@article{adams_collins_williams_holmes_hess_atkins_scheidemantle_liu_lodge_johnson_et al._2024, title={Myeloid cell MHC I expression drives CD8<SUP>+</SUP> T cell activation in nonalcoholic steatohepatitis}, volume={14}, ISSN={["1664-3224"]}, url={https://doi.org/10.3389/fimmu.2023.1302006}, DOI={10.3389/fimmu.2023.1302006}, abstractNote={Background & aimsActivated CD8+ T cells are elevated in Nonalcoholic steatohepatitis (NASH) and are important for driving fibrosis and inflammation. Despite this, mechanisms of CD8+ T cell activation in NASH are largely limited. Specific CD8+ T cell subsets may become activated through metabolic signals or cytokines. However, studies in NASH have not evaluated the impact of antigen presentation or the involvement of specific antigens. Therefore, we determined if activated CD8+ T cells are dependent on MHC class I expression in NASH to regulate fibrosis and inflammation.MethodsWe used H2Kb and H2Db deficient (MHC I KO), Kb transgenic mice, and myeloid cell Kb deficient mice (LysM Kb KO) to investigate how MHC class I impacts CD8+ T cell function and NASH. Flow cytometry, gene expression, and histology were used to examine hepatic inflammation and fibrosis. The hepatic class I immunopeptidome was evaluated by mass spectrometry.ResultsIn NASH, MHC class I isoform H2Kb was upregulated in myeloid cells. MHC I KO demonstrated protective effects against NASH-induced inflammation and fibrosis. Kb mice exhibited increased fibrosis in the absence of H2Db while LysM Kb KO mice showed protection against fibrosis but not inflammation. H2Kb restricted peptides identified a unique NASH peptide Ncf2 capable of CD8+ T cell activation in vitro. The Ncf2 peptide was not detected during fibrosis resolution.ConclusionThese results suggest that activated hepatic CD8+ T cells are dependent on myeloid cell MHC class I expression in diet induced NASH to promote inflammation and fibrosis. Additionally, our studies suggest a role of NADPH oxidase in the production of Ncf2 peptide generation.}, journal={FRONTIERS IN IMMUNOLOGY}, author={Adams, Victoria R. and Collins, Leonard B. and Williams, Taufika Islam and Holmes, Jennifer and Hess, Paul and Atkins, Hannah M. and Scheidemantle, Grace and Liu, Xiaojing and Lodge, Mareca and Johnson, Aaron J. and et al.}, editor={Williams, Taufika Islam and Collins, Leonard B. and Kennedy, ArionEditors}, year={2024}, month={Jan} }
 @article{balbuena_milhem_kiremitci_williams_collins_shu_eroglu_2024, title={The Biochemical Effects of Carotenoids in Orange Carrots on the Colonic Proteome in a Mouse Model of Diet-induced Obesity}, url={https://publons.com/wos-op/publon/69870218/}, DOI={10.1101/2024.07.23.604335}, abstractNote={Carotenoids are naturally occurring pigments in plants and are responsible for the orange, yellow, and red color of fruits and vegetables. Carrots are one of the primary dietary sources of carotenoids. The biological activities of carotenoids in higher organisms are well documented in most tissues but not the large intestine. The gastrointestinal barrier acts as a line of defense against the systemic invasion of pathogenic bacteria, especially at the colonic level. Proteins involved in tight junction assembly between epithelial cells and mucus secretion from goblet cells are essential for maintaining intestinal barrier homeostasis. A high-fat diet can cause gut impairment by inducing barrier permeability, leading to low-grade chronic inflammation via metabolic endotoxemia. Our hypothesis for this study is that the dietary intake of carotenoid-rich foods can alleviate obesity-associated gut inflammation and strengthen the intestinal barrier function. Male C57BL/6J mice were randomized to one of four experimental diets for 20 weeks (n = 20 animals/group): Low-fat diet (LFD, 10% calories from fat), high-fat diet (HFD, 45% calories from fat), HFD with white carrot powder (HFD + WC), or HFD with orange carrot powder (HFD + OC). Colon tissues were harvested to analyze the biochemical effects of carotenoids in carrots. The distal sections were subjected to isobaric labeling-based quantitative proteomics in which tryptic peptides were labeled with tandem mass tags, followed by fractionation and LC-MS/MS analysis in an Orbitrap Eclipse Tribrid instrument. High-performance liquid chromatography results revealed that the HFD+WC pellets were carotenoid-deficient, and the HFD+OC pellets contained high concentrations of provitamin A carotenoids, specifically α-carotene and β-carotene. As a result of the quantitative proteomics, a total of 4410 differentially expressed proteins were identified. Intestinal barrier-associated proteins were highly upregulated in the HFD+OC group, particularly mucin-2 (MUC-2). Upon closer investigation into mucosal activity, other proteins related to MUC-2 functionality and tight junction management were upregulated by the HFD+OC dietary intervention. Collectively, our findings suggest that carotenoid-rich foods can prevent high-fat diet-induced intestinal barrier disruption by promoting colonic mucus synthesis and secretion in mammalian organisms. Data are available via ProteomeXchange with identifier PXD054150.}, journal={BioRxiv}, author={Balbuena, Emilio and Milhem, Fadia and Kiremitci, Buse Zeren and Williams, Taufika Islam and Collins, Leonard and Shu, Qingbo and Eroglu, Abdulkerim}, year={2024} }
 @article{williams_kowalchyk_collins_reading_2023, title={Discovery Proteomics and Absolute Protein Quantification Can Be Performed Simultaneously on an Orbitrap-Based Mass Spectrometer}, volume={3}, ISSN={["2470-1343"]}, url={https://doi.org/10.1021/acsomega.2c07614}, DOI={10.1021/acsomega.2c07614}, abstractNote={Mass spectrometry (MS) has steadily moved into the forefront of quantification-centered protein research. Protein cleavage isotope dilution MS is a proven way for quantifying proteins by using an isotope-labeled analogue of a peptide fragment of the parent protein as an internal standard. Parallel reaction monitoring (PRM) has become the go-to approach for such quantification on an Orbitrap-based instrument as it is assumed that the instrument sensitivity is enhanced. We performed a comparative study on data-dependent acquisition (DDA) and PRM-based workflows to quantify egg yolk protein precursors or vitellogenins (VTGs) Aa, Ab, and C in striped bass (Morone saxatilis). VTG proportions serve as a developmental measure of egg quality, possibly changing with the environment, and have been studied as an indicator of the health of North Carolina stocks. Based on single-factor analysis of variance comparisons of mean VTG amounts across fish from the same sample groupings, our results indicate that there is no statistical difference between MS1-based and MS2-based VTG quantification. We further conclude that DDA is able to deliver both discovery data and absolute quantification data in the same experiment.}, number={13}, journal={ACS OMEGA}, author={Williams, Taufika Islam and Kowalchyk, Cara and Collins, Leonard B. and Reading, Benjamin J.}, year={2023}, month={Mar} }
 @article{oh_mendola_choe_min_lavoie_sripada_williams_lee_yigzaw_seay_et al._2023, title={Identification and characterization of CHO host-cell proteins in monoclonal antibody bioprocessing}, volume={10}, ISSN={["1097-0290"]}, DOI={10.1002/bit.28568}, abstractNote={AbstractHost‐cell proteins (HCPs) are the foremost class of process‐related impurities to be controlled and removed in downstream processing steps in monoclonal antibody (mAb) manufacturing. However, some HCPs may evade clearance in multiple purification steps and reach the final drug product, potentially threatening drug stability and patient safety. This study extends prior work on HCP characterization and persistence in mAb process streams by using mass spectrometry (MS)‐based methods to track HCPs through downstream processing steps for seven mAbs that were generated by five different cell lines. The results show considerable variability in HCP identities in the processing steps but extensive commonality in the identities and quantities of the most abundant HCPs in the harvests for different processes. Analysis of HCP abundance in the harvests shows a likely relationship between abundance and the reproducibility of quantification measurements and suggests that some groups of HCPs may hinder the characterization. Quantitative monitoring of HCPs persisting through purification steps coupled with the findings from the harvest analysis suggest that multiple factors, including HCP abundance and mAb‐HCP interactions, can contribute to the persistence of individual HCPs and the identification of groups of common, persistent HCPs in mAb manufacturing.}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Oh, Young Hoon and Mendola, Kerri M. and Choe, Leila H. and Min, Lie and Lavoie, Ashton R. and Sripada, Sobhana A. and Williams, Taufika Islam and Lee, Kelvin H. and Yigzaw, Yinges and Seay, Alexander and et al.}, year={2023}, month={Oct} }
 @article{williams_2023, title={Identification and characterization of CHO host-cell proteins in monoclonal antibody bioprocessing}, journal={Biotechnology and Bioengineering}, year={2023}, month={Sep} }
 @article{durmusoglu_al'abri_li_islam williams_collins_martinez_crook_2023, title={Improving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach}, volume={22}, ISSN={["1475-2859"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85161032784&partnerID=MN8TOARS}, DOI={10.1186/s12934-023-02117-y}, abstractNote={AbstractThe probiotic yeastSaccharomyces boulardii(Sb) is a promising chassis to deliver therapeutic proteins to the gut due toSb’s innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineerSbstrains with enhanced levels of protein secretion. In this work, we explored genetic modifications in bothcis-(i.e. to the expression cassette of the secreted protein) andtrans-(i.e. to theSbgenome) that enhanceSb’s ability to secrete proteins, taking aClostridioides difficileToxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by sixfold (76–458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 and 463 mg/L. Then, guided by prior knowledge ofS. cerevisiae’s secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficientSbstrain that produces 5045 mg/L secretory NPA, an improvement of > tenfold over wild-typeSb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion inSband highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability ofSbto deliver therapeutics to the gut and other settings to which it is adapted.}, number={1}, journal={MICROBIAL CELL FACTORIES}, author={Durmusoglu, Deniz and Al'Abri, Ibrahim and Li, Zidan and Islam Williams, Taufika and Collins, Leonard B. and Martinez, Jose L. and Crook, Nathan}, year={2023}, month={Jun} }
 @article{sripada_elhanafi_collins_williams_linova_woodley_boi_menegatti_2023, title={Pseudo-affinity capture of K. phaffii host cell proteins in flow-through mode: Purification of protein therapeutics and proteomic study}, volume={326}, ISSN={1383-5866}, url={http://dx.doi.org/10.1016/j.seppur.2023.124777}, DOI={10.1016/j.seppur.2023.124777}, abstractNote={K. phaffii is a versatile expression system that is increasingly utilized to produce biological therapeutics – including enzymes, engineered antibodies, and gene-editing tools – that feature multiple subunits and complex post-translational modifications. Two major roadblocks limit the adoption of K. phaffii in industrial biomanufacturing: its proteome, while known, has not been linked to downstream process operations and detailed knowledge is missing on problematic host cell proteins (HCPs) that endanger patient safety or product stability. Furthermore, the purification toolbox has not evolved beyond the capture of monospecific antibodies, and few solutions are available for engineered antibody fragments and other protein therapeutics. To unlock the potential of yeast-based biopharmaceutical manufacturing, this study presents the development and performance validation of a novel adsorbent – PichiaGuard – functionalized with peptide ligands that target the whole spectrum of K. phaffii HCPs and designed for protein purification in flow-through mode. The PichiaGuard adsorbent features high HCP binding capacity (∼25 g per liter of resin) and successfully purified a monoclonal antibody and an ScFv fragment from clarified K. phaffii harvests, affording > 300-fold removal of HCPs and high product yields (70–80%). Notably, PichiaGuard outperformed commercial ion exchange and mixed-mode resins without salt gradients or optimization in removing high-risk HCPs – including aspartic proteases, ribosomal subunits, and other peptidases – thus demonstrating its value in modern biopharmaceutical processing.}, journal={Separation and Purification Technology}, publisher={Elsevier BV}, author={Sripada, Sobhana A. and Elhanafi, Driss and Collins, Leonard B. and Williams, Taufika I. and Linova, Marina Y. and Woodley, John M. and Boi, Cristiana and Menegatti, Stefano}, year={2023}, month={Dec}, pages={124777} }
 @article{bai_collins_andre_breitschwerdt_williams_2023, title={A bottom-up proteomics workflow for a system containing multiple organisms}, volume={1}, ISSN={["1097-0231"]}, url={https://doi.org/10.1002/rcm.9431}, DOI={10.1002/rcm.9431}, abstractNote={RationaleDiscovery proteomics has been popularized to be essential in the investigator's biological toolbox. Many biological problems involve the interplay of multiple organisms. Herein, a bottom‐up proteomics workflow was developed to study a system containing multiple organisms to promote a thorough understanding of how each interacts with the others.MethodsA label‐free quantification proteomics workflow was developed with nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC‐MS/MS). This protocol describes a bottom‐up proteomics workflow used to study differential protein expression in the context of fleas (Ctenocephalides felis felis) experimentally infected by the bacterium Bartonella henselae, the etiological agent of Cat Scratch Disease (CSD).ResultsStep‐by‐step instructions are provided for protein extraction, protein cleanup, total protein measurement, nanoLC‐MS/MS data acquisition, and data analysis using Proteome Discoverer software. Comprehensive and exhaustive details are included to promote the adoption of this proteomics workflow in other laboratories.ConclusionA proteomics protocol is detailed for a system containing multiple proteomes from different taxonomic lineages using CSD (cats bitten by fleas infected with Bartonella henselae) as a model. The operating protocol can be readily applied to other label‐free proteomics work involving multiple proteomes from taxonomically distinct organisms.}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bai, Hongxia and Collins, Leonard B. B. and Andre, Marcos Rogerio and Breitschwerdt, Edward B. B. and Williams, Taufika Islam}, year={2023}, month={Jan} }
 @article{venkatraman_filiano_xu_collins_luo_ripple_castro_boua_marius_giamberardino_et al._2022, title={Filtered Cerebrospinal Fluid From Patients With Amyotrophic Lateral Sclerosis Displays an Altered Proteome and Affects Motor Phenotype in a Mouse Model}, volume={12}, url={http://dx.doi.org/10.7759/cureus.32980}, DOI={10.7759/cureus.32980}, abstractNote={Introduction: Cerebrospinal fluid (CSF) has been implicated in amyotrophic lateral sclerosis (ALS) due to its ability to spread inflammatory proteins throughout the nervous system. We hypothesized that filtration of the CSF could remove pathogenic proteins and prevent them from altering motor phenotypes in a mouse model. Methods: We filtered the CSF from 11 ALS patients via 100 kilodaltons (kD) molecular weight cut-off filters. We used mass spectrometry-based discovery proteomics workflows to compare protein abundances before and after filtration. To test the effects of CSF filtration on motor function, we injected groups of mice with saline, filtered ALS-CSF, or unfiltered ALS-CSF (n=12 per group) and assessed motor function via pole descent and open field tests. Results: We identified proteins implicated in ALS pathogenesis and showed that these were removed in significant amounts in our workflow. Key filtered proteins included complement proteins, chitinases, serine protease inhibitors, and neuro-inflammatory proteins such as amyloid precursor protein, chromogranin A, and glial fibrillary acidic protein. Compared to the filtered ALS-CSF mice, unfiltered ALS-CSF mice took longer to descend a pole (10 days post-injection, 11.14 seconds vs 14.25 seconds, p = 0.02) and explored less on an open field (one day post-injection, 21.81 m vs 16.83 m, p = 0.0004). Conclusions:We demonstrated the ability to filter proteins from the CSF of ALS patients and identified potentially pathologic proteins that were reduced in quantity. Additionally, we demonstrated the ability of unfiltered ALS-CSF to induce motor deficits in mice on the pole descent and open field tests and showed that filtration could prevent this deficit. Given the lack of effective treatments for ALS, this could be a novel solution for patients suffering from this deadly and irreversible condition.}, journal={Cureus}, publisher={Cureus, Inc.}, author={Venkatraman, Vishal and Filiano, Anthony J and Xu, Li and Collins, Leonard and Luo, Emily and Ripple, Katelyn M and Castro, George C and Boua, Jane-Valeriane K and Marius, Choiselle and Giamberardino, Charles and et al.}, year={2022}, month={Dec} }
 @article{durmusoglu_al’abri_williams_collins_martínez_crook_2022, title={Improving Therapeutic Protein Secretion in the Probiotic YeastSaccharomyces boulardiiusing a Multifactorial Engineering Approach}, url={https://doi.org/10.1101/2022.12.30.522352}, DOI={10.1101/2022.12.30.522352}, abstractNote={AbstractThe probiotic yeastSaccharomyces boulardii(Sb) is a promising chassis to deliver therapeutic proteins to the gut due toSb’s innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineerSbstrains with enhanced levels of protein secretion. In this work, we explored genetic modifications in bothcis- (i.e., to the expression cassette of the secreted protein) andtrans- (i.e., to theSbgenome) that enhanceSb’s ability to secrete proteins, taking aClostridioides difficileToxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by 6-fold (76-458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 - 463 mg/L. Then, guided by prior knowledge ofS. cerevisiae’s secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficientSbstrain that produces 5045 mg/L secretory NPA, an improvement of >10-fold over wild-typeSb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion inSband highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability ofSbto deliver therapeutics to the gut and other settings to which it is adapted.}, journal={bioRxiv}, author={Durmusoglu, Deniz and Al’Abri, Ibrahim and Williams, Taufika Islam and Collins, Leonard B. and Martínez, José L. and Crook, Nathan}, year={2022}, month={Dec} }
 @article{muthusamy_williams_o'toole_brudvig_adler_weimer_muddiman_ghashghaei_2022, title={Phosphorylation-dependent proteome of Marcks in ependyma during aging and behavioral homeostasis in the mouse forebrain}, volume={1}, ISSN={["2509-2723"]}, url={http://dx.doi.org/10.1007/s11357-022-00517-3}, DOI={10.1007/s11357-022-00517-3}, abstractNote={Ependymal cells (ECs) line the ventricular surfaces of the mammalian central nervous system (CNS) and their development is indispensable to structural integrity and functions of the CNS. We previously reported that EC-specific genetic deletion of the myristoylated alanine-rich protein kinase C substrate (Marcks) disrupts barrier functions and elevates oxidative stress and lipid droplet accumulation in ECs causing precocious cellular aging. However, little is known regarding the mechanisms that mediate these changes in ECs. To gain insight into Marcks-mediated mechanisms, we performed mass spectrometric analyses on Marcks-associated proteins in young and aged ECs in the mouse forebrain using an integrated approach. Network analysis on annotated proteins revealed that the identified Marcks-associated complexes are in part involved in protein transport mechanisms in young ECs. In fact, we found perturbed intracellular vesicular trafficking in cultured ECs with selective deletion of Marcks (Marcks-cKO mice), or upon pharmacological alteration to phosphorylation status of Marcks. In comparison, Marcks-associated protein complexes in aged ECs appear to be involved in regulation of lipid metabolism and responses to oxidative stress. Confirming this, we found elevated signatures of inflammation in the cerebral cortices and the hippocampi of young Marcks-cKO mice. Interestingly, behavioral testing using a water maze task indicated that spatial learning and memory is diminished in young Marcks-cKO mice similar to aged wildtype mice. Taken together, our study provides first line of evidence for potential mechanisms that may mediate differential Marcks functions in young and old ECs, and their effect on forebrain homeostasis during aging.}, number={4}, journal={GEROSCIENCE}, publisher={Springer Science and Business Media LLC}, author={Muthusamy, Nagendran and Williams, Taufika I and O'Toole, Ryan and Brudvig, Jon J. and Adler, Kenneth B. and Weimer, Jill M. and Muddiman, David C. and Ghashghaei, H. Troy}, year={2022}, month={Jan} }
 @article{manley_phan_stewart_mosley_xue_cha_bai_lightfoot_rucker_collins_et al._2022, title={Self-sacrificial tyrosine cleavage by an Fe:Mn oxygenase for the biosynthesis of para-aminobenzoate in Chlamydia trachomatis}, volume={119}, ISSN={["1091-6490"]}, url={http://dx.doi.org/10.1073/pnas.2210908119}, DOI={10.1073/pnas.2210908119}, abstractNote={
            Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of
            para
            -aminobenzoate (pABA), an essential component of the folate cofactor that is required for the survival and proliferation of the human pathogen
            Chlamydia trachomatis
            . The pathway used by
            Chlamydiae
            for pABA synthesis differs from the canonical multi-enzyme pathway used by most bacteria that relies on chorismate as a metabolic precursor. Rather, recent work showed pABA formation by CADD derives from
            l
            -tyrosine. As a member of the emerging superfamily of heme oxygenase–like diiron oxidases (HDOs), CADD was proposed to use a diiron cofactor for catalysis. However, we report maximal pABA formation by CADD occurs upon the addition of both iron and manganese, which implicates a heterobimetallic Fe:Mn cluster is the catalytically active form. Isotopic labeling experiments and proteomics studies show that CADD generates pABA from a protein-derived tyrosine (Tyr27), a residue that is ∼14 Å from the dimetal site. We propose that this self-sacrificial reaction occurs through O
            2
            activation by a probable Fe:Mn cluster through a radical relay mechanism that connects to the “substrate” Tyr, followed by amination and direct oxygen insertion. These results provide the molecular basis for pABA formation in
            C. trachomatis
            , which will inform the design of novel therapeutics.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Manley, Olivia M. and Phan, Han N. and Stewart, Allison K. and Mosley, Dontae A. and Xue, Shan and Cha, Lide and Bai, Hongxia and Lightfoot, Veda C. and Rucker, Pierson A. and Collins, Leonard and et al.}, year={2022}, month={Sep} }
 @article{sripada_chu_williams_teten_mosley_carbonell_lenhoff_cramer_bill_yigzaw_et al._2022, title={Towards continuous mAb purification: Clearance of host cell proteins from CHO cell culture harvests via "flow-through affinity chromatography" using peptide-based adsorbents}, volume={119}, ISSN={["1097-0290"]}, url={https://doi.org/10.1002/bit.28096}, DOI={10.1002/bit.28096}, abstractNote={AbstractThe growth of advanced analytics in manufacturing monoclonal antibodies (mAbs) has highlighted the challenges associated with the clearance of host cell proteins (HCPs). Of special concern is the removal of “persistent” HCPs, including immunogenic and mAb‐degrading proteins, that co‐elute from the Protein A resin and can escape the polishing steps. Responding to this challenge, we introduced an ensemble of peptide ligands that target the HCPs in Chinese hamster ovary (CHO) cell culture fluids and enable mAb purification via flow‐through affinity chromatography. This study describes their integration into LigaGuard™, an affinity adsorbent featuring an equilibrium binding capacity of ~30 mg of HCPs per mL of resin as well as dynamic capacities up to 16 and 22 mg/ml at 1‐ and 2‐min residence times, respectively. When evaluated against cell culture harvests with different mAb and HCP titers and properties, LigaGuard™ afforded high HCP clearance, with logarithmic removal values (LRVs) up to 1.5, and mAb yield above 90%. Proteomic analysis of the effluents confirmed the removal of high‐risk HCPs, including cathepsins, histones, glutathione‐S transferase, and lipoprotein lipases. Finally, combining LigaGuard™ for HCP removal with affinity adsorbents for product capture afforded a global mAb yield of 85%, and HCP and DNA LRVs > 4.}, number={7}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, publisher={Wiley}, author={Sripada, Sobhana Alekhya and Chu, Wenning and Williams, Taufika Islam and Teten, Matthew A. and Mosley, Brian J. and Carbonell, Ruben G. and Lenhoff, Abraham M. and Cramer, Steven M. and Bill, Jerome and Yigzaw, Yinges and et al.}, year={2022}, month={Apr} }
 @article{andre_neupane_lappin_herrin_smith_williams_collins_bai_jorge_balbuena_et al._2022, title={Using Proteomic Approaches to Unravel the Response of Ctenocephalides felis felis to Blood Feeding and Infection With Bartonella henselae}, volume={12}, ISSN={["2235-2988"]}, url={http://dx.doi.org/10.3389/fcimb.2022.828082}, DOI={10.3389/fcimb.2022.828082}, abstractNote={Among the Ctenocephalides felis felis-borne pathogens, Bartonella henselae, the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of B. henselae as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect. Even though recent developments in vector and pathogen -omics have advanced the understanding of the genetic factors and molecular pathways involved at the tick-pathogen interface, leading to discovery of candidate protective antigens, only a few studies have focused on the interaction between fleas and flea-borne pathogens. Taking into account the period of time needed for B. henselae replication in flea digestive tract, the present study investigated flea-differentially abundant proteins (FDAP) in unfed fleas, fleas fed on uninfected cats, and fleas fed on B. henselae-infected cats at 24 hours and 9 days after the beginning of blood feeding. Proteomics approaches were designed and implemented to interrogate differentially expressed proteins, so as to gain a better understanding of proteomic changes associated with the initial B. henselae transmission period (24 hour timepoint) and a subsequent time point 9 days after blood ingestion and flea infection. As a result, serine proteases, ribosomal proteins, proteasome subunit α-type, juvenile hormone epoxide hydrolase 1, vitellogenin C, allantoinase, phosphoenolpyruvate carboxykinase, succinic semialdehyde dehydrogenase, glycinamide ribotide transformylase, secreted salivary acid phosphatase had high abundance in response of C. felis blood feeding and/or infection by B. henselae. In contrast, high abundance of serpin-1, arginine kinase, ribosomal proteins, peritrophin-like protein, and FS-H/FSI antigen family member 3 was strongly associated with unfed cat fleas. Findings from this study provide insights into proteomic response of cat fleas to B. henselae infected and uninfected blood meal, as well as C. felis response to invading B. henselae over an infection time course, thus helping understand the complex interactions between cat fleas and B. henselae at protein levels.}, journal={FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Andre, Marcos Rogerio and Neupane, Pradeep and Lappin, Michael and Herrin, Brian and Smith, Vicki and Williams, Taufika Islam and Collins, Leonard and Bai, Hongxia and Jorge, Gabriel Lemes and Balbuena, Tiago Santana and et al.}, year={2022}, month={Jan} }
 @article{lavoie_islam_blackburn_carbonell_menegatti_2021, title={Development of Peptide Ligands for Targeted Capture of Host Cell Proteins from Cell Culture Production Harvests}, volume={2261}, ISBN={["978-1-0716-1185-2"]}, ISSN={["1940-6029"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85099721618&partnerID=MN8TOARS}, DOI={10.1007/978-1-0716-1186-9_31}, abstractNote={Capture of host cell proteins (HCPs) from cell culture production harvests is critical to ensure the maximum levels specified by international regulatory bodies of product purity for therapeutic monoclonal antibodies (mAbs). Peptide ligands that selectively target the whole spectrum of the HCPs, while letting the mAb product flow through unbound, are an ideal complement to the affinity-based capture step via Protein A chromatography. In this work, we describe the development of HCP-binding peptide ligands, especially focusing on the steps of (1) peptide selection via library screening and (2) quantification of HCP removal via proteomics by mass spectrometry.}, journal={PROTEOMIC PROFILING, 2 EDITION}, author={Lavoie, R. Ashton and Islam, Taufika and Blackburn, Williams R. Kevin and Carbonell, Ruben G. and Menegatti, Stefano}, year={2021}, pages={489–506} }
 @article{mellinger_mccoy_minior_williams_2021, title={Discovery proteomics of human placental tissue}, volume={9}, ISSN={["1097-0231"]}, url={https://doi.org/10.1002/rcm.9189}, DOI={10.1002/rcm.9189}, abstractNote={We describe a label‐free proteomics protocol for the interrogation of the placental proteome. Step‐by‐step directions, including tissue cleanup and preparation, proteolytic digestion, nanoLC–MS/MS data collection and data analysis, are provided. The workflow has been applied toward exploring differential protein expression patterns in placentas from women who have been exposed to drugs during pregnancy relative to those who have not. We collected 20 tissue specimens, each representing a combination of spatially diverse sections across the placenta. These specimens were analyzed in the work described here, to survey information across the entire organ. This protocol can be scaled up or down as needed.}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, publisher={Wiley}, author={Mellinger, Allyson L. and McCoy, Krista and Minior, Duy An T. and Williams, Taufika Islam}, year={2021}, month={Dec} }
 @article{lavoie_chu_lavoie_hetzler_williams_carbonell_menegatti_2021, title={Removal of host cell proteins from cell culture fluids by weak partitioning chromatography using peptide-based adsorbents}, volume={257}, ISSN={["1873-3794"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85093930679&partnerID=MN8TOARS}, DOI={10.1016/j.seppur.2020.117890}, abstractNote={This work presents the removal of host cell proteins (HCPs) from a Chinese Hamster Ovary clarified cell culture fluid (CHO CCCF) containing a therapeutic monoclonal antibody (mAb) by weak partitioning chromatography (WPC). The chromatographic adsorbents were produced by functionalizing Toyopearl resin with HCP-binding tetrameric multipolar (4MP) or hexameric hydrophobic/cationic (6HP) peptides. The CCCF was loaded on columns packed with either 4MP-Toyopearl or 6HP-Toyopearl resin only, or a 4MP and 6HP resin mixture at different values of residence time (RT: 0.5, 1, 2, and 5 min). The temporal profiles of concentration of HCPs and mAb in the effluents confirmed the binding mechanism by WPC, where both HCPs and mAb are initially bound by the peptide ligands, but, as more CCCF is fed to the column, the incoming HCPs displace the bound mAbs. In particular, 4MP was shown to capture more selectively high molecular weight HCPs, while 6HP was more effective in binding low molecular weight HCPs. Under optimal loading conditions (~60–80 g of proteins per L of adsorbent; RT of 5 min), the 6HP+4MP-Toyopearl adsorbent provided mAb yield and purity of >80% and up to 90%, respectively. Conversely, the control resin Toyopearl SuperQ-650 M resulted in 70% yield and 75% purity under the same conditions. Proteomic analysis of the effluents demonstrated that 6HP+4MP-Toyopearl adsorbent removes HCPs known for their immunogenicity or IgG co-elution or degradation, demonstrating the potential of these peptide-based resins as HCP scrubbers in mAb purification processes.}, journal={SEPARATION AND PURIFICATION TECHNOLOGY}, author={Lavoie, R. Ashton and Chu, Wenning and Lavoie, Joseph H. and Hetzler, Zachary and Williams, Taufika Islam and Carbonell, Ruben and Menegatti, Stefano}, year={2021}, month={Feb} }
 @article{jaiswal_weber_yerke_xue_lehman_williams_xiao_haddad_williams_2019, title={A substitute variety for agronomically and medicinally important Serenoa repens (saw palmetto)}, volume={9}, ISSN={["2045-2322"]}, url={http://europepmc.org/abstract/med/30886216}, DOI={10.1038/s41598-019-41150-z}, abstractNote={AbstractSerenoa repens (saw palmetto) berries are one of the most consumed medicinal herbs in the United States and the wild green variety is used in the initial therapy of benign prostatic hyperplasia (BPH), globally. Use of saw palmetto is approved by the German Commission E, and several clinical trials are underway for evaluation of its efficacy. Exploitation of its habitats and over foraging imperil this plant, which only grows in the wild. This is the first study, to propose the use of the S. repens forma glauca (silver variety) as a qualitative substitute for the wild variety, to support its conservation. We compared tissue microstructures and lipid and water distribution through spatial imaging and examined metabolite distribution of three tissue domains and whole berries. This combined approach of 3D imaging and metabolomics provides a new strategy for studying phenotypic traits and metabolite synthesis of closely related plant varieties.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Jaiswal, Yogini and Weber, Daniel and Yerke, Aaron and Xue, Yanling and Lehman, Danielle and Williams, Taufika and Xiao, Tiqiao and Haddad, Daniel and Williams, Leonard}, year={2019}, month={Mar} }
 @inproceedings{williams_kowalchyk_fischer_reading_2019, place={Raleigh, NC}, title={Egg Characteristics and Striped Bass Fertility}, author={Williams, T.Islam and Kowalchyk, C. and Fischer, Jesse and Reading, Benjamin}, year={2019} }
 @inproceedings{williams_kowalchyk_fischer_reading_2019, place={Atlanta, GA}, title={Exploring Egg Characteristics of Striped Bass}, author={Williams, T.Islam and Kowalchyk, C. and Fischer, J. and Reading, B.}, year={2019} }
 @article{lavoie_fazio_williams_carbonell_menegatti_2020, title={Targeted capture of Chinese hamster ovary host cell proteins: Peptide ligand binding by proteomic analysis}, volume={117}, ISSN={["1097-0290"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85075219049&partnerID=MN8TOARS}, DOI={10.1002/bit.27213}, abstractNote={AbstractThe clearance of host cell proteins (HCPs) is of crucial importance in biomanufacturing, given their diversity in composition, structure, abundance, and occasional structural homology with the product. The current approach to HCP clearance in the manufacturing of monoclonal antibodies (mAbs) relies on product capture with Protein A followed by removal of residual HCPs in flow‐through mode using ion exchange or mixed‐mode chromatography. Recent studies have highlighted the presence of “problematic HCP” species, which are either difficult to remove (Group I), can degrade the mAb product (Group II), or trigger immunogenic reactions (Group III). To improve the clearance of these species, we developed a family of synthetic peptides that target HCPs and exhibit low binding to IgG product. In this study, these peptides were conjugated onto chromatographic resins and evaluated in terms of HCP clearance and mAb yield, using an industrial mAb‐producing CHO harvest as model supernatant. To gather detailed knowledge on the binding of individual HCPs, the unbound fractions were subjected to shotgun proteomic analysis by mass spectrometry. It was found that these peptide ligands exhibit superior HCP binding capability compared to those of the benchmark commercial resins commonly used in mAb purification. In addition, some peptide‐based resins resulted in much lower losses of product yield compared to these commercial supports. The proteomic analysis showed effective capture of many “problematic HCPs” by the peptide ligands, especially some that are weakly bound by commercial media. Collectively, these results indicate that these peptides show great promise toward the development of next‐generation adsorbents for safer and cost‐effective manufacturing of biologics.}, number={2}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Lavoie, R. Ashton and Fazio, Alice and Williams, Taufika Islam and Carbonell, Ruben and Menegatti, Stefano}, year={2020}, month={Feb}, pages={438–452} }
 @article{williams_2018, title={Conrad Bessant (Ed.): Proteome informatics}, volume={410}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/S00216-018-1009-7}, DOI={10.1007/S00216-018-1009-7}, number={14}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Williams, Taufika Islam}, year={2018}, month={Apr}, pages={3231–3233} }
 @article{williams_reading_amano_hiramatsu_schilling_salger_williams_gross_sullivan_2014, title={Proportional Accumulation of Yolk Proteins Derived From Multiple Vitellogenins is Precisely Regulated During Vitellogenesis in Striped Bass (Morone saxatilis)}, volume={321}, ISSN={["2471-5646"]}, url={http://europepmc.org/abstract/med/24648375}, DOI={10.1002/jez.1859}, abstractNote={ABSTRACTWe quantified three vitellogenins (VtgAa, VtgAb, VtgC) or their derived yolk proteins (YPs) in the liver, plasma, and ovary during pre‐vitellogenic (PreVG), mid‐vitellogenic (MVG), and late‐vitellogenic (LVG) oocyte growth and during post‐vitellogenesis (PostVG) in the striped bass (Morone saxatilis) using label‐free quantitative mass spectrometry (MS). Western blotting of the samples using antisera raised against gray mullet (Mugil cephalus) lipovitellins derived from VtgAa, VtgAb, and VtgC confirmed the MS results. Semi‐quantitative reverse transcription polymerase chain reaction (RT‐PCR) revealed liver as the primary site of expression for all three Vtgs, with extra‐hepatic transcription weakly detected in ovary, foregut, adipose tissue, and brain. Quantitative real‐time RT‐PCR confirmed vtgAb to be primarily expressed in liver and VtgAb proteins were predominant in liver and plasma from MVG to PostVG. However, the primary period of deposition into oocytes of VtgAb occurred up until MVG, whereas VtgAa was primarily deposited from MVG to LVG. The VtgC was gradually taken up by oocytes throughout vitellogenesis and was detected at trace levels in plasma. The ratio of yolk proteins derived from VtgAa, VtgAb, VtgC (YPAa/YPAb/YPC) in PostVG ovary is 1.4:1.4:1, which differs from ratios previously reported for other fish species in that YPC comprises a greater proportion of the egg yolk. Our results indicate that proportional accumulation of multiple Vtgs in the yolk may depend both on the precise rates of their hepatic secretion and specific uptake by oocytes. Furthermore, composition of the Vtg‐derived yolk may vary among Acanthomorph fishes, perhaps reflecting their different early life histories and reproductive strategies. J. Exp. Zool. 321A: 301–315, 2014. © 2014 Wiley Periodicals, Inc.}, number={6}, journal={JOURNAL OF EXPERIMENTAL ZOOLOGY PART A-ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY}, author={Williams, Valerie N. and Reading, Benjamin J. and Amano, Haruna and Hiramatsu, Naoshi and Schilling, Justin and Salger, Scott A. and Williams, Taufika Islam and Gross, Kevin and Sullivan, Craig V.}, year={2014}, month={Jul}, pages={301–315} }
 @article{reading_williams_chapman_williams_sullivan_2013, title={Dynamics of the Striped Bass (Morone saxatilis) Ovary Proteome Reveal a Complex Network of the Translasome}, volume={12}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/PR3010293}, DOI={10.1021/pr3010293}, abstractNote={We evaluated changes in the striped bass (Morone saxatilis) ovary proteome during the annual reproductive cycle using label-free quantitative mass spectrometry and a novel machine learning analysis based on K-means clustering and support vector machines. Modulated modularity clustering was used to group co-variable proteins into expression modules and Gene Ontology (GO) biological process and KEGG pathway enrichment analyses were conducted for proteins within those modules. We discovered that components of the ribosome along with translation initiation and elongation factors generally decrease as the annual ovarian cycle progresses toward ovulation, concomitant with a slight increase in components of the 26S-proteasome. Co-variation within more than one expression module of components from these two multi-protein complexes suggests that they are not only co-regulated, but that co-regulation occurs through more than one sub-network. These components also co-vary with subunits of the TCP-1 chaperonin system and enzymes of intermediary metabolic pathways, suggesting that protein folding and cellular bioenergetic state play important roles in protein synthesis and degradation. We provide further evidence to suggest that protein synthesis and degradation are intimately linked, and our results support function of a proteasome-ribosome supercomplex known as the translasome.}, number={4}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Reading, Benjamin J. and Williams, Valerie N. and Chapman, Robert W. and Williams, Taufika Islam and Sullivan, Craig V.}, year={2013}, month={Mar}, pages={1691–1699} }
 @inproceedings{kandhi_williams_2013, title={The North Carolina State University Mass Spectrometry Facility at the Cutting Edge of Scientific Research}, author={Kandhi, V. and Williams, T. Islam}, year={2013} }
 @article{booker_burkey_jones_2012, title={Re-evaluating the role of ascorbic acid and phenolic glycosides in ozone scavenging in the leaf apoplast of Arabidopsis thaliana L.}, volume={8}, url={http://europepmc.org/abstract/med/22380512}, DOI={10.1111/j.1365-3040.2012.02502.x}, abstractNote={ABSTRACTPhenolic glycosides are effective reactive oxygen scavengers and peroxidase substrates, suggesting that compounds in addition to ascorbate may have functional importance in defence responses against ozone (O3), especially in the leaf apoplast. The apoplastic concentrations of ascorbic acid (AA) and phenolic glycosides in Arabidopsis thaliana L. Col‐0 wild‐type plants were determined following exposure to a range of O3 concentrations (5, 125 or 175 nL L−1) in controlled environment chambers. AA in leaf apoplast extracts was almost entirely oxidized in all treatments, suggesting that O3 scavenging by direct reactions with reduced AA was very limited. In regard to phenolics, O3 stimulated transcription of numerous phenylpropanoid pathway genes and increased the apoplastic concentration of sinapoyl malate. However, modelling of O3 scavenging in the apoplast indicated that sinapoyl malate concentrations were too low to be effective protectants. Furthermore, null mutants for sinapoyl esters (fah1‐7), kaempferol glycosides (tt4‐1) and the double mutant (tt4‐1/fah1‐7) were equally sensitive to chronic O3 as Ler‐0 wild‐type plants. These results indicate that current understanding of O3 defence schemes deserves reassessment as mechanisms other than direct scavenging of O3 by extracellular AA and antioxidant activity of some phenolics may predominate in some plant species.}, journal={Plant, cell & environment}, author={Booker, FL and Burkey, KO and Jones, AM}, year={2012}, month={Mar} }
 @inproceedings{swarup_williams_anholt_2011, title={Behavioral Response Profiles of Odorant Binding Proteins in Drosophila melanogaster}, author={Swarup, S. and Williams, T.Islam and Anholt, R.R.H.}, year={2011} }
 @inproceedings{swarup_williams_anholt_2011, title={Functional Dissection of Odorant Binding Protein Genes in Drosophila melanogaster}, author={Swarup, S. and Williams, T.Islam and Anholt, R.R.H.}, year={2011} }
 @article{swarup_williams_anholt_2011, title={Functional dissection of Odorant binding protein genes in Drosophila melanogaster}, volume={10}, ISSN={["1601-183X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79961026622&partnerID=MN8TOARS}, DOI={10.1111/j.1601-183x.2011.00704.x}, abstractNote={Most organisms rely on olfaction for survival and reproduction. The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems and serves as a prototype for understanding insect olfaction. Olfaction in Drosophila is mediated by multigene families of odorant receptors and odorant binding proteins (OBPs). Although molecular response profiles of odorant receptors have been well documented, the contributions of OBPs to olfactory behavior remain largely unknown. Here, we used RNAi‐mediated suppression of Obp gene expression and measurements of behavioral responses to 16 ecologically relevant odorants to systematically dissect the functions of 17 OBPs. We quantified the effectiveness of RNAi‐mediated suppression by quantitative real‐time polymerase chain reaction and used a proteomic liquid chromatography and tandem mass spectrometry procedure to show target‐specific suppression of OBPs expressed in the antennae. Flies in which expression of a specific OBP is suppressed often show altered behavioral responses to more than one, but not all, odorants, in a sex‐dependent manner. Similarly, responses to a specific odorant are frequently affected by suppression of expression of multiple, but not all, OBPs. These results show that OBPs are essential for mediating olfactory behavioral responses and suggest that OBP‐dependent odorant recognition is combinatorial.}, number={6}, journal={GENES BRAIN AND BEHAVIOR}, author={Swarup, S. and Williams, T. I. and Anholt, R. R. H.}, year={2011}, month={Aug}, pages={648–657} }
 @inproceedings{williams_swarup_zhou_anholt_2011, place={Denver, CO}, title={Proteomics of Olfaction: Identification and Relative Quantification of Odorant Binding Proteins in the Antennae of Drosophila melanogaster}, author={Williams, T.Islam and Swarup, S. and Zhou, S. and Anholt, R.R.H.}, year={2011} }
 @inproceedings{williams_2009, title={Accurate Mass Measurements in FTMS with Automatic Gain Control}, author={Williams, T. Islam}, year={2009} }
 @article{zhao_ghosh_zheng_lyndon_williams_stang_2009, title={Construction of Coordination-Driven Self-Assembled [5+5] Pentagons Using Metal-Carbonyl Dipyridine Ligands}, volume={48}, ISSN={["1520-510X"]}, url={http://europepmc.org/abstract/med/19476323}, DOI={10.1021/ic900649m}, abstractNote={The coordination-driven self-assembly of two metal-carbonyl-cluster-coordinated dipyridyl donors, (4-C(5)H(4)N)(2)C[triple bond]CCo(2)(CO)(6) (1) and (4-C(5)H(4)N)(2)C[triple bond]CMo(2)Cp(2)(CO)(4) (2), with a linear diplatinum(II) acceptor ligand was investigated. The structures of the resulting self-assembled polygons were found to be controlled by the steric bulk of the metal-carbonyl cluster adduct. The use of a sterically less imposing ligand 1 resulted in a pentagon-hexagon mixture, which was characterized by electrospray ionization time-of-flight mass spectroscopy. The exclusive formation of a [5 + 5] pentagon was achieved by the self-assembly of the bulkier molybdenum donor ligand 2 with a linear organoplatinum(II) acceptor ligand. Molecular force field modeling was used to study the structural details of the pentagonal and hexagonal architectures. The first Fe(3)-Co(6)-Pt(6) trimetal [3 + 3] hexagon was also synthesized via the combination of 1 with a 120 degrees ferrocenyldiplatinum(II) acceptor.}, number={13}, journal={INORGANIC CHEMISTRY}, author={Zhao, Liang and Ghosh, Koushik and Zheng, Yaorong and Lyndon, Matthew M. and Williams, Taufika Islam and Stang, Peter J.}, year={2009}, month={Jul}, pages={5590–5592} }
 @inproceedings{williams_sun_yeh_sampson_muddiman_chiang_2009, title={Proteomic Profiling of Populus trichocarpa for the Interrogation of Molecular Mechanisms behind Wood Formation}, author={Williams, T.Islam and Sun, Y.-H. and Yeh, T.-F. and Sampson, J.S. and Muddiman, D.C. and Chiang, V.}, year={2009} }
 @inproceedings{bereman_williams_kalli_cliby_muddiman_2009, title={The Development of Nano LC Mass Spectrometric Methods for Profiling Glycans in Epithelial Ovarian Cancer (EOC) and Control Plasma}, author={Bereman, M.S. and Williams, T.Islam and Kalli, K.R. and Cliby, W.A. and Muddiman, D.C.}, year={2009} }
 @article{anholt_williams_2010, title={The Soluble Proteome of the Drosophila Antenna}, volume={35}, ISSN={1464-3553 0379-864X}, url={http://dx.doi.org/10.1093/chemse/bjp073}, DOI={10.1093/chemse/bjp073}, abstractNote={The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems. Identification of proteins contained in the third antennal segment, the main olfactory organ, has previously relied primarily on immunohistochemistry, and although such studies and in situ hybridization studies are informative, they focus generally on one or few gene products at a time, and quantification is difficult. In addition, purification of native proteins from the antenna is challenging because it is small and encased in a hard cuticle. Here, we describe a simple method for the large-scale detection of soluble proteins from the Drosophila antenna by chromatographic separation of tryptic peptides followed by tandem mass spectrometry with femtomole detection sensitivities. Examination of the identities of these proteins indicates that they originate both from the extracellular perilymph and from the cytoplasm of disrupted cells. We identified enzymes involved with intermediary metabolism, proteins associated with regulation of gene expression, nucleic acid metabolism and protein metabolism, proteins associated with microtubular transport, 8 odorant-binding proteins, protective enzymes associated with antibacterial defense and defense against oxidative damage, cuticular proteins, and proteins of unknown function, which represented about one-third of all soluble proteins. The procedure described here opens the way for precise quantification of any target protein in the Drosophila antenna and should be readily applicable to antennae from other insects.}, number={1}, journal={Chemical Senses}, publisher={Oxford University Press (OUP)}, author={Anholt, Robert R.H. and Williams, Taufika Islam}, year={2010}, month={Jan}, pages={21–30} }
 @inproceedings{williams_bereman_nielsen_kalli_cliby_muddiman_2008, title={A Combinatorial Approach: The Use of MALDI-MS and Nano LC-MS for Glycan Biomarker Discovery}, author={Williams, T.Islam and Bereman, M.S. and Nielsen, D.M. and Kalli, K.R. and Cliby, W.A. and Muddiman, D.C.}, year={2008} }
 @inproceedings{bereman_williams_hawkridge_muddiman_2008, title={Analysis of O-linked Glycans Derived from Normal and Diseased EOC Plasma by Nano LC-ESI-FTICR Mass Spectrometry}, author={Bereman, M.S. and Williams, T.Islam and Hawkridge, A.M. and Muddiman, D.C.}, year={2008} }
 @misc{williams_muddiman_2008, title={Applications of Carbohydrate Profiling in Ovarian Cancer Plasma Glycoproteins}, author={Williams, T.Islam and Muddiman, D.C.}, year={2008} }
 @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={43}, ISSN={["1096-9888"]}, url={http://europepmc.org/abstract/med/18563853}, DOI={10.1002/jms.1451}, abstractNote={AbstractOperation 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={Dec}, pages={1659–1663} }
 @article{bereman_williams_muddiman_2009, title={Development of a nanoLC LTQ Orbitrap Mass Spectrometric Method for Profiling Glycans Derived from Plasma from Healthy, Benign Tumor Control, and Epithelial Ovarian Cancer Patients}, volume={81}, ISSN={["1520-6882"]}, url={http://europepmc.org/abstract/med/19113831}, DOI={10.1021/ac802262w}, abstractNote={We report the development of split-less nano-flow liquid chromatography mass spectrometric analysis of glycans chemically cleaved from glycoproteins in plasma. Porous graphitized carbon operating under reverse-phase conditions and an amide-based stationary phase operating under hydrophilic interaction conditions are quantitatively compared for glycan separation. Both stationary phases demonstrated similar column efficiencies and excellent retention time reproducibility without an internal standard to correct for retention time shift. The 95% confidence intervals of the mean retention times were +/-4 s across 5 days of analysis for both stationary phases; however, the amide stationary phase was observed to be more robust. The high mass measurement accuracy of less than 2 ppm and fragmentation spectra provided highly confident identifications along with structural information. In addition, data are compared among samples derived from 10 healthy controls, 10 controls with a differential diagnosis of benign gynecologic tumors, and 10 diseased epithelial ovarian cancer patients (EOC). Two fucosylated glycans were found to be up-regulated in healthy controls and provided an accurate diagnostic value with an area under the receiver operator characteristic curve of 0.87. However, these same glycans provided a significantly less diagnostic value when used to differentiate EOC from benign tumor control samples with an area under the curve of 0.73.}, number={3}, journal={ANALYTICAL CHEMISTRY}, author={Bereman, Michael S. and Williams, Taufika Islam and Muddiman, David C.}, year={2009}, month={Feb}, pages={1130–1136} }
 @inproceedings{williams_muddiman_2008, title={Epithelial Ovarian Cancer Detection by Glycan Profiling in Blood}, author={Williams, T.Islam and Muddiman, D.C.}, year={2008} }
 @inproceedings{bereman_williams_kalli_cliby_muddiman_2008, place={Athens, GA}, title={Glycan Analysis by Nano LC-MS: Applications for Biomarker Discovery in Epithelial Ovarian Cancer (EOC)}, author={Bereman, M.S. and Williams, T.Islam and Kalli, K.R. and Cliby, W.A. and Muddiman, D.C.}, year={2008} }
 @inproceedings{williams_muddiman_2008, title={Glycan Profiling in Plasma: Fundamentals and Applications to Ovarian Cancer}, author={Williams, T.Islam and Muddiman, D.C.}, year={2008} }
 @inproceedings{williams_bereman_nielsen_kalli_cliby_muddiman_2008, place={San Diego, San Diego, CA}, title={In Search of Epithelial Ovarian Cancer Molecular Markers by MALDI-FT-ICR-MS and NANO-LC-LTQ-ORBITRAP-MS}, author={Williams, T.Islam and Bereman, M.S. and Nielsen, D.M. and Kalli, K.R. and Cliby, W.A. and Muddiman, D.C.}, year={2008} }
 @inproceedings{williams_bereman_williams_muddiman_2008, title={Innovative Technology Development Directed at the Elucidation of Biomarkers for the Detection of Early-Stage Ovarian Cancer}, author={Williams, T.Islam and Bereman, M.S. and Williams, D.Keith and Muddiman, D.C.}, year={2008} }
 @article{williams_saggese_toups_frahm_an_li_lebrilla_muddiman_2008, title={Investigations with O-linked protein glycosylations by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={43}, ISSN={["1076-5174"]}, url={http://europepmc.org/abstract/med/18324610}, DOI={10.1002/jms.1398}, abstractNote={AbstractPosttranslational modifications such as glycosylation can play a fundamental role in signaling pathways that transform an ordinary cell into a malignant one. The development of a protocol to detect these changes in the preliminary stages of disease can lead to a sensitive and specific diagnostic for the early detection of malignancies such as ovarian cancer in which differential glycan patterns are linked to etiology and progression. Small variations in instrument parameters and sample preparation techniques are known to have significant influence on the outcome of an experiment. For an experiment to be effective and reproducible, these parameters must be optimized for the analyte(s) under study. We present a detailed examination of sample preparation and matrix‐assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI‐FT‐ICR‐MS) analysis of O‐linked glycans globally cleaved from mucin glycoproteins. Experiments with stable isotope‐labeled biomolecules allowed for the establishment of appropriate acquisition times and excitation voltages for MALDI‐FT‐ICR‐MS of oligosaccharides. Quadrupole ion guide optimization studies with mucin glycans identified conditions for the comprehensive analysis of the entire mass range of O‐linked carbohydrates in this glycoprotein. Separately optimized experimental parameters were integrated in a method that allowed for the effective study of O‐linked glycans. Copyright © 2008 John Wiley & Sons, Ltd.}, number={9}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Williams, Taufika Islam and Saggese, Diana A. and Toups, Kristina L. and Frahm, Jennifer L. and An, Hyun Joo and Li, Bensheng and Lebrilla, Carlito B. and Muddiman, David C.}, year={2008}, month={Sep}, pages={1215–1223} }
 @inproceedings{williams_nielsen_cliby_kalli_muddiman_2008, place={Denver, CO}, title={Mining the Plasma Glycome for Epithelial Ovarian Cancer Biomarker Discovery}, author={Williams, T.Islam and Nielsen, D.M. and Cliby, W.A. and Kalli, K.R. and Muddiman, D.C.}, year={2008} }
 @article{williams_saggese_muddiman_2008, title={Studying O-linked protein glycosylations in human plasma}, volume={7}, ISSN={["1535-3893"]}, url={http://europepmc.org/abstract/med/18422354}, DOI={10.1021/pr800066e}, abstractNote={Recent investigations have implicated aberrant glycosylations in various malignancies, including epithelial ovarian cancer (EOC). The protocol here identifies O-linked carbohydrate patterns in EOC plasma glycoproteins through chemical cleavage and purification of these glycans. Dialyzed plasma is subjected to reductive beta-elimination with alkaline borohydride to release O-linked oligosaccharides from glycoproteins. Enrichment of released glycans, as well as removal of peptide and other contaminants, is followed by carbohydrate pattern analysis with MALDI-FT-ICR-MS.}, number={6}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Williams, Taufika Islam and Saggese, Diana A. and Muddiman, David C.}, year={2008}, month={Jun}, pages={2562–2568} }
 @inproceedings{bereman_williams_muddiman_2008, title={The Development of a Nano-LC Mass Spectrometric Method for Profiling Glycans in Epithelial Ovarian Cancer (EOC) and Control Plasma}, author={Bereman, M.S. and Williams, T.Islam and Muddiman, D.C.}, year={2008} }
 @inproceedings{chadwick_williams_williams_muddiman_2007, title={Calibration Laws Based on Multiple Linear Regression Applied to MALDI-FT-ICR-MS}, author={Chadwick, M.A. and Williams, T.Islam and Williams, D.K., Jr. and Muddiman, D.C.}, year={2007} }
 @article{bereman_williams_muddiman_2007, title={Carbohydrate analysis by desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={79}, ISSN={["0003-2700"]}, url={http://europepmc.org/abstract/med/17918969}, DOI={10.1021/ac0713858}, abstractNote={We report the use of desorption electrospray ionization hybrid Fourier transform ion cyclotron resonance mass spectrometry (DESI-FT-ICR-MS) for the analysis of carbohydrates. Spectra of neat carbohydrates are presented along with their mass measurement accuracies and limits of detection. Furthermore, a comparison is made between the analyses of O-linked glycans from mucin by DESI-FT-ICR-MS and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Finally, glycans from mucin are identified by using the high mass measurement accuracy and tandem MS capabilities afforded by the hybrid FT-ICR-MS platform.}, number={22}, journal={ANALYTICAL CHEMISTRY}, author={Bereman, Michael S. and Williams, Taufika Islam and Muddiman, David C.}, year={2007}, month={Nov}, pages={8812–8815} }
 @inproceedings{bereman_williams_muddiman_2007, title={Characterization and Biological Applications of Desorption Electrospray Ionization Coupled to Hybrid FT-ICR Mass Spectrometry}, author={Bereman, M.S. and Williams, T.Islam and Muddiman, D.C.}, year={2007} }
 @article{williams_saggese_wilcox_martin_muddiman_2007, title={Effect of matrix crystal structure on ion abundance of carbohydrates by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={21}, ISSN={["0951-4198"]}, url={http://europepmc.org/abstract/med/17279479}, DOI={10.1002/rcm.2904}, abstractNote={AbstractSample preparation techniques for carbohydrate analysis using matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) are explored, with particular emphasis on analyte/matrix co‐crystallization procedures. While carbohydrates are known to prefer 2,5‐dihydroxybenzoic acid (2,5‐DHB) as the matrix of choice, these analytes are quite specific about matrix crystal structure, which in turn is dependent on the rate of drying of analyte/matrix spots on the MALDI target. With N‐acetylglucosamine (GlcNAc) and N‐acetylneuraminic acid (sialic acid or NeuAc) as test monosaccharides, significant increases in ion abundances are demonstrated with 2,5‐DHB/NeuAc spots (>10‐fold improvement) and 2,5‐DHB/GlcNAc spots (∼5‐fold improvement) with active drying. The fine structure of crystals generated in active and passive drying was investigated using powder diffraction. Passively dried samples were shown to consist of an ordered polymorph, crystallizing in the space group P21/a, while the actively dried samples produced a disordered phase crystallizing in the space group Pa. These data provide the wherewithal to engineer a matrix best suited for carbohydrate analyses. Copyright © 2007 John Wiley & Sons, Ltd.}, number={5}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Williams, Taufika Islam and Saggese, Diana A. and Wilcox, Robert J. and Martin, James D. and Muddiman, David C.}, year={2007}, pages={807–811} }
 @misc{williams_toups_saggese_kalli_cliby_muddiman_2007, title={Epithelial ovarian cancer: Disease etiology, treatment, detection, and investigational gene, metabolite, and protein biomarkers}, volume={6}, ISSN={["1535-3907"]}, url={http://europepmc.org/abstract/med/17583933}, DOI={10.1021/pr070041v}, abstractNote={Cancer research in recent years has immensely benefited from the development of novel technologies that enable scientists to perform detailed investigations of genomes, transcriptomes, proteomes, and metabolomes. This has invariably furthered knowledge of tumorigenesis and etiology of cancer. The resulting information can, in the foreseeable future, effect a significant change in the pace of cancer research, thereby producing improvements in patient care. Ovarian cancer in particular has received the interest of the scientific community, being the most frequent cause of death from gynecological cancers, characterized by few early symptoms, diagnosis at an advanced stage, as well as poor prognosis. Ovarian cancer is a malignancy in which normal ovarian cells begin to grow in an uncontrolled, abnormal manner and produce tumors in one or both ovaries. Epithelial cancers, the most common ovarian cancers (>80%), develop from cells lining the ovarian surface. Most ovarian cancer research is primarily focused on the early detection and treatment of epithelial ovarian cancer, the more common ovarian malignancy. This review offers an introduction to ovarian cancer, with particular emphasis on human epithelial ovarian cancer. Current methods of detection and therapy are discussed. A survey of promising new protein, gene, and metabolite biomarkers on the horizon is provided. Future prospects for improved diagnosis are offered.}, number={8}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Williams, Taufika Islam and Toups, Kristina L. and Saggese, Diana A. and Kalli, Kimberly R. and Cliby, William A. and Muddiman, David C.}, year={2007}, month={Aug}, pages={2936–2962} }
 @inproceedings{saggese_williams_wilcox_martin_an_li_lebrilla_muddiman_2007, title={Investigations with O-linked Protein Glycosylations by MALDI-FT-ICR-MS}, author={Saggese, D.A. and Williams, T.Islam and Wilcox, R.J. and Martin, J.D. and An, H.J. and Li, B. and Lebrilla, C.B. and Muddiman, D.C.}, year={2007} }
 @inproceedings{toups_williams_zheng_frahm_muddiman_2007, title={MALDI-FT-ICR-MS Quantification of Peptides and Oligosaccharides using Stable-Isotope Labels}, author={Toups, K.L. and Williams, T.Islam and Zheng, J. and Frahm, J.L. and Muddiman, D.C.}, year={2007} }
 @inproceedings{williams_sampson_hawkridge_cliby_muddiman_2007, title={O-linked Protein Glycosylations in Plasma as Biomarkers for Epithelial Ovarian Cancer}, author={Williams, T.Islam and Sampson, J.S. and Hawkridge, A.M. and Cliby, W.A. and Muddiman, D.C.}, year={2007} }
 @inproceedings{muddiman_hawkridge_williams_cliby_burnett_2007, title={Plasma Biomarker Discovery and Analysis using FT-ICR Mass Spectrometry}, author={Muddiman, D.C. and Hawkridge, A.M. and Williams, T.Islam and Cliby, W.A. and Burnett, J.}, year={2007} }
 @inproceedings{bereman_williams_muddiman_2007, title={The Development and Characterization of a Desorption Electrospray Ionization Source Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (DESI-FT-ICR-MS) for Biological Analyses}, author={Bereman, M.S. and Williams, T.Islam and Muddiman, D.C.}, year={2007} }
 @article{williams_combs_thakur_strobel_lynn_2006, title={A novel Bicine running buffer system for doubled sodium dodecyl sulfate – polyacrylamide gel electrophoresis of membrane proteins}, volume={27}, ISSN={0173-0835 1522-2683}, url={http://dx.doi.org/10.1002/elps.200500730}, DOI={10.1002/elps.200500730}, abstractNote={AbstractA novel, Bicine‐based SDS‐PAGE buffer system was developed for the analysis of membrane proteins. The method involves molecular weight‐based separations of fully denatured and solubilized proteins in two dimensions. This doubled SDS‐PAGE (dSDS‐PAGE) approach produced a diagonal arrangement of protein spots and successfully circumvented problems associated with membrane proteome analysis involving traditional gel‐based methods. Membrane proteins from the anaerobic bacterium Clostridium thermocellum were used for these investigations. Tricine‐dSDS‐PAGE and the newly developed Bicine‐dSDS‐PAGE were compared with the standard glycine‐dSDS‐PAGE (Laemmli protocol) in their suitability to separate C. thermocellum membrane proteins. Large‐format gel experiments using optimized gel preparation and running buffer conditions revealed a 112% increase in protein spot count for Tricine‐dSDS‐PAGE and a 151% increase for Bicine‐dSDS‐PAGE, compared to glycine‐dSDS‐PAGE. The data clearly indicated that Bicine‐dSDS‐PAGE is a superior method for the analysis of membrane proteins, providing enhanced resolution and protein representation.}, number={14}, journal={Electrophoresis}, publisher={Wiley}, author={Williams, Taufika Islam and Combs, Jennifer C. and Thakur, Anup P. and Strobel, Herbert J. and Lynn, Bert C.}, year={2006}, month={Jul}, pages={2984–2995} }
 @article{williams_combs_lynn_strobel_2007, title={Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum}, volume={74}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/S00253-006-0689-7}, DOI={10.1007/s00253-006-0689-7}, abstractNote={Clostridium thermocellum, a cellulolytic, thermophilic anaerobe, has potential for commercial exploitation in converting fibrous biomass to ethanol. However, ethanol concentrations above 1% (w/v) are inhibitory to growth and fermentation, and this limits industrial application of the organism. Recent work with ethanol-adapted strains suggested that protein changes occurred during ethanol adaptation, particularly in the membrane proteome. A two-stage Bicine-doubled sodium dodecyl sulfate-polyacrylamide gel electrophoresis protocol was designed to separate membrane proteins and circumvent problems associated with membrane protein analysis using traditional gel-based proteomics approaches. Wild-type and ethanol-adapted C. thermocellum membranes displayed similar spot diversity and approximately 60% of proteins identified from purified membrane fractions were observed to be differentially expressed in the two strains. A majority (73%) of differentially expressed proteins were down-regulated in the ethanol-adapted strain. Based on putative identifications, a significant proportion of these down-regulated proteins were involved with carbohydrate transport and metabolism. Approximately one-third of the up-regulated proteins in the ethanol-adapted species were associated with chemotaxis and signal transduction. Overall, the results suggested that membrane-associated proteins in the ethanol-adapted strain are either being synthesized in lower quantities or not properly incorporated into the cell membrane.}, number={2}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Williams, Taufika Islam and Combs, Jennifer C. and Lynn, Bert C. and Strobel, Herbert J.}, year={2007}, month={Nov}, pages={422–432} }
 @article{williams_lovell_lynn_2005, title={Analysis of derivatized biogenic aldehydes by LC tandem mass spectrometry.}, volume={5}, url={http://europepmc.org/abstract/med/15889933}, DOI={10.1021/ac048265+}, abstractNote={Lipid peroxidation has been linked to the etiology of several diseases, including Alzheimer's disease (AD). End products of this phenomenon include low molecular weight, water-soluble aldehydes, compounds that covalently modify proteins and nucleic acids, thereby altering function. Aliphatic aldehydes (C3-C10) are generated during lipid peroxidation, along with alpha,beta-unsaturated aldehydes, including acrolein and 4-hydroxynonenal (HNE). The Hantzsch reaction was used to produce heterocyclic aldehyde derivatives that can be conveniently analyzed with mass spectrometry. Liquid chromatographic analyses revealed increasing retention times from derivatized methanal to octanal. HNE derivatives were observed to elute between heptanal and octanal derivatives, while the acrolein derivatives had a retention time similar to the propanal derivative. Smaller aliphatic aldehyde derivatives fragmented in a similar manner to produce a base peak of m/z 273, while the larger derivatives yielded m/z 274 as the base peak. Acrolein and HNE derivatives fragmented in a slightly different manner compared to their aliphatic counterparts. Calibration plots of aliphatic and unsaturated aldehydes were linear (r2 >/= 0.99) in the concentration range explored (approximately 5-1500 pg on column). The LC-MS/MS methodology developed here will be used in subsequent studies to determine aldehyde concentrations for comparing age-matched controls to AD tissues from human subjects.}, number={10}, journal={Analytical chemistry}, author={Williams, TI and Lovell, MA and Lynn, BC}, year={2005}, month={May}, pages={3383–3389} }
 @article{williams_lynn_markesbery_lovell_2006, title={Increased levels of 4-hydroxynonenal and acrolein, neurotoxic markers of lipid peroxidation, in the brain in Mild Cognitive Impairment and early Alzheimer's disease}, volume={27}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33744935554&partnerID=MN8TOARS}, DOI={10.1016/j.neurobiolaging.2005.06.004}, abstractNote={Previous studies show increased levels of lipid peroxidation and neurotoxic by-products of lipid peroxidation including 4-hydroxynonenal (HNE) and acrolein in vulnerable regions of the Alzheimer's disease (AD) brain. To determine if lipid peroxidation occurs early in progression of AD, we analyzed levels of HNE and acrolein in the hippocampus/parahippocampal gyrus (HPG), superior and middle temporal gyrus (SMTG) and cerebellum (CER) of 7 subjects with Mild Cognitive Impairment (MCI), six subjects with early AD (EAD) and sevem age-matched control subjects using liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI/MS/MS). Our data show that there is a statistically significant (P < 0.05) increase in HNE in HPG, SMTG and CER in MCI compared to age-matched control subjects. Specimens of SMTG also showed a significant increase in levels of acrolein in MCI. Comparison of EAD and control subjects showed a statistically significant increase in HNE in HPG and SMTG and a significant increase in acrolein in all three brain regions studied. We did not observe any statistically significant differences between MCI and EAD specimens. These results suggest that lipid peroxidation occurs early in the pathogenesis of AD.}, number={8}, journal={Neurobiology of Aging}, author={Williams, TI and Lynn, BC and Markesbery, WR and Lovell, MA}, year={2006}, pages={1094–1099} }
 @phdthesis{methods development in biological mass spectrometry: applications in  small molecule research and  proteomics_2005, url={https://uknowledge.uky.edu/cgi/viewcontent.cgi?referer=&httpsredir=1&article=1291&context=gradschool_diss}, year={2005}, month={Dec} }
 @misc{williams_lynn_2005, title={Methods Development in Biological Mass Spectrometry: Applications in Small Molecule Research and Proteomics}, author={Williams, T.Islam and Lynn, B.C.}, year={2005} }
 @inproceedings{williams_combs_lynn_strobel_2005, title={Proteomic Profile Changes in Membranes of Ethanol-Tolerant Clostridium thermocellum}, author={Williams, T.Islam and Combs, J.C. and Lynn, B.C. and Strobel, H.J.}, year={2005} }
 @inproceedings{williams_combs_strobel_lynn_2005, title={The Membrane Proteome of Clostridium Thermocellum by MALDI-TOF-MS}, author={Williams, T.Islam and Combs, J.C. and Strobel, H.G. and Lynn, B.C.}, year={2005} }
 @inproceedings{williams_lovell_lynn_2004, title={Analysis of Derivatized Biogenic Aldehydes by HPLC Tandem Mass Spectrometry}, author={Williams, T.Islam and Lovell, M.A. and Lynn, B.C.}, year={2004} }
 @inproceedings{williams_liu_lynn_2003, title={Analysis of Aldehydes and Aldehyde-DNA Adducts by HPLC Tandem Mass Spectrometry}, author={Williams, T.Islam and Liu, X. and Lynn, B.C.}, year={2003} }
 @article{williams_denault_cooks_2001, title={Proton affinity of deuterated acetonitrile estimated by the kinetic method with full entropy analysis}, volume={210}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035860247&partnerID=MN8TOARS}, DOI={10.1016/S1387-3806(01)00455-9}, abstractNote={Branching ratios for the dissociation of proton-bound dimers of selected alkyl nitriles, [R1CN⋯H+⋯NCR2], have been measured as a function of collision energy, using a triple quadrupole mass spectrometer. The system shows a small collision energy dependence consistent with small differences in entropy requirements for the competing fragmentation channels. The extended form of the kinetic method provides a value for the proton affinity and an approximate value for the relative entropy difference between the two dissociation channels (which corresponds approximately to the relative entropy of protonation of the two bases). A comparison is made between these results and those from earlier standard kinetic method data treatments. The proton affinity of d3-acetonitrile, estimated by the extended kinetic method, is 186.3 ± 1.2 (±1.4) kcal mol−1, where the standard deviation is given, followed by the 90% confidence limits in parentheses. The proton affinity of acetonitrile, estimated using the extended kinetic method as 188.2 ± 1.2 (±1.4) kcal mol−1, is statistically the same as that obtained for d3-acetonitrile. The relative entropies of protonation, Δ(ΔS), for d3-acetonitrile and acetonitrile, referenced to a series of alkyl nitriles, are 1.8 ± 0.3 (±0.3) and −1.1 ± 0.3 (±0.3) cal mol−1 K−1, respectively. Direct comparison of the isotopomers of acetonitrile using the standard and extended kinetic methods was employed to arrive at a more accurate value for the proton affinity difference between d3-acetonitrile and acetonitrile, and this method yielded a difference of ∼0.2 kcal mol−1. The direct comparison was also used to show that the proton affinity difference is a result of isotopic substitution. Normal secondary kinetic isotope effects were observed for the dissociation of the proton-bound dimer, CH3CN⋯H+⋯CD3CN. The branching ratio, kH/kD, was constant at 1.2 over the laboratory collision energy range of 5–50 eV.}, number={211}, journal={International Journal of Mass Spectrometry}, author={Williams, T.I. and Denault, J.W. and Cooks, R.G.}, year={2001}, pages={133–146} }
 @inproceedings{islam_chambers_1998, title={Electrochemical Analysis of DNA Bioconjugates}, author={Islam, T. and Chambers, J.Q.}, year={1998} }
 @misc{williams_chambers_1997, title={Electrochemical Analysis of DNA Bioconjugates}, author={Williams, T.Islam and Chambers, J.Q.}, year={1997} }
 @inproceedings{dupuy_flueck_islam_seebach_1997, place={San Francisco, CA}, title={Promoting Science for Fun at a Local Inner City School}, author={Dupuy, W. and Flueck, M. and Islam, T. and Seebach, D.L.}, year={1997} }