Selective intercalation of polymers in carbon nanotubes

A room-temperature, open-air method is devised to selectively intercalate relatively low-molecular-weight polymers (approximately 10-100 kDa) from dilute, volatile solutions into open-end, as-grown, wettable carbon nanotubes with 50-100 nm diameters. The method relies on a novel self-sustained diffusion mechanism driving polymers from dilute volatile solutions into carbon nanotubes and concentrating them there. Relatively low-molecular-weight polymers, such as poly(ethylene oxide) (PEO, 600 kDa) and poly(caprolactone) (PCL, 80 kDa), were encapsulated in graphitic nanotubes as confirmed by transmission electron microscopy, which revealed morphologies characteristic of mixtures in nanoconfinements affected by intermolecular forces. Whereas relatively small, flexible polymer molecules can conform to enter these nanotubes, larger macromolecules (approximately 1000 kDa) remain outside. The selective nature of this process is useful for filling nanotubes with polymers and could also be valuable in capping nanotubes.     

Coupling electrospray corona discharge, charge reduction and ion mobility mass spectrometry: From peptides to large macromolecular protein complexes

We present the design and implementation of a home-built point-to-plane corona discharge probe, which rapidly and efficiently charge reduces biological ions generated by electrospray ionization (ESI). The molecules analysed ranged from small peptides such as Glu-fibrinopeptide B (1.5 kDa), small proteins such as myoglobin (16.9 kDa), polymers such as polyethylene glycol (PEG 10 k) which all showed intense singly charged ions; to large native multiprotein complexes such as GroEL (802 kDa) which show a broad range of charge-reduced species. The corona discharge probe operates at atmospheric pressure and was directly interfaced with a standard-ESI or nanoflow-ESI source of quadrupole ion mobility time-of-flight mass spectrometer. The corona discharge probe is completely modular and could potentially be mounted to any commercial or research grade mass spectrometer with an ESI source. The level of charge reduction is precisely controlled by the applied voltage and/or probe gas flow rate and when in operation, results in approximately a 50 % reduction in total ion current. We also present the combination of corona discharge and travelling wave ion mobility and assign helium collision cross-section values (Ω_He) to the charge reduced species of the native protein complex pyruvate kinase. It would appear that the Ω_He of the +20 charge state for pyruvate kinase is approximately 20 % smaller than the +35 charge state. Finally, we discuss the potential benefits and concerns of utilising charge reduced protein species as a means of extending the travelling wave collision cross-section calibration range over that which is already published.     

Highly efficient monolithic silica capillary columns modified with poly(acrylic acid) for hydrophilic interaction chromatography

Monolithic silica capillary columns for hydrophilic interaction liquid chromatography (HILIC) were prepared by on-column polymerization of acrylic acid on monolithic silica in a fused silica capillary modified with anchor groups. The products maintained the high permeability (K=5 x 10(-14)m(2)) and provided a plate height (H) of less than 10 microm at optimum linear velocity (u) and H below 20 microm at u=6mm/s for polar solutes including nucleosides and carbohydrates. The HILIC mode monolithic silica capillary column was able to produce 10000 theoretical plates (N) with column dead time (t(0)) of 20s at a pressure drop of 20 MPa or lower. The total performance was much higher than conventional particle-packed HILIC columns currently available. The gradient separations of peptides by a capillary LC-electrospray mass spectrometry system resulted in very different retention selectivity between reversed-phase mode separations and the HILIC mode separations with a peak capacity of ca. 100 in a 10 min gradient time in either mode. The high performance observed with the monolithic silica capillary column modified with poly(acrylic acid) suggests that the HILIC mode can be an alternative to the reversed-phase mode for a wide range of compounds, especially for those of high polarity in isocratic as well as gradient elution.     

An improved sodium dodecyl sulfate-polyacrylamide gel electrophoresis system for the analysis of membrane protein complexes

Membrane protein complexes such as the reaction center complexes of oxygenic photosynthesis or the complex I of mitochondira are composed of many subunit polypeptides. To analyze their polypeptide compositions by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), a wide range of molecular sizes has to be resolved, especially in the low molecular mass range. We have improved the traditional Tris/HCI buffer systems adopting a Tris/2-(N-morpholino)ethanesulfonic acid (MES) buffer system containing 6 M urea. This gel system was used with an 18-24% acrylamide gradient for the separation of polypeptides with molecular masses from below 5 kDa to over 100 kDa. This buffer system can also be applied to the usual uniform concentration of acrylamide gel and also to minislab gels.     

Comparing monolithic and microparticular capillary columns for the separation and analysis of peptide mixtures by liquid chromatography-mass spectrometry

A mixture of ten proteins was trypsinized and injected onto poly-(styrene-divinylben-zene) monolithic columns (60 x 0.20 or 0.10 mm ID) and a column packed with C18 silica particles (75 x 0.075 mm ID), respectively. The columns were eluted at 200-2000 nL/min with gradients of ACN in 0.050% TFA. Eluting peptides were detected by ESI-MS/MS and subsequently identified by database searching. The 100 microm ID monolithic column showed the highest cumulative Mowse scores based on the highest ion scores for the peptides and the largest number of identified peptides. It is shown that the number of identified peptides strongly depends on the dynamic range within the peptide mixture. In consequence, all proteins were identified in a mixture of relatively balanced analyte amounts (12.5-80 fmol) whereas only peptides for six out of ten proteins were found in a sample of high-dynamic range (0.65-270 fmol). The 100 microm monolithic column showed the highest reproducibility for peptide identifications in three consecutive runs. Depending on sample amount, 57-72% of the identified peptides were detectable in each of the three runs of triplicate analyses. The results demonstrate the high suitability of 100 microm monolithic columns for high-resolution peptide separations in proteomic research.     

Micellar electrokinetic chromatography of fluorescently labeled proteins on poly(dimethylsiloxane)-based microchips

MEKC of standard proteins was investigated on PDMS microfluidic devices. Standard proteins were labeled with AlexaFluor(R) 488 carboxylic acid tetrafluorophenyl ester and filtered through a size-exclusion column to remove any small peptides and unreacted label. High-efficiency MEKC separations of these standard proteins were performed using a buffer consisting of 10 mM sodium tetraborate, 25 mM SDS, and 20% v/v ACN. A separation of BSA using this buffer in a 3.0 cm long channel generated a peak with a plate height of 0.38 microm in <20 s. Additional fast separations of myoglobin, alpha-lactalbumin, lysozyme, and cytochrome c also yielded peaks with plate heights ranging from 0.54 to 0.72 microm. All proteins migrated with respect to their individual pIs. To improve the separations, we used a PDMS serpentine chip with tapered turns and a separation distance of 25 cm. The number of plates generated increased linearly with increasing separation distance on the extended separation channel chips; however, the resolution reached an asymptotic value after about 7 cm. This limited the peak capacity of the separation technique to 10-12.     

High-speed separation of proteins by microchip electrophoresis using a polyethylene glycol-coated plastic chip with a sodium dodecyl sulfate-linear polyacrylamide solution

In this paper, we describe a method for size-based electrophoretic separation of sodium dodecyl sulfate (SDS)-protein complexes on a polymethyl methacrylate (PMMA) microchip, using a separation buffer solution containing SDS and linear polyacrylamide as a sieving matrix. We developed optimum conditions under which protein separations can be performed, using polyethylene glycol (PEG)-coated polymer microchips and electrokinetic sample injection. We studied the performance of protein separations on the PEG-coated PMMA microchip. The electrophoretic separation of proteins (21.5-116.0 kDa) was completed with separation lengths of 3 mm, achieved within 8 s on the PEG-coated microchip. This high-speed method may be applied to protein separations over a large range of molecular weight, making the PEG-coated microchip approach applicable to high-speed proteome analysis systems.     

A graphical method for understanding the kinetics of peak capacity production in gradient elution liquid chromatography

A novel graphical method for assessing the compromise between conditional peak capacity and separation speed for packed bed columns under gradient conditions has been developed and applied to the separation of peptides. This approach is analogous to and complements the conventional "Poppe plot" used to study plate count in isocratic separations. The use of the new plot can assist the design of appropriate column formats (e.g. particle size and column length) for both dimensions in gradient elution two-dimensional liquid chromatography (2DLC). Particularly for the second dimension of 2DLC, we find that smaller particles provide faster separations even though fast separations based on particles smaller than 2 microm are practically limited by the required miniscule column length. We also find that high temperatures strongly enhance the kinetics of peak capacity production whereas higher pressures help achieve larger absolute peak capacities albeit at the cost of longer analysis time.     

Restricted-access material-based high-molecular-weight protein depletion coupled on-line with nano-liquid chromatography-mass spectrometry for proteomics applications

Proteomics samples often contain both abundant proteins and low-level proteins and peptides. Highly abundant proteins can mask and/or bind those of lower abundance and thereby hinder their analysis. In particular, we were concerned with samples containing large amounts of albumin (up to 4.0 microM). In this study, a novel set-up for multidimensional nano-liquid chromatography-mass spectrometry (nanoLC-MS) with three columns coupled on-line was developed and characterised. A 1-mm-I.D. restricted-access-material (RAM) cartridge and a 100-microm-I.D. reversed-phase trap column are coupled in forward-flush mode to remove albumin before on-line separation on a 50 microm I.D. reversed-phase capillary analytical column. Volumes up to 100 microL of a complex matrix (containing 0.4 or 4.0 microM albumin) could be injected onto this system, enabling a 5000-fold volume reduction. Up to 99.7% of the albumin present in samples could be efficiently removed over the RAM cartridge. The total analysis time was about 40 min. Using Substance P as a model peptide, separations were efficient, with a peak width of 10s at half height. Moreover, separations were highly reproducible (relative standard deviation (RSD) on retention time approximately 3% over 1 week). The set-up proved to be robust and was used for about 750 analyses without exchanging one of the columns. Flexibility with respect to the stationary phase material in the sample preparation cartridge allows for other separation modes to be applied as well.     

A novel sodium bis(2-ethylhexyl) sulfosuccinate-PAGE system suitable for the separation of small peptides

A novel sodium bis(2-ethylhexyl) sulfosuccinate-PAGE (AOT-PAGE) system which delivers high resolution and sensitivity for small peptides with molecular masses of 0.8-17 kDa is described. Small peptides migrate more slowly and are less prone to leakage than in conventional SDS-PAGE, thus allowing for the in-gel detection with CBB R 250 of 0.5 mug of peptide. The system is also compatible with electroblotting, activity staining in renatured gels, and the peptide analysis by MALDI-MS. AOT-PAGE is simpler, more rapid, and cheaper than the generally adopted Tricine-SDS-PAGE method.     

Fritless capillary electrochromatography

The preparation of packed capillaries with stable frits of good quality can be a hurdle to obtain efficient separations in capillary electrochromatography (CEC). Especially with particles smaller than 3 microm, frit preparation is cumbersome. Highly efficient separations using packed capillaries without frits are presented. Under appropriate CEC conditions the particles were retained by electrophoretic attraction towards the anode by a tapered capillary inlet, without the need of a frit at the outlet end. Such fritless capillaries, packed with 1.5 microm nonporous reversed-phase particles, allowed separations with efficiencies of more than 500,000 plates/m. Once the capillaries were conditioned properly, more than 100 separations could be performed with good repeatability. With respect to separation efficiency, fritless capillaries packed with 3 microm particles were comparable with standard CEC capillaries with frits. Examples of separations of steroids, a pesticide and its by-products, and cardiac glycosides under various CEC conditions are shown.     

Structural analysis of protein complexes with sodium alkyl sulfates by small-angle scattering and polyacrylamide gel electrophoresis

Small-angle X-ray (SAXS) and neutron (SANS) scattering is used to probe the structure of protein-surfactant complexes in solution and to correlate this information with their performance in gel electrophoresis. Proteins with sizes between 6.5 to 116 kDa are denatured with sodium alkyl sulfates (SC(x)S) of variable tail lengths. Several combinations of proteins and surfactants are analyzed to measure micelle radii, the distance between micelles, the extension of the complex, the radius of gyration, and the electrophoretic mobility. The structural characterization shows that most protein-surfactant complexes can be accurately described as pearl-necklace structures with spherical micelles. However, protein complexes with short surfactants (SC(8)S) bind with micelles that deviate significantly from spherical shape. Sodium decyl (SC(10)S) and dodecyl (SC(12)S, more commonly abbreviated as SDS) sulfates result in the best protein separations in standard gel electrophoresis. Particularly, SC(10)S shows higher resolutions for complexes of low molecular weight. The systematic characterization of alkyl sulfate surfactants demonstrates that changes in the chain architecture can significantly affect electrophoretic migration so that protein-surfactant structures could be optimized for high resolution protein separations.     

Molecule-specific imaging with mass spectrometry and a buckminsterfullerene probe: application to characterizing solid-phase synthesized combinatorial libraries

We employ a newly developed buckminsterfullerene (C(60)) primary ion beam with time-of-flight secondary ion mass spectrometry to create molecule-specific images of resin particles employed in the solid-phase synthesis of peptide combinatorial libraries. This new cluster ion source, when operated at an incident energy of 20 keV, is remarkably effective at desorbing small peptides directly from a polymer surface and opens new possibilities for characterizing large arrays of diverse sets of molecules. In addition, the C(60) ion beam may be focused to a spot of 1.5 microm in diameter, enabling molecule-specific images of single 100 microm resin particles to be acquired. We report three significant aspects associated with utilizing the C(60) projectile that show how this technology can be taken to a more advanced level, especially when compared to results obtained with more conventional atomic primary ions. First, the useful yield of molecular ions is generally observed to be enhanced by at least 3 orders of magnitude over those previously possible. Second, the energy dissipation process associated with the C(60) impact is most efficient at desorbing molecules on soft substrates such as polymer surfaces rather than harder substrates such as metals or semiconductors. Third, there is a greatly reduced tendency for insulating surfaces to build up excess charge, obviating the need for charge compensation. Using a small five-member peptide library as a model, we show that by utilizing the focusing properties of the C(60) beam, it is possible to assay the surface composition of 100-microm polymer beads at a rate of up to 10 particles/s. Moreover, even at the picomole level, there are enough sequence ions in the mass spectrum to determine a unique composition. The results illustrate the ability to quickly assay large libraries without the use of tags and suggest the strategy may be applicable to a range of high-throughput experiments.     

Sequential hydration of small protonated peptides

The sequential addition of water molecules to a series of small protonated peptides was studied by equilibrium experiments using electrospray ionization combined with drift cell techniques. The experimental data were compared to theoretical structures of selected hydrated species obtained by molecular mechanics simulations. The sequential water binding energies were measured to be of the order of 7-15 kcal/mol, with the largest values for the first water molecule adding to either a small nonarginine containing peptide (e.g., protonated dialanine) or to a larger peptide in a high charge state (e.g., triply protonated neurotensin). General trends are (a) that the first water molecules are more strongly bound than the following water molecules, (b) that very small peptides (2-3 residues) bind the first few water molecules more strongly than larger peptides, (c) that the first few water molecules bind more strongly to higher charge states than to lower charge states, and (d) that water binds less strongly to a protonated guanidino group (arginine containing peptides) than to a protonated amino group. Experimental differential entropies of hydration were found to be of the order of -20 cal/mol/K although values vary from system to system. At constant experimental conditions the number of water molecules adding to any peptide ion is strongly dependent on the peptide charge state (with higher charge states adding proportionally more water molecules) and only weakly dependent on the choice of peptide. For small peptides molecular mechanics calculations indicate that the first few water molecules add preferentially to the site of protonation until a complete solvation shell is formed around the charge. Subsequent water molecules add either to water molecules of the first solvation shell or add to charge remote functional groups of the peptide. In larger peptides, charge remote sites generally compete more effectively with charge proximate sites even for the first few water molecules.     

Optimum concentration of trifluoroacetic acid for reversed-phase liquid chromatography of peptides revisited

Trifluoroacetic acid (TFA) remains the dominant mobile phase additive for reversed-phase high-performance liquid chromatography (RP-HPLC) of peptides after more than two decades since its introduction to this field. Generally, TFA has been employed in a concentration range of 0.05-0.1% (6.5-13 mM) for the majority of peptide separations. In order to revisit the question as to whether such a concentration range is optimum for separations of peptide mixtures containing peptides of varying net positive charge, the present study examined the effect of varying TFA concentration on RP-HPLC at 25 and 70 degrees C of three groups of synthetic 10-residue synthetic peptides containing either one (+1) or multiple (+3, +5) positively charged groups. The results show that the traditional range of TFA concentrations employed for peptide studies is not optimum for many, perhaps the majority, of peptide applications. For efficient resolution of peptide mixtures, particularly those containing peptides with multiple positive charges, our results show that 0.2-0.25% TFA in the mobile phase will achieve optimum resolution. In addition, the use of high temperature as a complement to such TFA concentration levels is also effective in maximizing peptide resolution.     

Ion-transfer voltammetry at silicon membrane-based arrays of micro-liquid-liquid interfaces

Microporous silicon membranes, fabricated by lithographic patterning and wet and dry silicon etching processes, were used to create arrays of micro-scale interfaces between two immiscible electrolyte solutions (muITIES) for ion-transfer voltammetry. These membranes served the dual functions of interface stabilization and enhancement of the rate of mass-transport to the interface. The pore radii were 6.5 microm, 12.8 microm and 26.6 microm; the pore-pore separations were ca. 20- to 40-times the pore radii and the membrane thickness was 100 microm. Deep reactive ion etching (DRIE) was used for pore drilling through the silicon, which had been previously selectively thinned by potassium hydroxide etching. DRIE produces hydrophobic fluorocarbon-coated internal pore walls. The small pore sizes and large pore-pore separations used resulted in steady-state voltammograms for the transfer of tetramethylammonium cation (TMA(+)) from the aqueous to the organic phase, whereas the reverse voltammetric sweeps were peak-shaped. These asymmetric voltammograms are consistent with the location of the ITIES at the aqueous side of the silicon membrane such that the organic phase fills the micropores. Comparison of the experimental currents to calculated currents for an inlaid disc micro-interface revealed that the interfaces were slightly recessed, up to 10 microm (or 10% of the pore length) in one case. Facilitated ion transfer, with an organic-phase ionophore, confirmed the location of the organic phase within the pores. These microporous silicon membranes offer opportunities for various analytical operations, including enhancing the rate of mass transport to ITIES-based sensing devices and stabilization of the ITIES for hydrodynamic applications.     

Two-dimensional strong cation exchange/porous layer open tubular/mass spectrometry for ultratrace proteomic analysis using a 10 microm id poly(styrene- divinylbenzene) porous layer open tubular column with an on-line triphasic trapping column

This study expands the capabilities for ultratrace proteomic analysis of our previous work by incorporating on-line sample desalting using a triphasic (RP/strong cation exchange (SCX)/micro-SPE) trapping column connected to a 3.2 m x 10 microm id poly(styrene-divinylbenzene) (PS-DVB) porous layer open tubular (PLOT) column. To minimize extra sample handling steps, C18 RP packing was incorporated in the capillary tubing upstream of the SCX column for the on-line desalting. For the micro-SPE column, a 50 microm id PS-DVB monolithic column was positioned downstream of the SCX column. High-performance separation was achieved on the PLOT column at a mobile phase flow rate of 20 nL/min. The sensitivity and high resolution capability of the new multidimensional platform was evaluated using an in-gel tryptic digested sample of a cervical cancer (SiHa) cell line. For the injected amount of 1200 cells ( approximately 500 ng), over 2700 peptides covering greater than 850 unique proteins were identified from the triphasic SCX/PLOT/MS analysis of a single SDS gel section (>40 kDa). The 2-D LC/MS platform demonstrated good separation performance, such that more than 85% of the identified peptides were detected from only one salt fraction. In a triplicate analysis of the above >40 kDa gel section, 4497 peptides and 1209 unique proteins were identified when applying stringent filtering criteria, with a false-positive rate of 2.4%. When all three SDS-PAGE gel sections of the lysed SiHa cells were analyzed, 5047 peptides and 1857 unique proteins (false-positive rate 1.8%), including cancer-related proteins such as MAP kinases, were identified.     

Ultratrace liquid chromatography/mass spectrometry analysis of large peptides with post-translational modifications using narrow-bore poly(styrene-divinylbenzene) monolithic columns and extended range proteomic analysis

This paper describes approaches to optimize the chromatographic performance for our recently developed LC-MS platform, extended range proteomic analysis (ERPA), for comprehensive protein characterization at the ultratrace level. Large digested peptide fragments up to 10 kDa (e.g., from lysyl endopeptidase digestion) with or without modifications were well separated with high resolution using narrow bore (20 and 50 microm I.D.) poly(styrene-divinylbenzene) (PS-DVB) monolithic columns constructed by in situ solution polymerization. Importantly, the macroporous structure of the monolithic columns facilitated mass transport of large peptides with improved recovery relative to small pore size reversed-phase packings. High sequence coverage (>95%), including identification of phosphorylated and glycosylated particles was achieved for beta-casein and epidermal growth factor receptor (EGFR) at the 4 and 20 fmol levels per injection, respectively, using the 20 microm I.D. PS-DVB monolithic column. For peptides with greater ionization efficiency, the detection limit could be lowered to approximately 400 zmol. Typically, the separation system produced a peak capacity of approximately 200 for a 10 cm column. This paper demonstrates that narrow-bore monolithic columns are suitable for high sensitivity and high-resolution separation of large peptide fragments by LC-MS analysis.     

PRESUMED PHOTORECEPTOR PROTEIN AND ULTRASTRUCI'URE OF THE PHOTORECEPTOR ORGANELLE IN THE CILIATED PROTOZOAN, Blepharisma

Abstract-The red pigment granule of Belpharisma japonicum is believed to be a photoreceptor organelle mediating photodispersal. Freeze-fracture and thin section electron microscopy revealed that the pigment granules contained a honeycomb-like structure constructed of folded membranes. In the fracture face of the honeycomb-like structure, small membrane particles were observed, which might correspond to pigment—protein complexes. The pigment granules were isolated and detergent-solubilized. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that the pigment granules mainly contained a 200 kDa membrane protein. The complex of red pigment and 200 kDa protein was isolated by gel-filtration chromatography of the detergent-solubilized components, and the protein was subjected to SDS-PAGE and amino acid analysis. The 200 kDa protein could not be dissociated into subunits by 2-mercaptoethanol, indicating that the protein is composed of a single polypeptide chain. Hydrophobic amino acids contained in the 200 kDa protein were not dominant, suggesting that only partial domains may extend across the membrane of the honeycomb-like structure.     

Enantiomer separations by capillary electrochromatography using chiral stationary phases

The applicability of capillary electrochromatography (CEC) using packed capillary column to enantiomer separations was investigated. As chiral stationary phases, OD type packing materials of 5 and 3 microm particle diameters, originally designed for conventional high-performance liquid chromatography (HPLC) were employed. The chiral packing materials were packed by a pressurized method into a 100 microm I.D. fused-silica capillary. Several racemic enantiomers, such as acidic, neutral and basic drug components, were successfully resolved, typically by using acidic or basic solutions containing acetonitrile as mobile phases. The separation efficiencies for some enantiomers in the chiral CEC system using the 5 microm OD type packing were superior to those obtained in HPLC using chiral packings. The plate heights obtained for several enantiomers were 8-13 microm or the reduced plate height of 1.6-2.6, which indicates the high efficiency of this chiral CEC system.