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.     

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.     

Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry

We have developed an analytical method, consisting of ion-pair liquid chromatography coupled to electrospray ionization mass spectrometry (IP-LC-ESI-MS), for the simultaneous quantitative analysis of several key classes of polar metabolites, like nucleotides, coenzyme A esters, sugar nucleotides, and sugar bisphosphates. The use of the ion-pair agent hexylamine and optimization of the pH of the mobile phases were critical parameters in obtaining good retention and peak shapes of many of the above-mentioned polar and acidic metabolites that are impossible to analyze using standard reversed-phase LC/MS. Optimum conditions were found when using a gradient from 5 mM hexylamine in water (pH 6.3) to 90% methanol/10% 10 mM ammonium acetate (pH 8.5). The IP-LC-ESI-MS method was extensively validated by determining the linearity (R2 > 0.995), sensitivity (limit of detection 0.1-1 ng), repeatability, and reproducibility (relative standard deviation <10%). The IP-LC-ESI-MS method was shown to be a useful tool for microbial metabolomics, i.e., the comprehensive quantitative analysis of metabolites in extracts of microorganisms, and for the determination of the energy charge, i.e., the cellular energy status, as an overall quality measure for the sample workup and analytical protocols.     

Optimization and evaluation of a sheathless capillary electrophoresis-electrospray ionization mass spectrometry platform for peptide analysis: comparison to liquid chromatography-electrospray ionization mass spectrometry

In this study we have evaluated the suitability of a sheathless capillary electrophoresis-electrospray ionization mass spectrometry (CE-ESI-MS) interface with a porous tip as the nanospray emitter for use in peptide analysis. A positively charged capillary coating and 0.1% formic acid as background electrolyte were used for separation upstream from mass spectrometry characterization. The influence of the distance between emitter tip and MS inlet, ESI voltage applied, and of the electroosmotic flow (EOF) on electrospray performance and efficiency of the system was investigated in detail. Under optimized conditions, less than 30 amol of a model peptide (angiotensin I) was required for a detection in the base peak electropherogram and positive identification via tandem MS. Three different cationic capillary coatings were investigated for stability, resolution, and EOF and were found to enable reproducible separations by CE-ESI-MS. After optimizing MS settings, the effectiveness of the CE-ESI-MS method developed was compared with a state-of-the-art nano-liquid chromatography (LC)-ESI-MS method by analyzing Arg-C-digested rat testis linker histones with both systems. With comparable amounts of sample applied, the number of identified peptides increased by more than 60% when using CE-ESI-MS. We found that low molecular mass peptides (below 1400 Da) were preferentially identified by CE-ESI-MS, since this group of peptides poorly interacted with the reversed-phase material in the nano-LC system. Finally, total analysis time in LC-ESI-MS for three runs including equilibration was nearly 4 times longer than that of CE-ESI-MS: 246 versus 66 min.     

Analysis of nucleic acids by capillary ion-pair reversed-phase HPLC coupled to negative-ion electrospray ionization mass spectrometry

Ion-pair reversed-phase high-performance liquid chromatography was successfully coupled to negative-ion electrospray ionization mass spectrometry by using 60 × 0.20 mm i.d. capillary columns packed with 2.3-μm micropellicular, octadecylated poly(styrene/divinylbenzene) particles as stationary phase and gradients of acetonitrile in 50 mM aqueous triethylammonium bicarbonate as mobile phase. Systematic variation of the eluent composition, such as concentration of ion-pair reagent, anion in the ion-pair reagent, solution pH, and acetonitrile concentration led to the conclusion that most parameters have opposite effects on chromatographic and mass spectrometric performances. The use of acetonitrile as sheath liquid enabled the rapid and highly efficient separation and detection of phosphorylated and nonphosphorylated oligonucleotides ranging in size from 8 to 40 nucleotides. High-quality full-scan mass spectra showing little cation adduction were acquired from which the molecular masses of the separated oligonucleotides were calculated with an accuracy of 0.011%. With calibration curves being linear over at least 2 orders of magnitude, the lower limits of detection for a oligodeoxythymidine 16-mer were 104 fmol with full scan and 710 amol with selected-ion-monitoring data acquisition. The potential of ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry was demonstrated for mixed-sequence oligomers by the characterization of a reaction mixture from solid-phase synthesis of a 40-mer oligonucleotide.     

Quantitative detection of trichloroacetic acid in human urine using isotope dilution high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

The chemical disinfection of drinking water to control microbial contaminants results in the formation of disinfection byproducts (DBPs). The volatile trihalomethanes and the nonvolatile haloacetic acids (HAAs) are the most prevalent DBPs. It is important to monitor human exposure to HAAs because of their potential adversehealth effects, such as cancer. Among the HAAs, urinary trichloroacetic acid (TCAA) is a potential valid biomarker for assessing chronic ingestion exposure to HAAs from drinking water. We have developed a rugged, high-throughput, sensitive, accurate, and precise assay for the measurement of trace levels of TCAA in human urine using a simple solid-phase extraction (SPE) cleanup followed by isotope dilution high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). TCAA is extracted from the urine using SPE, separated from other extract components by reversed-phase HPLC, and analyzed by negative ion electrospray ionization-isotope dilution-MS/MS using a multiple reaction monitoring experiment. The method is simple and fast and is not labor intensive (sample preparation and analysis can be performed in approximately 15 min) with a limit of detection of 0.5 ng/mL in 1 mL of urine.     

Comparative sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry.

An algorithm was developed for the computer-aided interpretation of fragment ion spectra from collision-induced dissociation of multiply charged oligodeoxynucleotide ions generated by electrospray ionization. The method compares the experimental spectrum to the m/z values predicted by employing established fragmentation pathways from a known reference sequence. The closeness of matching between the measured spectrum and the predicted set of fragment ions is characterized by the fitness, which takes into account the difference between measured and predicted m/z values, the intensity of the fragment ions, the number of fragments assigned, and the number of nucleotide positions not covered by fragment ions in the experimental spectrum. Smaller values for the fitness indicate a closer match between measured spectrum and predicted m/z values. To substantiate the identity of investigated sequence and reference sequence, or to identify point mutations or insertions/deletions, the reference sequence is systematically varied by incorporating all four possible nucleotides A, T, G, and C at each position in the sequence followed by identification of the correct sequence by the lowest fitness value. Collision energy was shown to have a major impact on the interpretability of the tandem mass spectra by the comparative sequencing algorithm, and the optimal collision energy depended on the length of the fragmented oligodeoxynucleotide. The analytical system was successfully applied to verify DNA sequences as well as to detect and localize point mutations or insertions/deletions in 5-51-mer oligodeoxynucleotides.     

Classification of cultivation locations of Panax quinquefolius L samples using high performance liquid chromatography-electrospray ionization mass spectrometry and chemometric analysis

Panax quinquefolius L ( P. quinquefolius L) samples grown in the United States and China were analyzed with high performance liquid chromatography-mass spectrometry (HPLC-MS). Prior to classification, the two-way data sets were subjected to pretreatment including baseline correction and retention time (RT) alignment. Principal component analysis (PCA) and projected difference resolution (PDR) metrics were used to evaluate the data quality and the pretreatment effects. A fuzzy rule-building expert system (FuRES) classifier was used to classify the P. quinquefolius L samples grown in the United States and China with the optimized partial least-squares (o-PLS) classifier as the positively biased control method. A classification rate as high as 98 ± 3% with FuRES was obtained after baseline correction and RT alignment, which is equivalent to the result obtained by using the positively biased o-PLS control method (98 ± 3%). RT alignment improved the classification rates for both FuRES and o-PLS classifiers (18% improvement for the FuRES classification rate and 10% improvement for the o-PLS classification rate with baseline correction). From the rule obtained to classify the P. quinquefolius L samples grown in the United States and China, peaks were identified that can be prospective biomarkers for differentiating samples from different growth regions. HPLC-MS with chemometric analysis has the potential to be used as an authentication method for P. quinquefolius L grown in China and the United States.     

Characterization of phosphoantigens by high-performance anion-exchange chromatography-electrospray ionization ion trap mass spectrometry and nanoelectrospray ionization ion trap mass spectrometry

New phosphorylated microbial metabolites referred to as phosphoantigens activate immune responses in humans. Although these molecules have leading applications in medical research, no direct method allows their rapid and unambiguous structural identification. Here, we interfaced online HPAEC (high performance anion-exchange chromatography) with ESI-ITMS (electrospray ionization ion trap mass spectrometry) to identify such pyrophosphorylated molecules. A self-regenerating anion suppressor located upstream of electrospray ionization enabled the simultaneous detection of pyrophosphoester by conductimetry, UV and MS. By HPAEC-ITMS and HPAEC-ITMS2, a single run permitted characterization of reference phosphoantigens and of related structures. Although all compounds were resolved by HPAEC, MS enabled their detection and identification by [M-H]- and fragment ions. Isobaric phosphoantigen analogues were also separated by HPAEC and distinguished by MS2. The relevance of this device was demonstrated for phosphoantigens analysis in human urine and plasma. Furthermore, identification of natural phosphoantigens by automatically generated 2D mass spectra from nano-ESI-ITMS is presented. This last technique permits the simultaneous performance of molecular screening of natural phosphoantigen extracts and their identification.     

High-efficiency liquid chromatographic separation utilizing long monolithic silica capillary columns

Long monolithic silica-C18 capillary columns of 100 microm i.d. were prepared, and the efficiency was examined using reversed-phase HPLC under a pressure of up to 47 MPa. At linear velocities of 1-2 mm/s, 100,000-500,000 theoretical plates could be generated with a single column (90-440 cm in length) using an acetonitrile-water (80/20) mobile phase with a column dead time (t0) of 5-40 min. It was possible to prepare columns with a minimum plate height of 8.5 +/- 0.5 microm and permeability of (1.45 +/- 0.09) x 10(-13) m(2). The chromatographic performance of a long octadecylsilylated monolithic silica capillary column was demonstrated by the high-efficiency separations of aromatic hydrocarbons, benzene derivatives, and a protein digest. The efficiency for a peptide was maintained for an injection of up to 0.5-2 ng. When three 100 microm i.d. columns were connected to form a 1130-1240 cm column system, 1,000,000 theoretical plates were generated for aromatic hydrocarbons with retention factors of up to 2.4 with a t0 of 150 min. The fact that very high efficiencies were obtained for the retained solutes suggests the practical utility of these long monolithic silica capillary columns.     

Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry

Herein we report a novel method for determining genomic DNA methylation that utilizes liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to measure 5-methyl-2'-deoxycytidine levels following enzymatic hydrolysis of genomic DNA. LC separation of 5-methyl-2'-deoxycytidine from the four deoxyribonucleosides, the four ribonucleosides, and 5-methyl-2'-cytidine, a RNA methylation product, has been achieved within 15 min. In combination with ESI-MS/MS detection, the reported method is highly specific and extremely sensitive with a limit of detection (LOD) of 0.2 fmol and a quantification linearity range from 1 fmol to 20 pmol. Genomic DNA methylation was expressed as the ratio of 5-methyl-2'-deoxycytidine to 2'-deoxyguanosine and was determined directly using 2'-deoxyguanosine as the internal standard. Because deoxycytidine methylation typically ranges from 2 to 6% in mammalian genomes, and pharmacological or genetic manipulations have not achieved levels lower than 0.1%, we validated the assay for methylation levels ranging from 0.05 to 10%. Importantly, both RNA contamination and incomplete DNA hydrolysis had no appreciable effect on 5-methyl-2'-deoxycytidine quantification. LOD studies indicate that only 4 ng of DNA is required for this assay. This LOD should permit the use of this method for applications having limiting amounts of DNA that were not previously candidates for global genomic DNA methylation analysis, e.g., clinical trial samples, or cells collected by laser capture microdissection.     

Quantification of intracellular phosphorylated carbohydrates in HT29 human colon adenocarcinoma cell line using liquid chromatography-electrospray ionization tandem mass spectrometry

The quantitative understanding of the role of sugar phosphates in regulating tumor energetic metabolism at the proteomic and genomic level is a prerequisite for an efficient rational design in combined drug chemotherapy. Therefore, it is necessary to determine accurately the concentration of the main sugar phosphate pools at the lower concentrations present in the often-limited volume of tumor cell samples. Taking as an example the human adenocarcinoma cell line HT29, we here report a fast and reliable quantitative method based on the use of liquid nitrogen, a weak acid extraction, and liquid chromatography-electrospray ionization tandem mass spectrometry to quantify simultaneously the intracellular concentration of sugar phosphate pools. The method was set up using standard addition curves. Thus, it is possible to identify and quantify hexose phosphate, pentose phosphate, and triose phosphate pools up to 0.02-0.10 ng x microL(-1), depending on the analyte. The method developed was here used for the quantitative study of changes in phosphorylated carbohydrates of central carbon metabolism when high or low glucose concentration conditions are induced in vitro in the HT29 human colon adenocarcinoma cell line.     

Capillary-scale frontal affinity chromatography/MALDI tandem mass spectrometry using protein-doped monolithic silica columns

Frontal affinity chromatography (FAC) interfaced with electrospray mass spectrometry (ESI-MS) has been reported as a potential method for screening of compound mixtures against immobilized target proteins. However, the interfacing of bioaffinity columns to ESI-MS requires that the eluent that passes through the protein-loaded column have a relatively low ionic strength to produce a stable spray. Such low ionic strength solvents can cause serious problems with protein stability and may also affect binding constants and lead to high nonspecific binding to the column. Herein, we report on the interfacing of bioaffinity columns to matrix-assisted laser desorption/ionization (MALDI) MS/MS as a new platform for FAC/MS studies. Capillary columns containing a monolithic silica material with entrapped dihydrofolate reductase were used for frontal affinity chromatography of small-molecule mixtures. The output from the column was combined with a second stream containing alpha-cyano-hydoxycinnamic acid in methanol and was deposited using a nebulizer-assisted electrospray method onto a conventional MALDI plate that moved relative to the column via a computer-controlled x-y stage, creating a semipermanent record of the FAC run. The use of MALDI MS/MS allowed for buffers with significantly higher ionic strength to be used for FAC studies, which reduced nonspecific binding of ionic compounds and allowed for better retention of protein activity over multiple runs. Following deposition, MALDI analysis required only a fraction of the chromatographic run time, and the deposited track could be rerun multiple times to optimize ionization parameters and allow signal averaging to improve the signal-to-noise ratio. Furthermore, high levels of potential inhibitors could be detected via MALDI with limited ion suppression effects. Both MALDI- and ESI-based analysis showed similar retention of inhibitors present in compound mixtures when using identical ionic strength conditions. The results show that FAC/MALDI-MS should provide advantages over FAC/ESI-MS for high-throughput screening of compound mixtures.     

Determination of carbamazepine and its metabolites in aqueous samples using liquid chromatography-electrospray tandem mass spectrometry

A quantitative method is described for solid-phase extraction (SPE) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the simultaneous analysis of carbamazepine and its five metabolites, 10,11-dihydro-10,11-epoxycarbamazepine, 10,11-dihydro-10,11-dihydroxycarbamazepine, 2-hydroxycarbamazepine, 3-hydroxycarbamazepine, and 10,11-dihydro-10-hydroxycarbamazepine. An SPE procedure was used to concentrate target compounds from aqueous samples collected from sewage treatment plant (STP) wastewater and surface water. Extracts were analyzed using electrospray LC-MS/MS with time-scheduled selected reaction monitoring. The recoveries of the analytes were 83.6-102.2% from untreated sewage (influent), 90.6-103.5% from treated sewage (effluent), and 95.7-102.9% from surface water samples. The instrumental detection limits were 0.8-4.8 pg for the analytes. Matrix effects were investigated for the analytes in HPLC-grade water, surface water, and STP influent and effluent. Ion suppression increased for analytes in order of surface water to STP effluent to STP influent, but no ion suppression was observed for analytes in HPLC-grade water. The developed method was validated by analysis of environmental aqueous samples: STP influent and effluent and surface water. Carbamazepine and all five metabolites were detected in STP influent and effluent samples. Only carbamazepine and 10,11-dihydro-10,11-dihydroxycarbamazepine were detected in the surface water sample. Notably, 10,11-dihydro-10,11-dihydroxycarbamazepine was detected at approximately 3 times higher concentrations than the parent drug, carbamazepine, in all of the aqueous samples. To our knowledge, this is the first report on the simultaneous determination of carbamazepine and its metabolites in environmental samples.     

Analysis of alkylphenol ethoxylate metabolites in the aquatic environment using liquid chromatography-electrospray mass spectrometry

A quantitative method is described for the analysis of the metabolites of alkylphenol ethoxylate (APEO) surfactants in estuarine water and sediment samples using reversed-phase high-performance liquid chromatography with electrospray mass spectrometry detection. Nonyl- and octylphenols, nonyl- and octylphenol mono-, di-, and triethoxylates, halogenated nonylphenols, and nonylphenol ethoxycarboxylates were concentrated from water samples using a C18 solid-phase extraction procedure. A novel, continuous-flow, high-temperature, sonicated extraction system was developed to isolate APEO metabolites from sediment samples. Quantitative LC-MS was performed in the negative ion mode for nonylphenols, octylphenols, and halogenated nonylphenols and in the positive ion mode for nonyl- and octylphenol ethoxylates using selected ion monitoring with isotopically labeled surrogate standards. Recoveries for sediment and water analyses ranged between 78 and 94%, and detection limits for APEO metabolites were between 1 and 20 pg injected on column. This is a significant improvement over previously reported methods. Suppression of analyte response was encountered in the presence of matrix components in sediment samples, but this effect was eliminated by careful selection of surrogate and internal standards. Individual APEO metabolite concentrations of 1-320 ng/L and 5-2000 ng/g are reported for water and sediment samples, respectively, from Jamaica Bay, NY.     

A method for quantitatively differentiating crude natural extracts using high-performance liquid chromatography-electrospray mass spectrometry

This paper describes a method for quantitatively differentiating crude natural extracts using high-performance liquid chromatography-electrospray mass spectrometry (HPLC-ESI-MS). The method involves performing an HPLC-MS analysis using standard reversed-phase C18 gradient separation on the crude extract. The HPLC system used in this study was a dual-column system designed to optimize throughput. Using image analysis techniques, the data are reduced to a list containing the m/z value and retention time of each ion. The ion lists are then compared in a pairwise fashion to compute a sample similarity index between two samples. The similarity index is based on the number of ions common to both and is scaled from 0 to 1. Extract controls were analyzed throughout a run of 88 unknown fungal extracts. The controls provided information about column and spectrometer stability and overall sensitivity. Pairwise comparison of all control samples indicates that the similarity index is high (0.8) for replicate samples. Comparison between the unknown extract samples produces a distribution of similarities ranging from replicates (0.8) to very dissimilar (0.1). This information can be used to judge the chemical diversity of natural extract samples, which is one approach to determining the quality of libraries being used for drug discovery via high-throughput screening.     

Identification of phosphorylation sites in insulin receptor substrate-1 by hypothesis-driven high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

Serine phosphorylation of insulin receptor substrate-1 (IRS-1) can regulate tyrosine phosphorylation of IRS-1 and subsequent insulin signaling. The 182 serine and 60 threonine residues in IRS-1 make position-by-position analysis of potential phosphorylation sites by mutagenesis difficult. Tandem mass spectrometry provides a more efficient way to identify phosphorylated residues in IRS-1. Toward this end, we overexpressed glutathione S-transferase-IRS-1 fusion proteins in E. coli and treated them in vitro with various kinases followed by identification of phosphorylation sites using high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. Nine phosphorylation sites were detected in the tryptic digests of middle and C-terminal regions of IRS-1 treated with protein kinase A or extracellular signal-regulated kinase 2. Of these sites, five have not previously been detected by any method and provide novel candidates for identification in cells or in vivo.     

Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry

We have developed a new procedure for fabricating fused-silica emitters for electrospray ionization-mass spectrometry (ESI-MS) in which the end of a bare fused-silica capillary is immersed into aqueous hydrofluoric acid, and water is pumped through the capillary to prevent etching of the interior. Surface tension causes the etchant to climb the capillary exterior, and the etch rate in the resulting meniscus decreases as a function of distance from the bulk solution. Etching continues until the silica touching the hydrofluoric acid reservoir is completely removed, essentially stopping the etch process. The resulting emitters have no internal taper, making them much less prone to clogging compared to, e.g., pulled emitters. The high aspect ratios and extremely thin walls at the orifice facilitate very low flow rate operation; stable ESI-MS signals were obtained for model analytes from 5-microm-diameter emitters at a flow rate of 5 nL/min with a high degree of interemitter reproducibility. In extensive evaluation, the etched emitters were found to enable approximately four times as many LC-MS analyses of proteomic samples before failing compared with conventional pulled emitters. The fabrication procedure was also employed to taper the ends of polymer monolith-containing silica capillaries for use as ESI emitters. In contrast to previous work, the monolithic material protrudes beyond the fused-silica capillaries, improving the monolith-assisted electrospray process.     

Characterizing organic monolithic columns using capillary flow porometry and scanning electron microscopy

Polyethylene glycol diacrylate monoliths prepared using different amounts of monomer, porogen ratio, and capillary dimensions were characterized using capillary flow porometry (CFP) and scanning electron microscopy (SEM). Our results reveal good agreement between SEM and CFP measurements for through-pore size distribution. The CFP measurements for monoliths prepared by the same procedure in capillaries with different diameters (i.e., 75, 150, and 250 μm) clearly confirmed a change in through-pore size distribution with capillary diameter, thus, certifying the need for in-column measurement techniques over bulk measurements (e.g., mercury intrusion porosimetry). The mean through-pore size varied from 3.52 to 1.50 μm with a change in capillary diameter from 75 to 250 μm. Consistent mean through-pore size distribution for capillary columns with the same internal diameter but with different lengths (1.5, 2, and 3 cm) confirms the high interconnectivity of the pores and independence of CFP measurements with respect to capillary length. CFP and SEM measurements not only allow pore structure analysis but also prediction of relative column performance. Monoliths with narrow through-pore size distribution (0.8-1.2 μm), small mean through-pore size, and thin skeletal size (0.55 μm) gave the best performance in terms of efficiency for polyethylene glycol diacrylate monoliths.