse-driven droplet deposition of LC fractions onto a MALDI sample plate. At room temperature the interface allows the coupling of capillary LC separations (i.e., flow rate of <5 microL/min) with MALDI MS. With heating, it can be used to combine microbore LC operated at a relatively high flow rate of up to 50 microL/min with MALDI MS. The collected fractions can be analyzed by MALDI MS and MS/MS instruments, such as time-of-flight (TOF) and quadrupole-TOF MS. Performance of the interface was examined using several peptide and protein standards. It was shown that, using MALDI-TOF MS, [GLU1]-fibrinopeptide B could be detected with a total injection amount of 5 fmol to microbore LC. Chromatographic performance was also monitored. A peak width of 12 s at half-height for [GLU1]-fibrinopeptide B showed no evidence of band broadening due to the interface. The ability of the interface to mitigate ion suppression was studied using a mixture of 100 fmol of [GLU1]-fibrinopeptide B and 10 pmol of cytochrome c tryptic digest. Although fully suppressed under direct MALDI conditions, LC-MALDI analysis was able to detect the 100 fmol peptide with 10 s fraction collection. Finally, the ability to inject relatively large sample amounts to improve detectability of low-abundance peptides was illustrated in the analysis of phosphopeptides from alpha-casein tryptic digests. A digest loaded on column to 2.4 microg and analyzed by LC-MALDI MS/MS resulted in 82% sequence coverage and detection of all nine phosphoserine residues. It is concluded that, being able to handle both high- and low-flow LC separations, the impulse-driven heated-droplet interface provides the flexibility to carry out MALDI analysis of peptides and proteins depending on the information sought after, analysis speed, and sample size.     

Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS: exclusion of redundant peptides from MS/MS analysis in replicate runs

Due to the complexity of proteome samples, only a portion of peptides and thus proteins can be identified in a single LC-MS/MS analysis in current shotgun proteomics methodologies. It has been shown that replicate runs can be used to improve the comprehensiveness of the proteome analysis; however, high-intensity peptides tend to be analyzed repeatedly in different runs, thus reducing the chance of identifying low-intensity peptides. In contrast to commonly used online ESI-MS, offline MALDI decouples the separation from MS acquisition, thus allowing in-depth selection for specific precursor ions. Accordingly, we extended a strategy for offline LC-MALDI MS/MS analysis using a precursor ion exclusion list consisting of all identified peptides in preceding runs. The exclusion list eliminated redundant MS/MS acquisitions in subsequent runs, thus reducing MALDI sample depletion and allowing identification of a larger number of peptide identifications in the cumulative dataset. In the analysis of the digest of an Escherichia coli lysate, the exclusion list strategy resulted in a 25% increase in the number of unique peptide identifications in the second run, in contrast to simply pooling MS/MS data from two replicate runs. To reduce the increased LC analysis time for repeat runs, a four-column multiplexed LC system was developed to carry out separation simultaneously. The multiplexed LC-MALDI MS provides a high-throughput platform to utilize the exclusion list strategy in proteome analysis.     

High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies

The use of tetrahydrofuran/decanol as porogens for the fabrication of micropellicular poly(styrene/divinylbenzene) monoliths enabled the rapid and highly efficient separation of peptides and proteins by reversed-phase high-performance liquid chromatography (RP-HPLC). In contrast to conventional, granular, porous stationary phases, in which the loading capacity is a function of molecular mass, the loadability of the monoliths both for small peptides and large proteins was within the 0.40.9-pmol range for a 60- x 0.2-mm capillary column. Lower limits of detection obtained by measuring UV-absorbance at 214 nm with a 3-nl capillary detection cell were 500 amol for an octapeptide and 200 amol for ribonuclease A. Upon reduction of the concentration of trifluoroacetic acid in the eluent from the commonly used 0.1-0.2 to 0.05%, the separation system was successfully coupled to electrospray ionization mass spectrometry (ESI-MS) at the cost of only a small decrease in separation efficiency. Detection limits for proteins with ESI-MS were in the lower femtomole range. High-quality mass spectra were extracted from the reconstructed ion chromatograms, from which the masses of both peptides and proteins were deduced at a mass accuracy of 50-150 ppm. The applicability of monolithic column technology in proteomics was demonstrated by the mass fingerprinting of tryptic peptides of bovine catalase and human transferrin and by the analysis of membrane proteins related to the photosystem II antenna complex of higher plants.     

Nanofractionation spotter technology for rapid contactless and high-resolution deposition of LC eluent for further off-line analysis

The development of a contactless postcolumn spotter technology capable of rapidly and accurately depositing LC eluent onto another platform (e.g., 1536-well microtiter plates) is described. Many detection methodologies are suitable for online analysis, such as mass spectrometry, UV-vis, and fluorescence. In some cases, when online analysis is less suitable, off-line postcolumn analysis is the methodology of choice and usually relies on LC-based fractionation prior to detection (e.g., MALDI-MS, Raman spectrsocopy, biochemical assays). As fractionation generally involves loss in resolution, the technology described here allows high-resolution contactless fractionation by tailoring the fractionation frequency to the chromatographic peaks and mixing in of postcolumn reagents. Droplet ejection at frequencies of at least 6 Hz could be performed in the nanoliter to low microliter range with repeatabilities of ～6%. Furthermore, multiple droplets can be ejected at the same position thereby allowing adjustment of fractionation volume and speed. The technology was evaluated, optimized, and validated prior to two proof-of-principle demonstrations comprising off-line chemical detection of injected fluorescein and off-line postcolumn biochemical detection of acetylcholine-binding protein ligands, both based on 1536-well plate reader analysis.     

Methodology utilizing MS signal intensity and LC retention time for quantitative analysis and precursor ion selection in proteomic LC-MALDI analyses

This study describes a methodology for performing relative quantitation in large-scale proteomic sample comparisons using an LC-MALDI mass spectrometry analytical platform without the use of isotope tagging reagents. The method utilizes replicate analyses of a sample to create a profile of constituent components that are aligned based on LC elution time and mass. Once components from individual runs have been grouped as common "features", the Student's t test is used to determine which components are systematically different between samples. In this study, five HPLC runs of human plasma were compared to five HPLC runs of human serum. About 3889 components were detected in all 10 runs. Of these, 1831 corresponded to approximately 100 known serum proteins, based on MS/MS analysis of one run each from serum and plasma. As expected, fibrinogen alpha, beta, and gamma chains accounted for many of the most significant differences. Therefore, using MALDI, samples containing thousands of peptides can be compared in a minimal amount of time. Moreover, the results of the comparison can be used to guide further MS/MS mode sample interrogation in a result dependent manner.     

Low-attomole electrospray ionization MS and MS/MS analysis of protein tryptic digests using 20-microm-i.d. polystyrene-divinylbenzene monolithic capillary columns

This work explores the use of 20-microm-i.d. polymeric polystyrene-divinylbenzene monolithic nanocapillary columns for the LC-ESI-MS analysis of tryptic digest peptide mixtures. In contrast to the packing of microparticles, capillary columns were prepared, without the need of high pressure, in fused-silica capillaries, by thermally induced in situ copolymerization of styrene and divinylbenzene. The polymerization conditions and mobile-phase composition were optimized for chromatographic performance leading to efficiencies over 100000 plates/m for peptide separations. High mass sensitivity (approximately 10 amol of peptides) in the MS and MS/MS modes using an ion trap MS was found, a factor of up to 20-fold improvement over 75-microm-i.d. nanocolumns. A wide linear dynamic range (approximately 4 orders of magnitude) was achieved, and good run-to-run and column-to-column reproducibility of isocratic and gradient elution separations were found. As samples, both model proteins and tissue extracts were employed. Gradient nano-LC-MS analysis of a proteolytic digest of a tissue extract, equivalent to a sample size of approximately 1000 cells injected, is presented.     

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry

Advances in Fourier transform mass spectrometry have made the acquisition of high-resolution and accurate mass measurements routine on a chromatographic time scale. Here we report an algorithm, Hardkl?r, for the rapid and robust analysis of high-resolution mass spectra acquired in shotgun proteomics experiments. Our algorithm is demonstrated in the analysis of an Escherichia coli enriched membrane fraction. The mass spectrometry data of the respective peptides are acquired by microcapillary HPLC on an LTQ-orbitrap mass spectrometer with data-dependent acquisition of MS/MS spectra. Hardkl?r detects 211,272 total peptide isotope distributions over a 2-h analysis (75-min gradient) in only a small fraction of the time required to acquire the data. From these data there are 13,665 distinct, chromatographically persistent peptide isotope distributions. Hardkl?r is also used to assess the quality of the product ion spectra and finds that more than 11.2% of the MS/MS spectra are composed of fragment ions from multiple different molecular species. Additionally, a method is reported that enzymatically labels N-linked glycosylation sites on proteins, creating a unique isotope signature that can be detected with Hardkl?r. Using the protein invertase, Hardkl?r identifies 18O-labeled peptide isotope distributions of four glycosylation sites. The speed and robustness of the algorithm create a versatile tool that can be used in many different areas of mass spectrometry data analysis.     

Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow

We have developed an information-dependent, iterative MS/MS acquisition (IMMA) tool for improving MS/MS efficiency, increasing proteome coverage, and shortening analysis time for high-throughput proteomics applications based on the LC-MALDI MS/MS platform. The underlying principle of IMMA is to limit MS/MS analyses to a subset of molecular ions that are likely to identify a maximum number of proteins. IMMA reduces redundancy of MS/MS analyses by excluding from the precursor ion peak lists proteotypic peptides derived from the already identified proteins and uses a retention time prediction algorithm to limit the degree of false exclusions. It also increases the utilization rate of MS/MS spectra by removing "low value" unidentifiable targets like nonpeptides and peptides carrying large loads of modifications, which are flagged by their "nonpeptide" excess-to-nominal mass ratios. For some samples, IMMA increases the number of identified proteins by ～20-40% when compared to the data dependent methods. IMMA terminates an MS/MS run at the operator-defined point when "costs" (e.g., time of analysis) start to overrun "benefits" (e.g., number of identified proteins), without prior knowledge of sample contents and complexity. To facilitate analysis of closely related samples, IMMA's inclusion list functionality is currently under development.     

Ultratrace LC/MS proteomic analysis using 10-microm-i.d. Porous layer open tubular poly(styrene-divinylbenzene) capillary columns

In this paper, the preparation and performance of long, high-efficiency poly(styrene-divinylbenzene) (PS-DVB), 10-microm-i.d. porous layer open tubular (PLOT) capillary columns are described. PLOT capillaries ( approximately 3% RSD column-to-column retention time), with relatively high permeability, were prepared by in-situ polymerization. Relatively high loading capacities, approximately 100 fmol for angiotensin I and approximately 50 fmol for insulin, were obtained with a 4.2 m x 10-microm-i.d. PLOT column. Low detection levels (attomole to sub-attomole) were achieved when the column was coupled on-line with a linear ion trap MS (LTQ). Analysis of human epidermal growth factor receptor (EGFR), a large transmembrane tyrosine kinase receptor with heterogeneous phosphorylation and glycosylation structures, was obtained at the 25 fmol level. The PLOT column yielded a peak capacity of approximately 400 for the separation of a complex tryptic digest mixture when the sample preparation included a 50-microm-i.d. PS-DVB monolithic precolumn and ESI-MS detection. As an example of the power of the column, 3046 unique peptides covering 566 distinct Methanosarcina acetivorans proteins were identified from a 50 ng in-gel tryptic digest sample combining five cuts in a single LC/MS/MS analysis using the LTQ. The results demonstrate the potential of the PLOT column for high-resolution LC/MS at the ultratrace level.     

Interface for direct and continuous sample-matrix deposition onto a MALDI probe for polymer analysis by thermal field flow fractionation and off-line MALDI-MS

A simple interface based on an oscillating capillary nebulizer (OCN) is described for direct deposition of eluate from a thermal field-flow fractionation (ThFFF) system onto a matrix-assisted laser desorption/ionization (MALDI) probe. In this study, the polymer-containing eluent from the ThFFF system was mixed on-line with MALDI matrix solution and deposited directly onto a moving MALDI probe. The result was a continuous sample track representative of the fractionation process. Subsequent off-line MALDI-mass spectrometry analysis was performed in automated and manual modes. Polystyrene samples of broad polydispersity were used to characterize the overall system performance. The OCN interface is easy to build and operate without the use of heaters or high voltages and is compatible with any MALDI probe format.     

A high-throughput continuous sample introduction interface for microfluidic chip-based capillary electrophoresis systems

The development of efficient sample introduction and pretreatment systems for microfluidic chip-based analytical systems is important for their application to real-life samples. In this work, world-to-chip interfacing was achieved by a novel flow-through sampling reservoir featuring a guided overflow design. The flow-through reservoir was fabricated on a 30 x 60 x 3 mm planar glass chip of crossed-channel design used for capillary electrophoresis separations. The 20-microL sample reservoir was produced from a section of plastic pipet tip and fixed at one end of the sampling channel. Sample change was performed by pumping 80-microL samples sandwiched between air segments at approximately 0.48 mL/min flow rate through the flow-through reservoir, introduced from an access hole on the bottom side of the chip. A filter paper collar wrapped tightly around the reservoir guided the overflowing sample solution into a plastic trough surrounding the reservoir and then to waste. The performance of the system was demonstrated in the separation and determination of FITC-labeled arginine, glycine, phenylalanine, and glutamic acid with LIF detection, by continuously introducing a train of different samples through the system without electrical interruption. Employing a separation channel of 4 cm (2-cm effective separation length) and 1.4-kV separation voltage, maximum throughputs of 80/h were achieved with <4.1% carryover and precisions ranging from 1.5% for arginine to 2.6% RSD (n = 11) for glycine. The sampling system was tested in the continuous monitoring of the derivatizing process of amino acids by FITC over a period of 4 h, involving 166 analytical cycles. An outstanding overall precision of 4.8% RSD (n = 166) was achieved for the fluorescein internal standard.     

Pesticide residue analysis by off-line SPE and on-line reversed-phase LC-GC using the through-oven-transfer adsorption/desorption interface

A new method to determine pesticide residue in water is presented. The described method includes using off-line solid-phase extraction (SPE) and on-line reversed-phase liquid chromatography-gas chromatography (RPLC-GC). An interface, based on a modified programmed temperature vaporizer (PTV) injector, packed with a suitable trapping material, is used for on-line RPLC-GC. The changes made in the PTV injector affect the pneumatic system, sample introduction, and solvent elimination. The new interface is easily capable of automation. Methanol/wate (70/30) is used as the eluent in the LC preseparation step. The LC column flow during elution is different from the flow during the transfer step. The transferred volumes range from 500 to 1400 microL (volume of the fractions of interest). Solvent elimination is almost 100% before the sample reaches the GC column. The described system does not show any variation of the peak retention times. The detection limit for real samples ranges from 0.04 to 1.5 ng/L, using NP detection.     

Optimal conditions for protein array deposition using continuous flow

Optimal conditions for depositing protein microarrays using a continuous-flow microfluidic device, the continuous-flow microspotter (CFM), have been determined using a design of experiments approach. The amount of protein deposited on the surface depends on the rates of convective and diffusive transport to the surface and binding at the surface. These rates depend on parameters such as the flow rate, time, and capture mechanism at the surface. The process parameters were optimized, and uniform protein spots were obtained at a protein concentration of 10 microg/mL and even at 0.4 microg/mL. A 150-fold dilution in protein concentration in the sample solution decreased surface concentration by a factor of only 16. If the capture mechanism of the protein on the substrate is nonspecific, optimal deposition is obtained at higher flow rates for short periods of time. If the capture mechanism is specific, such as biotin-avidin, deposition is optimal at medium flow rates with little advantage beyond 30 min. The CFM can be used to deposit protein arrays with good spot morphology, spot-to-spot uniformity and enhanced surface concentration. The CFM was used to deposit an array of various antibodies, and their interactions with an antigen were studied using surface plasmon resonance (SPR). Affinity values were obtained at low antibody concentrations (5 microg/mL) with low coefficients of variation. Thus, the CFM can be used to effectively capture proteins and antibodies from dilute samples while depositing multiple spots, thereby increasing the quality of spots in protein microarrays and especially improving screening throughput of SPR.     

Hydrophilic interaction chromatography using methacrylate-based monolithic capillary column for the separation of polar analytes

A porous zwitterionic monolith was prepared by thermal copolymerization of N,N-dimethyl-N-methacryloxyethyl-N-(3-sulfopropyl)ammonium betaine and ethylene dimethacrylate inside a 100-mum-i.d. capillary. The resulting monolith was evaluated as a hydrophilic liquid chromatography (HILIC) stationary phase. No evidence of swelling or shrinking of the monolith in different polarity solvents was observed. A typical HILIC mechanism was observed at higher organic solvent content (ACN% > 60%). The poly(SPE-co-EDMA) monolith showed very good selectivity for neutral, basic, and acidic polar analytes. For charged analytes, both hydrophilic interactions and electrostatic interactions contributed to their retention, which provide chromatographers more choice to optimize the separations.     

MicroSPE-nanoLC-ESI-MS/MS using 10-microm-i.d. silica-based monolithic columns for proteomics

Silica-based monolithic capillary columns (25 cm x 10 microm i.d.) with integrated nanoESI emitters have been developed to provide high-quality and robust microSPE-nanoLC-ESI-MS analyses. The integrated nanoESI emitter adds no dead volume to the LC separation, allowing stable electrospray operation at flow rates of approximately 10 nL/min. In an initial application with a linear ion trap MS, we identified 5510 unique peptides that covered 1443 distinct Shewanella oneidensis proteins from a 300-ng tryptic digest sample in a single 4-h LC-MS/MS analysis. The use of an integrated monolithic ESI emitter provided enhanced resistance to clogging and provided good run-to-run reproducibility.     

Chlorinated phenol analysis using off-line solid-phase extraction and capillary electrophoresis coupled with amperometric detection and a boron-doped diamond microelectrode

The analysis of chlorinated phenols (2-chlorophenol, 3-chlorophenol, 4-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, pentachlorophenol) in river water was accomplished using off-line solid-phase extraction (SPE) and capillary electrophoresis coupled with electrochemical detection. A key to the sensitive, reproducible, and stable detection of these pollutants was the use of a boron-doped diamond microelectrode in the amperometric detection mode. An off-line SPE procedure was utilized to extract and preconcentrate the pollutants prior to separation and detection, with ENVI-Chrom P, a highly cross-linked styrene-divinylbenzene copolymer, being employed as the sorbent. Pollutant recoveries in the 95-100% range with relative standard deviations of 1-4% were achieved. The diamond microelectrode provided a low and stable background current with low peak-to-peak noise. The oxidative detection of the pollutants was accomplished at +1.05 V vs Ag/AgCl without the need for electrode pretreatment. The method was evaluated in terms of the linear dynamic range, sensitivity, limit of quantitation, response precision, and response stability. A reproducible electrode response was observed during multiple injections of the chlorinated phenol solutions with a relative standard deviation of < or =5.4%. Good electrode response stability was observed over many days of continuous use with no significant electrode deactivation or fouling. The separation efficiencies for all six pollutants were greater than 170,000 plates/m. The minimum concentration detectable for all six ranged from 0.02 to 0.2 ppb (S/N > or = 3) using a 250:1 preconcentration factor.     

A low-flow ce/electrospray ionization MS interface for capillary zone electrophoresis,large-volume sample stacking,and micellar electrokinetic chromatography

A simple and versatile low-flow interface has been developed for interfacing capillary electrophoresis (CE) with electrospray ionization (ESI) mass spectrometry. This low-flow interface showed better sensitivity than a conventional sheath liquid interface, primarily attributed to a low dilution factor and a reduction in the sprayer orifice size. The interface was also found to be more tolerant to the presence of nonvolatile salts. Because of tolerance to the surfactant SDS, this interface can be used to couple micellar electrokinetic chromatography (MEKC) with ESI-MS. The performance of the interface in an MEKC-MS application, as demonstrated in the analysis of triazines, was significantly better than that obtained with a conventional sheath liquid interface. Moreover, this interface can be easily used for large-volume sample-stacking (LVSS) applications. Using a series of phenols as a test case, an approximate 500-fold enrichment was achieved by LVSS in conjunction with the low-flow CE/MS interface described.     

Surface-alkylated polystyrene monolithic columns for peptide analysis in capillary liquid chromatography-electrospray ionization mass spectrometry

Macroporous poly(styrene-divinylbenzene) (PS-DVB) monoliths were prepared by in situ polymerization in PEEK, fused silica, or stainless steel tubing having an inner diameter of 75 or 125 microm. A process is described for subsequent alkylation of the flow-contacting surfaces of the monoliths. The process treats all the surfaces including through-pore surfaces of the rigid macroporous monolith with a solution containing a dissolved Friedel-Crafts catalyst, an alkyl halide (1-chlorooctadecane), and an organic solvent. This process produces an improved reversed-phase liquid chromatographic separation of peptides compared to an unmodified monolithic PS-DVB column. The surface octadecylation is not necessary for a reversed-phase separation of proteins since both unmodified and modified columns provide comparable results. Tryptic protein digests, standard proteins, and standard peptides were used to evaluate the monolithic columns by employing electrospray mass spectrometry detection. Potential applications in proteomics studies by mass spectrometry, which use the alkylated monolithic column engaged onto the nanofabricated electrospray ionization chip, are also discussed.     

Hydrophobic,pellicular, monolithic capillary columns based on cross-linked polynorbornene for biopolymer separations

Monolithic capillary columns were prepared by transition metal-catalyzed ring-opening metathesis copolymerization of norborn-2-ene and 1,4,4a,5,8,8a-hexahydro-1,4,5,8-exo,endo-dimethanonaphthalene inside a silanized 200-microm-i.d. fused-silica capillary using a mixture of toluene and 2-propanol as porogen and Cl2(PCy3)2Ru(=CHPh) as initiator. The synthesized columns allowed the rapid and highly efficient separation of single- and double-stranded nucleic acids by ion-pair reversed-phase high-performance liquid chromatography and of proteins by reversed-phase high-performance liquid chromatography. Compared to 3-mm-i.d. analytical columns synthesized from an identical polymerization mixture, a considerable improvement in the peak widths at half-height of oligonucleotides in the order of 60-80% was obtained. Significant differences in morphology between the capillary column, where the surface of the monolith was rather soft and rugulose, and the analytical column, where the surface was very sharp and smooth, were observed, most probably due to differences in polymerization kinetics. The synthesized monoliths were successfully applied to the separation of the diastereomers of phosphorothioate oligodeoxynucleotides. To confirm the identity of the eluting compounds on the basis of their intact molecular masses, the chromatographic separation system was on-line hyphenated to electrospray ionization mass spectrometry.     

On-column coaxial flow chemiluminescence detection for underivatized amino acids by pressurized capillary electrochromatography using a monolithic column

A new method for pressurized capillary electrochromatography (pCEC) coupling with chemiluminescence (CL) detection using a modified on-column coaxial flow detection interface was developed. To evaluate the feasibility and reliability of the experimental setup, the typical CL compounds luminol and isoluminol were separated and detected by using this pCEC-CL system. A detailed investigation of CL detection interface and postcolumn CL reagent flow rate parameters was described. The excellent resolution and detection sensitivity was achieved by using 3-microm ODS-C18 packed column with 30% ACN (v/v), 5 mmol/L phosphate buffer (pH 8.0). Moreover, with the presence of Co(II) (1.0 x 10(-4) mol/L) in the mobile phase, the linear range of the concentration for luminol was 2.0 x 10(-9)-2.0 x 10(-6) mol/L with a detection limit (S/N = 3) of 2.0 x 10(-10) mol/L, and 2.5 x 10(4) theoretical plates was achieved. In addition, separation and detection of the underivatized amino acids (l-threonine and l-tyrosine) were accomplished by using a polymerized monolithic column based on the principle of the luminol-H2O2-Cu(II)-amino acid CL system. Under the optimum conditions, the mixture of amino acids was efficiently separated with satisfactory results.