Julie Horner | Indiana University (original) (raw)

Papers by Julie Horner

Applied Spectroscopy, 1999

A 22 mm torch has been developed and characterized for use in inductively coupled plasma atomic e... more A 22 mm torch has been developed and characterized for use in inductively coupled plasma atomic em ission spectrom etry. A stability curve (radio-frequency power vs. outer-gas¯ow rate) was constructed for the modi® ed torch which indicates that the larger torch can be operated at¯ow rates and powers sim ilar to those for an 18 m m torch. Four operating parameters were optimized by m eans of a sim plex algorithm. Several criteria for optimization were used, including net signal intensity for Ca II); signal-to-background noise (S/N B ) for Ca(II), Mg(II), and Fe(II); and the Mg(II)/Mg(I) lineintensity ratio. The resu lts from these sim plex optimizations are com pared. Mg(II)/Mg(I) was used as the ® nal criterion for optimization for both the 22 mm and the conventional 18 mm torches. Two-dim ensional spatial images of the larger plasma were compared with those of a conventional plasma (18 m m) for a variety of plasma em ission features. Detection limits were determ ined in two ways for a suite of analytes under conditions optimized for the Mg(II)/Mg(I) ratio. The 18 mm torch affords the better limits of detection by an averaged factor of 1.5 because its sm aller volume gives a lower background level. Finally, nitrogen molecular-ion emission m aps were collected from both the 22 m m and a conventional 18 m m plasma as an indicator of the degree of air entrainm ent in the plasma. Several spatial regions of the plasm a have been evaluated on the basis of the local intensity of N 2 1 emission for their applicability for use in atomic em ission and atomic m ass spectrometry. The 22 m m torch shows a larger region in and around the central channel of low or zero N 2 1 emission and so m ay be better suited for sampling into a mass spectro meter. Index Headings: ICP-AES; Torch design; 22 m m torch.

The quantitative assessment of metabolites in samples from development in vivo studies has become... more The quantitative assessment of metabolites in samples from development in vivo studies has become an area of increasing study with the release of guidances from regulatory bodies (MIST and M3 R2) and their subsequent interpretation and implementation. The hurdles faced in metabolite identification are joined by obtaining quantitative levels on relevant metabolites for which absolute structure may not be known and for which reference standards are not available. The challenges of matrix suppression, analyte stability, and MS detector response factor make quantitation of metabolites based on a parent drug standard almost impossible. We have applied a UV correlation to assign concentrations to metabolites identified from in vitro generated samples and used the results to quantify plasma samples on the same instrument. Initially, metabolites of dextromethorphan were generated in vitro through incubations with human liver S9 fraction (2 mg/mL). Dextromethorphan was incubated for 2 hours ...

Molecular Cell, 2015

Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interact... more Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interactions remains limited. We systematically used affinity purification/mass spectrometry to define the host interactions of all ten HCV proteins in hepatoma cells. We combined these studies with RNAi knockdown of corresponding genes using a two-step scoring approach to generate a map of 139 high-confidence HCV-host protein-protein interactions. We found mitochondrial proteins highly involved in HCV infection and characterized an interaction between the viral core protein and host protein within bgcn homolog (WIBG). Expression of core prevents WIBG from binding its regular interaction partners Y14 and Magoh, two known mediators of the nonsense-mediated mRNA decay pathway. We discovered that this surveillance pathway is disrupted in HCV-infected cells, causing potentially harmful transcripts to accumulate. Our study provides a comprehensive view of HCV-host interactions and uncovers mechanisms for how HCV perturbs host functions during infection.

Molecular Cell, 2015

Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipula... more Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipulate host machinery and how numerous cellular processes are regulated. DNA viruses such as herpesviruses have relatively large coding capacity and thus can target an extensive network of cellular proteins. To identify the host proteins hijacked by this pathogen, we systematically affinity tagged and purified all 89 proteins of Kaposi's sarcoma-associated herpesvirus (KSHV) from human cells. Mass spectrometry of this material identified over 500 virus-host interactions. KSHV causes AIDS-associated cancers, and its interaction network is enriched for proteins linked to cancer and overlaps with proteins that are also targeted by HIV-1. We found that the conserved KSHV protein ORF24 binds to RNA polymerase II and brings it to viral late promoters by mimicking and replacing cellular TATA-box-binding protein (TBP). This is required for herpesviral late gene expression, a complex and poorly understood phase of the viral lifecycle.

Spectrochimica Acta Part B: Atomic Spectroscopy, 2008

ABSTRACT Recent experiments involving aerosol introduction into the inductively coupled plasma ha... more ABSTRACT Recent experiments involving aerosol introduction into the inductively coupled plasma have shown that intact droplets and solute particles cause enormous fluctuations in analyte emission and mass-spectral signals. Here, particle-vaporization kinetics are simulated as a detailed function of the operating conditions, fundamental properties and spatial location in the inductively coupled plasma, and as a function of several of the properties of the particles themselves: diameter, chemical composition and size distribution. These simulations portray the particle vaporization as proceeding nominally linearly with respect to the particle radius when the particles are small, but roughly quadratically with radius when the particles are very large. Further, the heat- and mass-transfer-limited rates of vaporization are roughly equal for the typical gas-temperature range in the plasma tail flame, so that at any height either process might limit the rate of vaporization. This similarity gives rise to a dynamic, competitive picture of plasma vaporization kinetics.

Spectrochimica Acta Part B: Atomic Spectroscopy, 2000

False-color spatial maps of experimentally determined and simulated values of electron number den... more False-color spatial maps of experimentally determined and simulated values of electron number density n , e Ž .

Spectrochimica Acta Part B: Atomic Spectroscopy, 2002

A mathematical model for the desolvation of solvent droplets has been used in conjunction with an... more A mathematical model for the desolvation of solvent droplets has been used in conjunction with an existing code for simulation of ICP fundamental parameters. The combination has been used for the calculation of droplet histories and desolvation behavior along the central channel of an ICP. Calculations have been performed for droplets of various sizes and under a variety of ICP operating conditions. As central-channel gas flow rate increases, the point of complete desolvation of the droplet shifts upward in the plasma, away from the load coil. This relationship is fairly linear. As forward power increases, the point of complete desolvation moves down in the discharge, closer to the load coil. This is approximately an inverse relationship. Finally, simulation of behavior for a log-normal size distribution of a large number of droplets (10 ) shows that the number of surviving droplets falls sigmoidally with 8 height above the load coil. For most nebulizeryspray chamber systems, the desolvation process is complete at a welldefined height in the plasma. ᮊ

Spectrochimica Acta Part B: Atomic Spectroscopy, 1995

ABSTRACT A useful plasma diagnostic is the measurement of electron number density. One way to acc... more ABSTRACT A useful plasma diagnostic is the measurement of electron number density. One way to accomplish such measurements is to determine the contribution to the broadening of a spectral line due to the Stark effect. To simplify and extend such electron density measurements across computer platforms, a program that calculates electron number density from the Stark-broadened hydrogen-beta line has been written for the LabVIEW® environment. This program calculates electron number densities from the field strength that would be exerted on a hydrogen atom immersed in a plasma. Using the new program, the electron number density in a glow discharge is calculated for two different operating conditions. Not surprisingly, the results indicate that to increase the current density in the discharge, the source electrodes must be reduced in surface area. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by one disk with an executable program (written for Apple Macintosh), data and text files including a manual.

Journal of Chromatography A, 2004

In this paper we describe results based on the combination of atmospheric pressure photoionizatio... more In this paper we describe results based on the combination of atmospheric pressure photoionization (APPI) with atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI). The main purpose of combining more than one ionizer is to extend the range of compounds that can be simultaneously analyzed. Three modes of operation are presented; use of either ionizer, simultaneous use of two

Journal of Analytical Atomic Spectrometry, 1988

... The authors thank Peter Wentzell, Mike Hatton and Barbara Faggetter for their assistance with... more ... The authors thank Peter Wentzell, Mike Hatton and Barbara Faggetter for their assistance with this work. A. PW thanks the UBC Chemistry Department for partially funding this work. MWB acknowledges financial support from ...

Applied Spectroscopy, 2000

ABSTRACT An unambiguous comparison has been made of the spatial features of a 27.12 and a 40.68 M... more ABSTRACT An unambiguous comparison has been made of the spatial features of a 27.12 and a 40.68 MHz inductively coupled plasma. Experiments were carried out with a switchable-frequency, solid-state radio-frequency generator from the Leco 2000 system. Several features of analytical significance have been evaluated in a spatially resolved fashion. Results from optimization of the magnesium ion-to-atom (Mg II/Mg I) line-intensity ratio have been compared. The volume of the two discharges was estimated from molecular nitrogen-ion emission, and a spatially resolved map of the Fe(I) excitation temperature was determined by means of a Boltzmann analysis at each spatial location. Calcium and magnesium ion-to-atom line-intensity ratios have been calculated throughout both plasmas. Finally, limits of detection are presented. The results indicate that the plasma operated at 40.68 MHz provides slightly better figures of merit, although fundamental parameters suggest a lower degree of analyte excitation. This difference is explained by examining the results of a simulation of plasmas operated at 27.12 and 40.68 MHz.

Spectrochimica Acta Part B: Atomic Spectroscopy, 1995

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electroni... more This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by a diskette with data files and text files with the hardcopy paper in Word for Windows 2.0 and ASCII format, and a disclaimer. The text details the purpose of the work, and the appendix provides essential information for accessing the diskette and using programs and data. An automated simplex optimization program was written in an attempt to relieve the monotonous human effort required to optimize an inductively coupled plasma atomic emission spectroscopic (ICP-AES) instrument. The program controls the operating conditions of a solid-state ICP while a monochromatic imaging spectrometer collects two-dimensional response images. In the work described in this article, four of the most important ICP operating parameters are optimized automatically: radio frequency (rf) power, intermediate Ar flow rate, nebulizer flow rate and sample uptake rate. Optimization of these parameters is based first on the response of the Ca II net signal and, independently, on the response of the Ca II net signal-to-background noise ratio (SNB). Since the best height and off-axis positions of the designated response are known from the optimal two-dimensional response image, two spatial parameters are indirectly optimized through use of a CCD camera. Optimal operating conditions are reported for the CA II net signal and Ca II SNB as well as the Mg IIMg I ratio.

Spectrochimica Acta Part B: Atomic Spectroscopy, 1997

A description is given of an imaging-based instrument capable of mapping several fundamental prop... more A description is given of an imaging-based instrument capable of mapping several fundamental properties of analytical plasmas, especially the inductively coupled plasma. The plasma fundamental parameters include electron temperature and number density, heavy-particle gas-kinetic temperature, analyte and argon atom and ion concentrations, and analyte emission intensities. These parameters can be measured on the same plasma running under identical operation conditions. The techniques to probe the basic plasma properties include Thomson scattering (for electron concentration and temperature), Rayleigh scattering (for heavy-particle temperature), computer-aided optical tomography (for three-dimensional emission maps), and laser-induced saturated fluorescence (for analyte and argon atom and ion number densities). A brief description of these techniques is presented. Also, a new approach to determining absolute number densities from fluorescence measurements is introduced. This novel method is based on normalizing a measured fluorescence intensity by the room-temperature Rayleighscattering signal.

Analytical Chemistry, 1999

Unlike the genome, the proteome is exquisitely sensitive to cellular conditions and will consist ... more Unlike the genome, the proteome is exquisitely sensitive to cellular conditions and will consist of proteins having abundances dependent upon stage in the cell cycle, cell differentiation, response to environmental conditions (nutrients, temperature, stress etc.), or disease state(s). Therefore, the study of proteomes under well-defined conditions can provide a better understanding of complex biological processes and inference of protein function. Thus, much faster, more sensitive, and precise capabilities for the characterization of cellular constituents are desired. We describe progress in the development and initial application of the powerful combination of capillary isoelectric focusing (CIEF) and Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for measurements of the proteome of the model system Escherichia coli. Isotope depletion of the growth media has been used to improve mass measurement accuracy, and the comparison of CIEF-FTICR results for the analysis of cell lysates harvested from E. coli cultured in normal and isotopically depleted media are presented. The initial studies have revealed 400-1000 putative proteins in the mass range 2-100 kDa from total injections of approximately 300 ng of E. coli proteins in a single CIEF-FTICR analysis.

Analytical Chemistry, 2009

The understanding and control of the in-source collision-induced dissociation (CID) of analytes i... more The understanding and control of the in-source collision-induced dissociation (CID) of analytes is important for the accurate LC-MS/MS quantitation of drugs and metabolites in biological samples. Accordingly, it was of interest to us to establish whether such in-...

Analytical Chemistry, 2012

We report the implementation of front-end higher energy collision induced dissociation (fHCD) on ... more We report the implementation of front-end higher energy collision induced dissociation (fHCD) on a bench-top dual pressure linear ion trap. Software and hardware modifications were employed, described in detail vide-infra, to allow isolated ions to undergo collisions with ambient gas molecules in an intermediate multipole (q00) of the instrument. Results comparing the performance of fHCD and resonance excitation collision induced dissociation (RE-CID) in terms of injection time, total number of scans, efficiency, mass measurement accuracy (MMA), unique peptide identifications, and spectral quality of labile modified peptides are presented. fHCD is approximately 23% as efficient as RE-CID and, depending on the search algorithm, it identifies 6.6% more or 15% less peptides (q<0.01) from a soluble whole-cell lysate (Caenorhabditis elegans) than RE-CID using Mascot or Sequest search algorithms, respectively. fHCD offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater (p<0.05) than for spectra collected using RE-CID.

Applied Spectroscopy, 1999

A 22 mm torch has been developed and characterized for use in inductively coupled plasma atomic e... more A 22 mm torch has been developed and characterized for use in inductively coupled plasma atomic em ission spectrom etry. A stability curve (radio-frequency power vs. outer-gas¯ow rate) was constructed for the modi® ed torch which indicates that the larger torch can be operated at¯ow rates and powers sim ilar to those for an 18 m m torch. Four operating parameters were optimized by m eans of a sim plex algorithm. Several criteria for optimization were used, including net signal intensity for Ca II); signal-to-background noise (S/N B ) for Ca(II), Mg(II), and Fe(II); and the Mg(II)/Mg(I) lineintensity ratio. The resu lts from these sim plex optimizations are com pared. Mg(II)/Mg(I) was used as the ® nal criterion for optimization for both the 22 mm and the conventional 18 mm torches. Two-dim ensional spatial images of the larger plasma were compared with those of a conventional plasma (18 m m) for a variety of plasma em ission features. Detection limits were determ ined in two ways for a suite of analytes under conditions optimized for the Mg(II)/Mg(I) ratio. The 18 mm torch affords the better limits of detection by an averaged factor of 1.5 because its sm aller volume gives a lower background level. Finally, nitrogen molecular-ion emission m aps were collected from both the 22 m m and a conventional 18 m m plasma as an indicator of the degree of air entrainm ent in the plasma. Several spatial regions of the plasm a have been evaluated on the basis of the local intensity of N 2 1 emission for their applicability for use in atomic em ission and atomic m ass spectrometry. The 22 m m torch shows a larger region in and around the central channel of low or zero N 2 1 emission and so m ay be better suited for sampling into a mass spectro meter. Index Headings: ICP-AES; Torch design; 22 m m torch.

The quantitative assessment of metabolites in samples from development in vivo studies has become... more The quantitative assessment of metabolites in samples from development in vivo studies has become an area of increasing study with the release of guidances from regulatory bodies (MIST and M3 R2) and their subsequent interpretation and implementation. The hurdles faced in metabolite identification are joined by obtaining quantitative levels on relevant metabolites for which absolute structure may not be known and for which reference standards are not available. The challenges of matrix suppression, analyte stability, and MS detector response factor make quantitation of metabolites based on a parent drug standard almost impossible. We have applied a UV correlation to assign concentrations to metabolites identified from in vitro generated samples and used the results to quantify plasma samples on the same instrument. Initially, metabolites of dextromethorphan were generated in vitro through incubations with human liver S9 fraction (2 mg/mL). Dextromethorphan was incubated for 2 hours ...

Molecular Cell, 2015

Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interact... more Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interactions remains limited. We systematically used affinity purification/mass spectrometry to define the host interactions of all ten HCV proteins in hepatoma cells. We combined these studies with RNAi knockdown of corresponding genes using a two-step scoring approach to generate a map of 139 high-confidence HCV-host protein-protein interactions. We found mitochondrial proteins highly involved in HCV infection and characterized an interaction between the viral core protein and host protein within bgcn homolog (WIBG). Expression of core prevents WIBG from binding its regular interaction partners Y14 and Magoh, two known mediators of the nonsense-mediated mRNA decay pathway. We discovered that this surveillance pathway is disrupted in HCV-infected cells, causing potentially harmful transcripts to accumulate. Our study provides a comprehensive view of HCV-host interactions and uncovers mechanisms for how HCV perturbs host functions during infection.

Molecular Cell, 2015

Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipula... more Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipulate host machinery and how numerous cellular processes are regulated. DNA viruses such as herpesviruses have relatively large coding capacity and thus can target an extensive network of cellular proteins. To identify the host proteins hijacked by this pathogen, we systematically affinity tagged and purified all 89 proteins of Kaposi&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s sarcoma-associated herpesvirus (KSHV) from human cells. Mass spectrometry of this material identified over 500 virus-host interactions. KSHV causes AIDS-associated cancers, and its interaction network is enriched for proteins linked to cancer and overlaps with proteins that are also targeted by HIV-1. We found that the conserved KSHV protein ORF24 binds to RNA polymerase II and brings it to viral late promoters by mimicking and replacing cellular TATA-box-binding protein (TBP). This is required for herpesviral late gene expression, a complex and poorly understood phase of the viral lifecycle.

Spectrochimica Acta Part B: Atomic Spectroscopy, 2008

ABSTRACT Recent experiments involving aerosol introduction into the inductively coupled plasma ha... more ABSTRACT Recent experiments involving aerosol introduction into the inductively coupled plasma have shown that intact droplets and solute particles cause enormous fluctuations in analyte emission and mass-spectral signals. Here, particle-vaporization kinetics are simulated as a detailed function of the operating conditions, fundamental properties and spatial location in the inductively coupled plasma, and as a function of several of the properties of the particles themselves: diameter, chemical composition and size distribution. These simulations portray the particle vaporization as proceeding nominally linearly with respect to the particle radius when the particles are small, but roughly quadratically with radius when the particles are very large. Further, the heat- and mass-transfer-limited rates of vaporization are roughly equal for the typical gas-temperature range in the plasma tail flame, so that at any height either process might limit the rate of vaporization. This similarity gives rise to a dynamic, competitive picture of plasma vaporization kinetics.

Spectrochimica Acta Part B: Atomic Spectroscopy, 2000

False-color spatial maps of experimentally determined and simulated values of electron number den... more False-color spatial maps of experimentally determined and simulated values of electron number density n , e Ž .

Spectrochimica Acta Part B: Atomic Spectroscopy, 2002

A mathematical model for the desolvation of solvent droplets has been used in conjunction with an... more A mathematical model for the desolvation of solvent droplets has been used in conjunction with an existing code for simulation of ICP fundamental parameters. The combination has been used for the calculation of droplet histories and desolvation behavior along the central channel of an ICP. Calculations have been performed for droplets of various sizes and under a variety of ICP operating conditions. As central-channel gas flow rate increases, the point of complete desolvation of the droplet shifts upward in the plasma, away from the load coil. This relationship is fairly linear. As forward power increases, the point of complete desolvation moves down in the discharge, closer to the load coil. This is approximately an inverse relationship. Finally, simulation of behavior for a log-normal size distribution of a large number of droplets (10 ) shows that the number of surviving droplets falls sigmoidally with 8 height above the load coil. For most nebulizeryspray chamber systems, the desolvation process is complete at a welldefined height in the plasma. ᮊ

Spectrochimica Acta Part B: Atomic Spectroscopy, 1995

ABSTRACT A useful plasma diagnostic is the measurement of electron number density. One way to acc... more ABSTRACT A useful plasma diagnostic is the measurement of electron number density. One way to accomplish such measurements is to determine the contribution to the broadening of a spectral line due to the Stark effect. To simplify and extend such electron density measurements across computer platforms, a program that calculates electron number density from the Stark-broadened hydrogen-beta line has been written for the LabVIEW® environment. This program calculates electron number densities from the field strength that would be exerted on a hydrogen atom immersed in a plasma. Using the new program, the electron number density in a glow discharge is calculated for two different operating conditions. Not surprisingly, the results indicate that to increase the current density in the discharge, the source electrodes must be reduced in surface area. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by one disk with an executable program (written for Apple Macintosh), data and text files including a manual.

Journal of Chromatography A, 2004

In this paper we describe results based on the combination of atmospheric pressure photoionizatio... more In this paper we describe results based on the combination of atmospheric pressure photoionization (APPI) with atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI). The main purpose of combining more than one ionizer is to extend the range of compounds that can be simultaneously analyzed. Three modes of operation are presented; use of either ionizer, simultaneous use of two

Journal of Analytical Atomic Spectrometry, 1988

... The authors thank Peter Wentzell, Mike Hatton and Barbara Faggetter for their assistance with... more ... The authors thank Peter Wentzell, Mike Hatton and Barbara Faggetter for their assistance with this work. A. PW thanks the UBC Chemistry Department for partially funding this work. MWB acknowledges financial support from ...

Applied Spectroscopy, 2000

ABSTRACT An unambiguous comparison has been made of the spatial features of a 27.12 and a 40.68 M... more ABSTRACT An unambiguous comparison has been made of the spatial features of a 27.12 and a 40.68 MHz inductively coupled plasma. Experiments were carried out with a switchable-frequency, solid-state radio-frequency generator from the Leco 2000 system. Several features of analytical significance have been evaluated in a spatially resolved fashion. Results from optimization of the magnesium ion-to-atom (Mg II/Mg I) line-intensity ratio have been compared. The volume of the two discharges was estimated from molecular nitrogen-ion emission, and a spatially resolved map of the Fe(I) excitation temperature was determined by means of a Boltzmann analysis at each spatial location. Calcium and magnesium ion-to-atom line-intensity ratios have been calculated throughout both plasmas. Finally, limits of detection are presented. The results indicate that the plasma operated at 40.68 MHz provides slightly better figures of merit, although fundamental parameters suggest a lower degree of analyte excitation. This difference is explained by examining the results of a simulation of plasmas operated at 27.12 and 40.68 MHz.

Spectrochimica Acta Part B: Atomic Spectroscopy, 1995

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electroni... more This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by a diskette with data files and text files with the hardcopy paper in Word for Windows 2.0 and ASCII format, and a disclaimer. The text details the purpose of the work, and the appendix provides essential information for accessing the diskette and using programs and data. An automated simplex optimization program was written in an attempt to relieve the monotonous human effort required to optimize an inductively coupled plasma atomic emission spectroscopic (ICP-AES) instrument. The program controls the operating conditions of a solid-state ICP while a monochromatic imaging spectrometer collects two-dimensional response images. In the work described in this article, four of the most important ICP operating parameters are optimized automatically: radio frequency (rf) power, intermediate Ar flow rate, nebulizer flow rate and sample uptake rate. Optimization of these parameters is based first on the response of the Ca II net signal and, independently, on the response of the Ca II net signal-to-background noise ratio (SNB). Since the best height and off-axis positions of the designated response are known from the optimal two-dimensional response image, two spatial parameters are indirectly optimized through use of a CCD camera. Optimal operating conditions are reported for the CA II net signal and Ca II SNB as well as the Mg IIMg I ratio.

Spectrochimica Acta Part B: Atomic Spectroscopy, 1997

A description is given of an imaging-based instrument capable of mapping several fundamental prop... more A description is given of an imaging-based instrument capable of mapping several fundamental properties of analytical plasmas, especially the inductively coupled plasma. The plasma fundamental parameters include electron temperature and number density, heavy-particle gas-kinetic temperature, analyte and argon atom and ion concentrations, and analyte emission intensities. These parameters can be measured on the same plasma running under identical operation conditions. The techniques to probe the basic plasma properties include Thomson scattering (for electron concentration and temperature), Rayleigh scattering (for heavy-particle temperature), computer-aided optical tomography (for three-dimensional emission maps), and laser-induced saturated fluorescence (for analyte and argon atom and ion number densities). A brief description of these techniques is presented. Also, a new approach to determining absolute number densities from fluorescence measurements is introduced. This novel method is based on normalizing a measured fluorescence intensity by the room-temperature Rayleighscattering signal.

Analytical Chemistry, 1999

Unlike the genome, the proteome is exquisitely sensitive to cellular conditions and will consist ... more Unlike the genome, the proteome is exquisitely sensitive to cellular conditions and will consist of proteins having abundances dependent upon stage in the cell cycle, cell differentiation, response to environmental conditions (nutrients, temperature, stress etc.), or disease state(s). Therefore, the study of proteomes under well-defined conditions can provide a better understanding of complex biological processes and inference of protein function. Thus, much faster, more sensitive, and precise capabilities for the characterization of cellular constituents are desired. We describe progress in the development and initial application of the powerful combination of capillary isoelectric focusing (CIEF) and Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for measurements of the proteome of the model system Escherichia coli. Isotope depletion of the growth media has been used to improve mass measurement accuracy, and the comparison of CIEF-FTICR results for the analysis of cell lysates harvested from E. coli cultured in normal and isotopically depleted media are presented. The initial studies have revealed 400-1000 putative proteins in the mass range 2-100 kDa from total injections of approximately 300 ng of E. coli proteins in a single CIEF-FTICR analysis.

Analytical Chemistry, 2009

The understanding and control of the in-source collision-induced dissociation (CID) of analytes i... more The understanding and control of the in-source collision-induced dissociation (CID) of analytes is important for the accurate LC-MS/MS quantitation of drugs and metabolites in biological samples. Accordingly, it was of interest to us to establish whether such in-...

Analytical Chemistry, 2012

We report the implementation of front-end higher energy collision induced dissociation (fHCD) on ... more We report the implementation of front-end higher energy collision induced dissociation (fHCD) on a bench-top dual pressure linear ion trap. Software and hardware modifications were employed, described in detail vide-infra, to allow isolated ions to undergo collisions with ambient gas molecules in an intermediate multipole (q00) of the instrument. Results comparing the performance of fHCD and resonance excitation collision induced dissociation (RE-CID) in terms of injection time, total number of scans, efficiency, mass measurement accuracy (MMA), unique peptide identifications, and spectral quality of labile modified peptides are presented. fHCD is approximately 23% as efficient as RE-CID and, depending on the search algorithm, it identifies 6.6% more or 15% less peptides (q<0.01) from a soluble whole-cell lysate (Caenorhabditis elegans) than RE-CID using Mascot or Sequest search algorithms, respectively. fHCD offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater (p<0.05) than for spectra collected using RE-CID.