On-line solid phase extraction-liquid chromatography, with emphasis on modern bioanalysis and miniaturized systems.

On-line solid phase extraction (SPE)-liquid chromatography (LC) allows for automated, sensitive, precise and selective bioanalysis. It is a common feature in miniaturized- or nano LC systems, which are well suited for applications requiring high sensitivity and/or treatment of limited samples (laser micro-dissection samples, rare cancer stem cells, etc.). Traditionally, particles with reversed phase (RP) functional groups are used for the columns in SPE-LC systems. There is however an expanding diversity in SPE-LC combinations applied to meet today's bioanalytical challenges. Current online SPE-LC combinations employ, e.g. porous graphitic carbon (PGC) and hydrophilic interaction liquid chromatography (HILIC) materials for metabolomics and glycomics, restricted access media (RAM) columns coupled with nano LC for peptidomics, immunoaffinity trap columns for targeted proteomics and metal oxide affinity phases for phosphopeptide analysis. However, issues can arise when combining different phases in on-line SPE-LC, e.g. due to solvent incompatibilities between enrichment/separation principles and sample solvent requirements. Consequences can be low recovery and poor resolution, or need for additional instrumentation. On-line SPE-LC with very narrow columns (10-20 µm inner diameters) can be appropriate to obtain maximum sensitivity and information. In such highly miniaturized systems, non-particulate columns are arguably more suited (e.g. monolithic or porous layer open tubular (PLOT) columns) as e.g. hardware contributions resulting in extra column volumes are reduced. Basic SPE-LC systems can be configured/modified to perform quite complex analytical operations, and certain columns, configurations and hardware can improve robustness.

Large volume injection of aqueous peptide samples on a monolithic silica based zwitterionic-hydrophilic interaction liquid chromatography system for characterization of posttranslational modifications.

Zwitterionic-hydrophilic interaction liquid chromatography (HILIC) has been found very appropriate for separation of polar compounds and peptides with post-translational modifications (PTMs) such as phosphorylation and glycosylation. In this study, a column switching system based on zwitterionic-HILIC silica based monolith columns was used for enrichment and separation of peptides and characterization of N-linked glycosylation by higher-energy collisional dissociation (HCD) Orbitrap mass spectrometry (MS). Peptides were found to be retained on a zwitterionic-HILIC precolumn, even in an aqueous buffer due to electrostatic interactions. Thus, a novel approach of using a zwitterionic-HILIC precolumn, for introduction of an aqueous sample such as a tryptic digest, followed by HILIC separation of the peptides is presented. The repeatability and loadability of the zwitterionic-HILIC-zwitterionic-HILIC column switching system were explored using a tryptic digest of transferrin and a mixture of six proteins. The column switching system was furthermore used to enrich and separate a tryptic digested rat liver extract gel fraction, where in total 48 peptides corresponding to 14 proteins were identified. N-linked glycoforms were also identified, both in the standard test proteins (transferrin and six protein mixture digest) and the rat liver extract fraction. In all cases, the identified N-linked glycoforms were identified at the end of the gradient, at high aqueous buffer content in the mobile phase, showing the suitability of the developed method for characterization of glycosylated peptides in aqueous samples.

Comprehensive profiling of N-linked glycosylation sites in HeLa cells using hydrazide enrichment.

The adenocarcinoma cell line HeLa serves as a model system for cancer research in general and cervical cancer in particular. In this study, hydrazide enrichment in combination with state-of-the art nanoLC-MS/MS analysis was used to profile N-linked glycosites in HeLa cells. N-Linked glycoproteins were selectively enriched in HeLa cells by the hydrazide capture method, which isolates all glycoproteins independent of their glycans. Nonglycosylated proteins were removed by extensive washing. N-Linked glycoproteins were identified with the specific NXT/S motif and deamidated asparagine (N). Deglycosylation was carried out in both H(2)(16)O and H(2)(18)O to confirm the deamidation. NanoLC-MS/MS analysis indicated that the method selectively enriched at least 100 fold N-linked glycosites in HeLa cells. When both the membrane and cytosolic fractions were used, a total of 268 unique N-glycosylation sites were identified corresponding to 106 glycoproteins. Bioinformatic analysis revealed that most of the glycoproteins identified are known to have an impact on cancer and have been proposed as biomarkers.

High efficiency, high temperature separations on silica based monolithic columns.

The effect of temperature on separation using reversed-phase monolithic columns has been investigated using a nano-LC pumping system for gradient separation of tryptic peptides with MS detection. A goal of this study was to find optimal conditions for high-speed separations. The chromatographic performance of the columns was evaluated by peak capacity and peak capacity per time unit. Column lengths ranging from 20 to 100 cm and intermediate gradient times from 10 to 30 min were investigated to assess the potential of these columns in a final step separation, e.g. after fractionation or specific sample preparation. Flow rates from 250 to 2000 nL/min and temperatures from 20 to 120°C were investigated. Temperature had a significant effect on fast separations, and a flow rate of 2000 nL/min and a temperature of 80°C gave the highest peak capacity per time unit. These settings produced 70% more protein identifications in a biological sample compared to a conventional packed column. Alternatively, an equal amount of protein identifications was obtained with a 40% reduction in run time compared to the conventional packed column.

Critical assessment of accelerating trypsination methods.

In LC-MS based proteomics, several accelerating trypsination methods have been introduced in order to speed up the protein digestion, which is often considered a bottleneck. Traditionally and most commonly, due to sample heterogeneity, overnight digestion at 37 °C is performed in order to digest both easily and more resistant proteins. High efficiency protein identification is important in proteomics, hours with LC-MS/MS analysis is needless if the majority of the proteins are not digested. Based on preliminary experiments utilizing some of the suggested accelerating methods, the question of whether accelerating digestion methods really provide the same protein identification efficiency as the overnight digestion was asked. In the present study we have evaluated four different accelerating trypsination methods (infrared (IR) and microwave assisted, solvent aided and immobilized trypsination). The methods were compared with conventional digestion at 37 °C in the same time range using a four protein mixture. Sequence coverage and peak area of intact proteins were used for the comparison. The accelerating methods were able to digest the proteins, but none of the methods appeared to be more efficient than the conventional digestion method at 37 °C. The conventional method at 37 °C is easy to perform using commercially available instrumentation and appears to be the digestion method to use. The digestion time in targeted proteomics can be optimized for each protein, while in comprehensive proteomics the digestion time should be extended due to sample heterogeneity and influence of other proteins present. Recommendations regarding optimizing and evaluating the tryptic digestion for both targeted and comprehensive proteomics are given, and a digestion method suitable as the first method for newcomers in comprehensive proteomics is suggested.

Hydrophilic interaction chromatography of nucleoside triphosphates with temperature as a separation parameter.

Eight deoxynucleoside triphosphates (dNTPs) and nucleoside triphosphates (NTPs): ATP, CTP, GTP, UTP, dATP, dCTP, dGTP and dTTP, were separated with two 15 cm ZIC-pHILIC columns coupled in series, using LC-UV instrumentation. The polymer-based ZIC-pHILIC column gave significantly better separations and peak shape than a silica-based ZIC-HILIC column. Better separations were obtained with isocratic elution as compared to gradient elution. The temperature markedly affected the selectivity and could be used to fine tune separation. The analysis time was also affected by temperature, as lower temperatures surprisingly reduced the retention of the nucleotides. dNTP/NTP standards could be separated in 35 min with a flow rate of 200 µL/min. In Escherichia coli cell culture samples dNTP/NTPs could be selectively separated in 7 0min using a flow rate of 100 µL/min.

2-D hydrophilic interaction liquid chromatography-RP separation in urinary proteomics--minimizing variability through improved downstream workflow compatibility.

Optimization of every step in a bottom-up urinary proteomics approach was studied with respect to maximize the protein recovery and making the downstream steps in the workflow fully compatible without compromising on the amount of information obtained. Sample enrichment and desalting using centrifugal filtration (5 kDa cut-off) yielded protein recoveries up to 97% when 8 M urea was used. Although yielding lower recoveries (88%), addition of Tris-HCl/NaCl was considered a better choice due to good down-stream compatibility. The consecutive depletion of HSA, using an immunoaffinity column was successfully adapted for use in urine. Separation of the trypsin generated peptides in an off-line 2-D chromatographic system consisting of a hydrophilic interaction liquid chromatography column, followed by a RP chromatography column showed a high peak capacity and good repeatability in addition to a high degree of orthogonality. All operations were modified in order to keep sample handling between every step to a minimum, reducing the variability of each process. In order to test the suitability of the full method in an extensive proteomic experiment, a urine sample from a kidney-transplanted patient was analyzed (n=6). The total variability of the method was identified with RSD values ranging from 11 to 30%. Eventually, we identified a total of 1668 peptides and 438 proteins from a single urine sample despite the use of low-resolution MS/MS equipment. The optimized and "streamlined" complex method has shown potential for use in future urinary proteomic studies.

Improving the resolution of neuropeptides in rat brain with on-line HILIC-RP compared to on-line SCX-RP.

Our two already established on-line 2-D LC systems, a strong cation exchange-RP chromatography (SCX-RP) system and a hydrophilic interaction LC (HILIC)-RP 2-D LC system, were compared to explore which system is best suited for our further studies of differences in cerebral neuropeptide expression as a function of hypoxia-caused stress. The same mass spectrometer and database search parameters were applied in both systems. In total, 19 first dimension fractions were collected with the novel on-line HILIC-RP system, including a Hypercarb SPE column that was applied to trap the compounds not retained on a Kromasil C18 enrichment column. In contrast, six fractions were collected in the SCX-RP method, due to practical limitations of this traditional on-line 2-D LC system. With the on-line HILIC-RP system three times more peaks were detected. It was observed that most of the compounds eluted in the first two fractions in the SCX-RP method, while in the 2-D HILIC-RP method there seemed to be no correlation between peaks detected and fraction number. Thus, from this systematic study it seems that on-line HILIC-RP chromatography is the method of choice for comparative peptidomics of cerebral neuropeptides in future studies.

Identification of major metal complexing compounds in Blepharis aspera.

Verbascoside and isoverbascoside, present at 0.7% and 0.2% (w/w dryweight), were identified to be major compounds that could contribute to the metal complexation in Blepharis aspera collected in Botswana, Africa. The metallophyte B. aspera has high ability to cope with a high level of metal accumulation. The presence of metal complexing compounds and/or antioxidants can prevent oxidative reactions in lipids, proteins and DNA that take place due to the metal accumulation. On-line liquid chromatography-solid phase extraction-nuclear magnetic resonance (LC-SPE-NMR) was applied for the identification, while electrospray-mass spectrometry (ESI-MS) and UV-vis spectroscopy was used to assess whether these compounds can complex with metals. It was found that verbascoside and isoverbascoside may form complexes with nickel, iron (verbascoside only) and copper. Thus, the presence of verbascoside and isoverbascoside can explain the survival of B. aspera in mineral-rich areas.

On-line SPE-Nano-LC-Nanospray-MS for rapid and sensitive determination of perfluorooctanoic acid and perfluorooctane sulfonate in river water.

An instrumental set up including on-line solid-phase extraction, nano-liquid chromatography, and nanospray mass spectrometry is constructed to improve the sensitivity for quantitation of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) in surface water. Sample volumes of 1000 microL are loaded onto a microbore 1.0-mm i.d. x 5 mm, 5 microm Kromasil C(18) enrichment column by a carrier solution consisting of 10mM ammonium acetate in acetonitrile-water (10:90, v/v) at a flow rate of 250 microL/min, providing on-line analyte enrichment and sample clean-up. Backflushed elution onto a 0.1-mm i.d. x 150 mm, 3.5 microm Kromasil C(18) analytical column is conducted using an acetonitrile-10mM ammonium acetate solvent gradient from 30% to 70% acetonitrile. Water samples are added with internal standard (perfluoroheptanoic acid) and filtrated prior to injection. The mass limits of detection of PFOA and PFOS are 0.5 and 1 pg, respectively, corresponding to concentration limits of detection of 500 pg/L and 1 ng/L, respectively. The total time spent on sample preparation, chromatography, and detection is approximately 12 min per sample. The method was employed for the determination of PFOS and PFOA in urban river water.

An alternative multiple-trapping LC-SPE-NMR system.

In this paper, we describe approaches that make RP LC-SPE-NMR simpler, and in our opinion, result in more reliable methods for trapping and subsequent transfer of separated trace-level compounds to the NMR. An SPE unit based on a commercially available, low dead-volume 10 port high-pressure column selector gives the possibility of trapping compounds on nine individual SPEs that have standard fittings. This allows the operator to employ specific stationary phases that are not available as SPEs in commercially available LC-SPE-NMR systems. Multiple trappings of small compounds like monuron, 1-(4-chlorophenyl)-3-methylurea, and 4-chlorophenylurea were easily performed employing a porous-carbon SPE material. The system was optimized to elute the SPE-trapped compounds to the NMR probes in as small a volume as possible using back-flushing. The proper match of NMR probe volume and SPE column inner diameter and elution volume was discussed, as well as the necessity of drying loaded SPEs prior to NMR transfer when using porous-carbon SPE material.

Short communication controlling LC-SPE-NMR systems.

There are several stages of the LC-SPE-NMR process that should be monitored closely to ensure an efficient isolation and concentration of the target analyte, for instance analyte break-through and compound transfer from the LC-SPE to the NMR probe. In this study, analyte break-through monitoring was performed with a UV detector and a mass spectrometer placed after the SPE unit. Easy break-through was a problem when attempting multiple trapping of various compounds using C18 SPE cartridges with the original commercial system. However, on lowering the flow rate over the SPE system and using SPE cartridges packed with porous carbon, the number of trappings possible increased five-fold. To increase control over the on-line SPE-NMR transfer, a gradient pump-UV system was used to elute compounds trapped on an SPE to an NMR probe. The analyte band was placed in the active volume of the probe by a stop-flow mechanism. The modified LC-SPE system was also coupled with off-line NMR analysis for determination of a degradation product of the insecticide monuron, present in the low ppm range.