@article{yang_gurgel_williams_bobay_cavanagh_muddiman_carbonell_2010, title={Binding site on human immunoglobulin G for the affinity ligand HWRGWV}, volume={23}, number={3}, journal={Journal of Molecular Recognition}, author={Yang, H. O. and Gurgel, P. V. and Williams, D. K. and Bobay, B. G. and Cavanagh, J. and Muddiman, D. C. and Carbonell, R. G.}, year={2010}, pages={271–282} }
 @article{williams_muddiman_2009, title={Absolute Quantification of C-Reactive Protein in Human Plasma Derived from Patients with Epithelial Ovarian Cancer Utilizing Protein Cleavage Isotope Dilution Mass Spectrometry}, volume={8}, DOI={10.1021/pr800922p}, abstractNote={A method employing protein cleavage isotope dilution mass spectrometry (PC-IDMS) was developed for quantification of C-reactive protein (CRP) in human plasma. This method was completed without the use of immunoaffinity chromatography or size exclusion chromatography, as previous mass spectrometric methods for the quantification of CRP have employed. A total of 110 human plasma samples were analyzed with PC-IDMS via 1-D nanoLC-MS/MS using a 30 min gradient with a triple quadrupole mass spectrometer operated in selective reaction monitoring (SRM) mode. The results from this newly developed method were compared to results generated from an enzyme-linked immunosorbent assay (ELISA) performed by an independent CLIA certified laboratory. The comparison of these results generated an R(2) = 0.9708 which indicates successful quantification of CRP from human plasma utilizing the methodology described herein. Interestingly, the PC-IDMS method provided concentration values that were approximately 10x the concentration reported by the ELISA method, which demonstrated that the method of detection is an important consideration when determining reference ranges of a particular analyte. In addition, data is shown that illustrates that, as epithelial ovarian cancer (EOC) progresses from stage I to stage IV, mean levels of CRP increase.}, number={2}, journal={Journal of Proteome Research}, author={Williams, D. Keith and Muddiman, David C.}, year={2009}, month={Jan}, pages={1085–1090} }
 @article{williams_comins_whitten_muddiman_2009, title={Evaluation of the ALiPHAT method for PC-IDMS and correlation of limits-of-detection with nonpolar surface area}, volume={20}, DOI={10.1016/j.jasms.2009.07.019}, abstractNote={PC-IDMS experiments for two peptides, laminin nonapeptide and the N-terminal tryptic peptide of prostate specific antigen, were performed utilizing a variety of alkylating reagents. These experiments were conducted to investigate how hydrophobicity influences the limits-of-detection (LOD) by altering their electrospray ionization response. Nonpolar surface areas were calculated for both peptides and all alkylating reagents to provide an estimate of the hydrophobicity of the differently alkylated peptides. Decreases in LOD by 2-fold were observed for both peptides between the best and worst performing combination of alkylating reagent. However, while an increase in hydrophobicity was found to aid in decreasing LOD to an extent, beyond a certain hydrophobicity, we observed a decrease.}, number={11}, journal={Journal of the American Society for Mass Spectrometry}, author={Williams, D. Keith and Comins, Daniel L. and Whitten, Jerry L. and Muddiman, David C.}, year={2009}, month={Aug}, pages={2006–2012} }
 @article{williams_kovach_muddiman_hanck_2009, title={Utilizing artificial neural networks in matlab to achieve parts-per-billion mass measurement accuracy with a fourier transform ion cyclotron resonance mass spectrometer}, volume={20}, DOI={10.1016/j.jasms.2009.02.030}, abstractNote={Fourier transform ion cyclotron resonance mass spectrometry has the ability to realize exceptional mass measurement accuracy (MMA); MMA is one of the most significant attributes of mass spectrometric measurements as it affords extraordinary molecular specificity. However, due to space-charge effects, the achievable MMA significantly depends on the total number of ions trapped in the ICR cell for a particular measurement, as well as relative ion abundance of a given species. Artificial neural network calibration in conjunction with automatic gain control (AGC) is utilized in these experiments to formally account for the differences in total ion population in the ICR cell between the external calibration spectra and experimental spectra. In addition, artificial neural network calibration is used to account for both differences in total ion population in the ICR cell as well as relative ion abundance of a given species, which also affords mean MMA values at the parts-per-billion level.}, number={7}, journal={Journal of the American Society for Mass Spectrometry}, author={Williams, D. Keith and Kovach, Alexander L. and Muddiman, David C. and Hanck, Kenneth W.}, year={2009}, month={Mar}, pages={1303–1310} }
 @article{williams_chadwick_williams_muddiman_2008, title={Calibration laws based on multiple linear regression applied to matrix‐assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={12}, url={http://europepmc.org/abstract/med/18563853}, DOI={10.1002/jms.1451}, abstractNote={Abstract Operation of any mass spectrometer requires implementation of mass calibration laws to translate experimentally measured physical quantities into a m / z range. While internal calibration in Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS) offers several attractive features, including exposure of calibrant and analyte ions to identical experimental conditions (e.g. space charge), external calibration affords simpler pulse sequences and higher throughput. The automatic gain control method used in hybrid linear trap quadrupole (LTQ) FT‐ICR‐MS to consistently obtain the same ion population is not readily amenable to matrix‐assisted laser desorption/ionization (MALDI) FT‐ICR‐MS, due to the heterogeneous nature and poor spot‐to‐spot reproducibility of MALDI. This can be compensated for by taking external calibration laws into account that consider magnetic and electric fields, as well as relative and total ion abundances. Herein, an evaluation of external mass calibration laws applied to MALDI‐FT‐ICR‐MS is performed to achieve higher mass measurement accuracy (MMA). Copyright © 2008 John Wiley & Sons, Ltd.}, number={12}, journal={Journal of Mass Spectrometry}, author={Williams, D. Keith, Jr. and Chadwick, M. Ashley and Williams, Taufika Islam and Muddiman, David C.}, year={2008}, month={Jun}, pages={1659–1663} }
 @article{williams_meadows_bori_hawkridge_comins_muddiman_2008, title={Synthesis, characterization, and application of lodoacetamide derivatives utilized for the ALiPHAT strategy}, volume={130}, DOI={10.1021/jao076849y}, number={7}, journal={Journal of the American Chemical Society}, author={Williams, D. K. and Meadows, C. W. and Bori, I. D. and Hawkridge, A. M. and Comins, D. L. and Muddiman, David}, year={2008}, pages={2122-} }
 @article{d. keith williams_mcalister_good_coon_muddiman_2007, title={Dual Electrospray Ion Source for Electron-Transfer Dissociation on a Hybrid Linear Ion Trap−Orbitrap Mass Spectrometer}, volume={79}, DOI={10.1021/ac071444h}, abstractNote={A dual electrospray ionization source (ESI) has been modified to simultaneously produce cations and anions, one from each emitter, for performing rapid electron-transfer dissociation (ETD) ion/ion reactions on a hybrid linear ion trap-orbitrap mass spectrometer. Unlike the pulsed dual ESI sources that were used to generate ETD reagent ions, this source separates the emitters in space, rather than time, by physically switching which one is in front of the atmospheric inlet. The new arrangement allows for substantially enhanced spray stability and decreased switching times (<or=30 ms), allowing for more tandem-MS spectra per unit time. Herein, we demonstrate the stability of the ETD anion population and the ability to identify several c- and z-type product ions from multiply protonated peptide cations.}, number={20}, journal={Analytical Chemistry}, author={D. Keith Williams and McAlister, Graeme C. and Good, David M. and Coon, Joshua J. and Muddiman, David C.}, year={2007}, month={Sep}, pages={7916–7919} }
 @article{williams_muddiman_2007, title={Parts-Per-Billion Mass Measurement Accuracy Achieved through the Combination of Multiple Linear Regression and Automatic Gain Control in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer}, volume={79}, DOI={10.1021/ac0704210}, abstractNote={Fourier transform ion cyclotron resonance mass spectrometry has the ability to achieve unprecedented mass measurement accuracy (MMA); MMA is one of the most significant attributes of mass spectrometric measurements as it affords extraordinary molecular specificity. However, due to space-charge effects, the achievable MMA significantly depends on the total number of ions trapped in the ion cyclotron resonance (ICR) cell for a particular measurement. Even through the use of automatic gain control (AGC), the total ion population is not constant between spectra. Multiple linear regression calibration in conjunction with AGC is utilized in these experiments to formally account for the differences in total ion population in the ICR cell between the external calibration spectra and experimental spectra. This ability allows for the extension of dynamic range of the instrument and for the mean MMA values to remain less than 1 part-per-million (ppm). In addition, multiple linear regression calibration is used to account for both differences in total ion population in the ICR cell as well as relative ion abundance of a given species, which also affords mean MMA values at the parts-per-billion (ppb) level.}, number={13}, journal={Analytical Chemistry}, author={Williams, D. Keith and Muddiman, David C.}, year={2007}, month={Jun}, pages={5058–5063} }
 @article{williams_hawkridge_muddiman_2006, title={Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer}, volume={18}, DOI={10.1016/j.jasms.2006.08.014}, abstractNote={High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from -2.0 ppm to 1.1 ppm, with an average of -0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.}, number={1}, journal={Journal of the American Society for Mass Spectrometry}, author={Williams, D. Keith and Hawkridge, Adam M. and Muddiman, David C.}, year={2006}, month={Sep}, pages={1–7} }