D R Knapp

Medical University of South Carolina, Charleston, SC, United States

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Publications (93)295.58 Total impact

  • A.K. Sen, J. Darabi, D.R. Knapp
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    ABSTRACT: This work presents simulation of aerosol formation in electrospray ionization (ESI) using a carbon fiber (CF) emitter. The model predicts droplet fission and trajectories of the droplets in a steady medium, within a monodisperse EHD spray in a Lagrangian framework. The droplet fission is simulated based on the principle of minimum free energy and droplet trajectories are predicted using Lagrangian single-droplet tracking method. The numerical model is validated by comparing model predictions with experimental results. The aerosol formation process using the CF emitter is simulated and results are presented and discussed.
    IEEE Sensors Journal 01/2011; 11(10):2335-2341. · 1.48 Impact Factor
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    Ranu Nayak, Daniel R Knapp
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    ABSTRACT: A novel matrix-free LDI MS platform using a thin film of patterned nanostructured gold, capped with methyl- and carboxy-terminated self-assembled monolayers (SAMs) is presented. Calibration on the matrix-free LDI surface was performed using a peptide standard mixture available for MALDI analysis. MS analysis for limit of detection was performed using angiotensin I peptide. Peptide fragments from standard protein digests of bovine serum albumin, bovine catalase, and bovine lactoperoxidase were used to carry out peptide mass fingerprinting analysis. Sequence coverage of each protein digest and the number of detected peptide fragments were compared with conventional MALDI MS on a standard MALDI plate. Versatility of the nanostructured gold LDI substrate is illustrated by performing MS analysis on a protein digest using different enzymes and by small molecule MS analysis.
    Analytical Chemistry 09/2010; 82(18):7772-8. · 5.70 Impact Factor
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    A K Sen, J Darabi, D R Knapp
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    ABSTRACT: This paper presents design, microfabrication, and test of a microfluidic nebulizer chip for desorption electrospray ionization mass spectrometry (DESI-MS) in proteomic analysis. The microfluidic chip is fabricated using cyclic olefin copolymer (COC) substrates. The fluidic channels are thermally embossed onto a base substrate using a nickel master and then a top substrate is thermally bonded to seal the channels. Carbon ink embossed into the top COC substrate is used to established electrical connection between the external power supply and the liquid in the channel. The microfluidic chip to external capillary connection is fabricated using Nanoport() interconnection system. Preliminary leakage test was performed to demonstrate the interconnection system is leak-free and pressure test was performed to evaluate the burst pressure. Finally, the nebulizer chip was used to perform DESI-MS for analyzing peptides (BSA and bradykinin) and reserpine on the nanoporous alumina surface. DESI-MS performance of the microfluidic nebulizer chip is compared with that obtained using a conventional DESI nebulizer.
    Sensors and Actuators B Chemical 04/2009; 137(2):789-796. · 3.54 Impact Factor
  • Ranu Nayak, Jian Liu, Ashis K Sen, Daniel R Knapp
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    ABSTRACT: A gold coated nanoporous alumina surface was used for dual ionization mode mass spectrometric analysis using desorption electrospray ionization (DESI) and laser desorption ionization (LDI). DESI and LDI mass spectrometry (MS) from the nanoporous alumina surface were compared with conventional electrospray ionization (ESI) mass spectrometry and matrix assisted laser desorption ionization (MALDI) for analysis of tryptic digests of proteins. Combined use of DESI and LDI offer greater peptide coverage than either method alone and comparable peptide coverage as with dual MALDI and ESI. This dual ionization technique using a common platform with same sample spot demonstrates a potential time and cost-effective tool for improved shotgun proteomic analysis.
    Analytical Chemistry 11/2008; 80(22):8840-4. · 5.70 Impact Factor
  • Lashanda N Waller, Kevin Shores, Daniel R Knapp
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    ABSTRACT: Shotgun proteomic analysis usually employs multidimensional separations with the first dimension most commonly being strong cation exchange (SCX) liquid chromatography (LC). SCX-LC is necessarily a serial process for preparation of multiple samples. Here, we apply a newly available tool, off-gel electrophoresis (OGE), for first-dimension separation of peptide mixtures from digests of cerebrospinal fluid (CSF), a complex and low total protein-containing sample. OGE first-dimension fractionation enabled identification of a total of 156 unique proteins compared to 115 identified in previous work using first-dimension SCX fractionation. OGE can be used to process multiple samples unattended with easy retrieval of the separated fractions. Thus, shotgun analysis using OGE as the first-dimension separation offers a significant advantage both in terms of sample throughput as well as increased numbers of identified proteins.
    Journal of Proteome Research 10/2008; 7(10):4577-84. · 5.06 Impact Factor
  • Michael Schilling, Daniel R Knapp
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    ABSTRACT: Immobilized metal affinity chromatography (IMAC) based on Fe (3+) or Ga (3+) chelation is the most widely employed technique for the enrichment of phosphopeptides from biological samples prior to mass spectrometric analysis. An IMAC resin geared mainly toward phosphoprotein enrichment, Pro-Q Diamond, has been assessed for its utility in phosphopeptide isolation. Using both single phosphoprotein tryptic digests of beta-casein and ovalbumin and synthetic mixtures composed of tryptic digests of phosphorylated and nonphosphorylated protein standards, the selectivity and sensitivity of Pro-Q Diamond resin in an immobilized metal affinity-reversed phase microcolumn format were compared to an alternate titanium dioxide approach. The biphasic microcolumn method was found to be superior to metal oxide-based phosphopeptide capture in biological samples of increasing complexity. The lower limit of mass spectrometric detection for the immobilized metal affinity-reversed phase microcolumn approach was determined to be 10 pmol of beta-casein monophosphorylated peptide in 20 microL of a solution of human serum protein digest (from 200 microg total serum protein after digestion and desalting).
    Journal of Proteome Research 09/2008; 7(9):4164-72. · 5.06 Impact Factor
  • A K Sen, R Nayak, J Darabi, D R Knapp
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    ABSTRACT: This paper presents use of a nanoporous alumina surface for desorption electrospray ionization mass spectrometry (DESI MS). The DESI MS performance of the nanoporous alumina surface is compared with that of polymethylmethacrylate (PMMA), polytetrafluroethylene (PTFE) and glass, which are popular surfaces in DESI MS experiments. Optimized operating conditions were determined for each of these surfaces by studying the effects of flow rate, tip to surface and surface to MS capillary distance, and spray angle on the DESI MS performance. The analytes (reserpine and BSA tryptic digest) were analyzed on all the surfaces. The results show that the nanoporous alumina surface offers higher ion intensity and increased peptide detection as compared to the other surfaces. Additionally, comparison of ion intensities obtained from the nanoporus alumina and an alumina film confirms that improved performance is due to the inherent nature of the nanostructured surface. Limits of detection (LODs) were determined for the analytes on all the surfaces. It was observed that the nanoporous alumina surface offers improved limits of detection as compared to other surfaces. Another advantage of the nanoporous alumina surface is that it provides to faster analysis associated with rapid drying of liquid samples on the surface. Additionally, porous alumina surface can be used as a dual ionization platform for combined DESI/LDI analysis for further improved peptide detection in proteomic analysis.
    Biomedical Microdevices 09/2008; 10(4):531-8. · 2.72 Impact Factor
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    Guofang Chen, Frantisek Svec, Daniel R Knapp
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    ABSTRACT: A simple light-actuated microvalve using a quartz halogen illuminator with tungsten filament was introduced to manipulate flow path effectively in micro-total analysis systems, which reduces system complexity and the need for on-chip integration. The microvalve device in cyclic olefin copolymer (COC) microchip functions very well based on the thermo-responsive polymer, poly(N-isopropylacrylamide) (PNIPAAm), whose pressure-tolerance can be tuned by changing the mechanical strength of polymer monolith inside the microchannel with the choice of suitable amount of monomer and crosslinker. The response time and pressure resistance of the valve can be optimized by the tetrahydrofuran composition in the polymerization mixture as well. Very importantly, the microvalve can withstand the leakage pressure up to around 1350 psi, and its opening and closing response time is only 4.0 and 6.2 s respectively. Microchips with such valves will be very useful in drug delivery, chemical analysis and proteomic analysis.
    Lab on a Chip 08/2008; 8(7):1198-204. · 5.70 Impact Factor
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    ABSTRACT: Biological samples can contain proteins with concentrations that span more than 10 orders of magnitude. Given the limited dynamic range of analysis methods, observation of proteins present at the lower concentrations requires depletion of high-abundance proteins, or other means of reducing the dynamic range of concentrations. Hexapeptide diversity library beads have been used to bind proteins in a complex sample up to a given saturation limit, effectively truncating the maximum concentration of proteins at a desired level. To avoid the potential problem of susceptibility of the hexapeptides to cleavage by proteases in the sample and/or bacterial degradation, peptide analogues that exhibit similar binding characteristics to peptides can be used in place of peptides. We report here the use of hexameric peptoid diversity library beads to reduce the dynamic range of protein concentrations in human cerebrospinal fluid (CSF). Using this method in conjunction with 2D LC/MS/MS analyses, we identified 200 unique proteins, about twice the number identified in untreated CSF.
    Journal of Proteome Research 06/2008; 7(5):1922-31. · 5.06 Impact Factor
  • Kevin S Shores, Daniel R Knapp
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    ABSTRACT: Optimal proteomic analysis of human cerebrospinal fluid (CSF) requires depletion of high-abundance proteins to facilitate observation of low-abundance proteins. The performance of two immunodepletion (MARS, Agilent Technologies and ProteoSeek, Pierce Biotechnology) and one ultrafiltration (50 kDa molecular weight cutoff filter, Millipore Corporation) methods for depletion of abundant CSF proteins were compared using a graphical method to access the depth of analysis using "marker proteins" with known normal concentration ranges. Two-dimensional LC/MS/MS analysis of each depleted sample yielded 171 and 163 unique protein identifications using the MARS and ProteoSeek immunodepletion methods, respectively, while only 46 unique proteins were identified using a 50 kDa molecular weight cutoff filter. The relative abundance of the identified proteins was estimated using total spectrum counting and compared to the concentrations of 45 known proteins in CSF as markers of the analysis depth. Results of this work suggest a clear need for methodology designed specifically for depletion of high-abundance proteins in CSF, as depletion methods designed to deplete high-abundance serum proteins showed little improvement in analysis depth compared to analysis without depletion. The marker protein method should be generally useful for assessing depth of analysis in the comparison of proteomic analysis methods.
    Journal of Proteome Research 10/2007; 6(9):3739-51. · 5.06 Impact Factor
  • Ranu Nayak, Daniel R Knapp
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    ABSTRACT: Nanoporous aluminum oxide layers, grown by anodization of aluminum thin films on glass and then sputter-coated with gold, were used to study the effects of the thin-film structural parameters on laser desorption/ionization (LDI) mass spectrometry (MS) of peptides. Variation of MS signal intensity was examined as a function of alumina pore depth, pore width, and gold layer thickness. Peptide molecular ion intensity was optimal with porous alumina formed from aluminum films of approximately 600-nm thickness; thinner or thicker films gave significantly lower signals. Signals decreased when pore sizes were increased beyond the as-formed width of approximately 100 nm. The MS signal also varied with the thickness of the sputtered gold layer with an optimum thickness being approximately 90 nm. The results of these studies provide values for empirical optimization of LDI MS performance as well as potential clues to the LDI mechanism.
    Analytical Chemistry 08/2007; 79(13):4950-6. · 5.70 Impact Factor
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    A. K. Sen, J. Darabi, D. R. Knapp
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    ABSTRACT: In this work, we propose a novel carbon nanofiber (CNF) emitter for electrospray ionization (ESI)–mass spectrometry (MS) applications. The proposed emitter comprises an array of CNFs around the orifice of a microscale capillary. The electrospray ionization process is simulated using a CFD code based on Taylor–Melcher leaky-dielectric formulations for solving the electrohydrodynamics and volume-of-fluid (VOF) method for tracking the interface. The code is validated for a conventional multiple electrospray emitter and then applied to simulate the CNF emitter model. The modeling results show that under steady state condition, individual cone-jets are established around each of the CNFs resulting in an array of electrosprays. The approach being taken to fabricate the CNF emitter is briefly discussed. Effects of geometrical parameters including aspect ratio of CNFs, total number of CNFs and distribution pattern of the CNFs on the electrospray performance are studied. The influence of operating parameters such as flow rate, potential difference and physical properties of the solvent on the electrospray behavior is thoroughly investigated. The spray current, ‘onset’ potential and jet diameter are correlated with total number and distribution of CNFs and physical properties of the liquid. The correlation results are compared with the available results in the literature. Higher spray current and lower jet diameter indicate that the device can perform equivalent to nanospray emitters while using a micro-scale orifice. This allows higher sample throughput and eliminates potential clogging problem inherent in nano-capillaries.
    Microfluidics and Nanofluidics 05/2007; 3(3):283-298. · 3.22 Impact Factor
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    ABSTRACT: Palmitylation is a widespread modification in G-protein-coupled receptors and often a dynamic process. In rhodopsins, palmitylation is static on C322/C323. Red/green (M/LWS) cone opsins have no cysteines at corresponding positions and no palmitylation. Blue (SWS2) cone opsins have a single corresponding cysteine and mass spectrometric analysis showed partial palmitylation of salamander SWS2 cone opsin. Ultraviolet (SWS1) cone opsins have one corresponding cysteine, but only unpalmitylated opsin was observed for mouse and salamander. The results show that the static palmitylation found on rhodopsin is not found on cone opsins and suggest the possibility of an unidentified role for opsin palmitylation in cones.
    Vision Research 01/2007; 46(27):4493-501. · 2.14 Impact Factor
  • Jian Liu, Kyung-Won Ro, Ranu Nayak, Daniel R. Knapp
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    ABSTRACT: Electrospray from a channel exit at the edge of a fluorocarbon coated cycloolefin copolymer microfluidic device has been investigated. The fluorocarbon coating facilitated generation of a stable electrospray, thereby enhancing the detectability of electrospray ionization (ESI) mass spectrometry (MS). A microfluidic device of integrated ESI emitters and monolithic liquid chromatography columns has been fabricated on a cycloolefin copolymer chip. The monolithic columns were polymerized in situ using UV irradiation with a photomask to confine the porous polymer monolith to the desired regions of the channels. The monolithic stationary phase was homogenous and well bonded to the channel surfaces, which had been functionalized by graft polymerization. The ESI potential was applied within the channel via a carbon ink line. The performance of this microfluidic device was demonstrated by analysis of a tryptic digest of bovine serum albumin on an ion trap MS instrument.
    International Journal of Mass Spectrometry. 01/2007;
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    ABSTRACT: We have designed a laser cell deposition system that employs the phenomenon of laser guidance to place single cells at specific points in a variety of in vitro environments. Here, we describe the components of the system: the laser optics, the deposition chamber, the microinjection cell feeding system and our custom system control software application. We discuss the requirements and challenges involved in laser guidance of cells and how our present system overcomes these challenges. We demonstrate that the patterning system is accurate within one micrometer by repeatedly depositing polymer microspheres and measuring their position. We demonstrate its ability to create highly defined living patterns of cells by creating a defined pattern of neurons with neurite extensions displaying normal function. We found that the positional accuracy of our system is smaller than the variations in cell size and pattern disruptions that occur from normal cell movement during substrate adhesion. The laser cell deposition system is a potentially useful tool that can be used to achieve site- and time-specific placement of an individual cell in a cell culture for the systematic investigation of cell-cell and cell-extracellular matrix interactions.
    Biotechnology Journal 10/2006; 1(9):1007-13. · 3.45 Impact Factor
  • Kyung Won Ro, Ranu Nayak, Daniel R Knapp
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    ABSTRACT: Considerable effort has been invested in the development of integrated microfluidic devices for fast and highly efficient proteomic studies. Among various fabrication techniques for the preparation of analytical components (separation columns, reactors, extractors, valves, etc.) in integrated microchips, in situ fabrication of monolithic media is receiving increasing attention. This is mainly due to the ease and simplicity of preparation of monolithic media and the availability of various precursors and chemistries. In addition, UV-initiated photopolymerization technique enables the incorporation of multiple analytical components into specified parts of a single microchip using photomasks. This review summarizes preparation methods for monolithic media and their application as microfluidic analytical components in microchips.
    Electrophoresis 10/2006; 27(18):3547-58. · 3.26 Impact Factor
  • Kyung Won Ro, Jian Liu, Daniel R Knapp
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    ABSTRACT: A prototype array of monolithic liquid chromatography (LC) columns was prepared in a plastic microfluidic device for the off-line interface with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The microfluidic channels were fabricated on a cyclic olefin copolymer (COC) plate by hot embossing. An array of methacrylate monolithic columns was prepared in the microfluidic channels by UV-initiated polymerization. The deposition system employed a pulsed electric field to transfer the effluents from multiple columns directly onto MALDI targets with a non-contact deposition method reported by Ericson et al. [C. Ericson, Q.T. Phung, D.M. Horn, E.C. Peters, J.R. Fitchett, S.B. Ficarro, A.R. Salmon, L.M. Brill, A. Brock, Anal. Chem. 75 (2003) 2309]. To characterize the off-line interface of the multiple-channel microchip LC and the MALDI-MS for the analysis of peptide mixtures, the separation efficiency and reproducibility tests in each column were carried out by separating a peptide mixture from tryptic digested proteins and depositing the multiple effluents simultaneously on the MALDI target plate. Using a MALDI-TOF mass spectrometer with a mass accuracy of +/-1 Da for peptide assignments of digested bovine serum albumin (BSA), amino acid sequence coverage of around 59% was obtained for the microchip LC-MALDI-MS compared to 23% obtained by the MALDI-MS method without LC separation. In sensitivity tests for the detection of low abundance proteins in the presence of high concentration protein mixtures, as low as 10 fmol/mul (S/N = 10) of a spiked peptide in 1 microg of digested BSA could be detected. In the analysis of a mixture of three digested proteins (BSA, myoglobin, and cytochrome c), more than twice the amino acid sequence coverage was obtained for the microchip LC-MALDI-MS compared to MALDI-MS alone.
    Journal of Chromatography 05/2006; 1111(1):40-7. · 4.61 Impact Factor
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    ABSTRACT: We characterized the variable processing of the G protein gamma subunit isoforms associated with bovine brain G proteins, a primary mediator of cellular communication. Ggamma subunits were isolated from purified brain G proteins and characterized by Edman sequencing, by MALDI MS, by chemical and/or enzymatic fragmentation assayed by MALDI MS, and by MS/MS fragmentation and sequencing. Multiple forms of six different Ggamma isoforms were detected. Significant variation in processing was found at both the amino termini and particularly the carboxyl termini of the proteins. All Ggamma isoforms contain a carboxyl-terminal CAAX motif for prenylation, carboxyl-terminal proteolysis, and carboxymethylation. Characterization of these proteins indicates significant variability in the normal processing of all of these steps in the prenylation reaction, including a new variation of prenyl processing resulting from cysteinylation of the carboxyl terminus. These results have multiple implications for intracellular signaling mechanisms by G proteins, for the role of prenyl processing variation in cell signaling, and for the site of action and consequences of drugs that target the prenylation modification.
    Molecular &amp Cellular Proteomics 05/2006; 5(4):671-85. · 7.25 Impact Factor
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    A K Sen, J Darabi, D R Knapp, J Liu
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    ABSTRACT: A novel microscale emitter employing a pointed carbon fiber (CF) can be used for electrospraying in mass spectrometric (MS) analysis. The carbon fiber is located coaxial with a fused silica capillary tube of 360 µm OD and 75 µm ID with its sharp tip extending 30 µm beyond the tube terminus. The electrospray ionization (ESI) process is simulated using a computational fluid dynamics (CFD) code based on the Taylor–Melcher leaky-dielectric fluid model for solving the electrohydrodynamics and the volume of fluid (VOF) approach for tracking the liquid–gas interface. The CFD code is first validated for a conventional geometry and then used to simulate the CF emitter based ESI model. The simulated current–flow and current–voltage results are in good agreement with experimental results for the CF emitter. The effects of emitter geometry, potential difference, flow rate and the physical properties of the liquid on the electrospray behavior of the CF emitter are thoroughly investigated. The spray current and jet diameter are correlated with the flow rate, potential difference and physical properties of the liquid and the correlation results are quantitatively compared with the results reported in the literature.
    Journal of Micromechanics and Microengineering 01/2006; 16:620-630. · 1.79 Impact Factor
  • Zsolt Ablonczy, Rosalie K Crouch, Daniel R Knapp
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    ABSTRACT: Integral membrane proteins are among the most interesting molecules for biomedical research, as some of the most important cellular functions are inherently tied to biological membranes. One such example is the vast expanse of receptors on cell surfaces. However, due to difficulties in the biochemical purification and structure/function analysis of membrane proteins, caused by their hydrophobic or amphophilic nature, membrane proteins are still much less studied than soluble proteins. Our laboratory has successfully developed and applied a methodology for the mass spectrometric analysis of integral membrane proteins. Here, we present an improvement in the sensitivity of detection made possible by the advancement of mass spectrometric instrumentation and refinement of the chromatographic analysis. Subpicomolar samples of bovine rhodopsin purified from native membranes were successfully analyzed, obtaining complete sequence coverage and the detection and localization of posttranslational modifications. Therefore, it is demonstrated that the detection limits and sequence coverage for soluble and membrane proteins can be comparable. The methodology presented here allows mass spectrometric analysis of subpicomolar levels of photopigments or other integral membrane proteins either from their native membranes or as products of expression systems.
    Journal of Chromatography B 11/2005; 825(2):169-75. · 2.49 Impact Factor

Publication Stats

995 Citations
295.58 Total Impact Points


  • 1983–2010
    • Medical University of South Carolina
      • • Department of Cell and Molecular Pharmacology and Experimental Therapeutics (College of Medicine)
      • • Department of Ophthalmology
      Charleston, SC, United States
  • 1987–2009
    • University of South Carolina
      • Department of Mechanical Engineering
      Columbia, SC, United States
    • Vanderbilt University
      Nashville, Michigan, United States
  • 1972
    • University of Cincinnati
      Cincinnati, Ohio, United States