@article{andrews_dean_hawkridge_muddiman_2011, title={Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments}, volume={22}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-011-0075-2}, abstractNote={Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms.}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Andrews, Genna L. and Dean, Ralph A. and Hawkridge, Adam M. and Muddiman, David C.}, year={2011}, month={Apr}, pages={773–783} }
 @article{dixon_bereman_petitte_hawkridge_muddiman_2011, title={One-year plasma N-linked glycome intra-individual and inter-individual variability in the chicken model of spontaneous ovarian adenocarcinoma}, volume={305}, ISSN={["1387-3806"]}, url={http://europepmc.org/abstract/med/21845070}, DOI={10.1016/j.ijms.2010.05.023}, abstractNote={Spontaneous epithelial ovarian cancer (EOC) in the chicken presents a similar pathogenesis compared with humans including CA-125 expression and genetic mutational frequencies (e.g., p53). The high prevalence of spontaneous EOC chickens also provides a unique experimental model for biomarker discovery at the genomic, proteomic, glycomic, and metabolomic level. In an effort to exploit this unique model for biomarker discovery, longitudinal plasma samples were collected from chickens at three month intervals for one year. The study described herein involved cleaving the N-glycans from these longitudinal chicken plasma samples and analyzing them via nanoLC-FTMS/MS. Glycans identified in this study were previously found in human plasma and this work provides a promising methodology to enable longitudinal studies of the N-linked plasma glycome profile during EOC progression. The structure, abundance, and intra-variability and inter-variability for 35 N-linked glycans identified in this study are reported. The full potential of the chicken model for biomarker discovery has yet to be realized, but the initial interrogation of longitudinally-procured samples provides evidence that supports the value of this strategy in the search for glycomic biomarkers.}, number={2-3}, journal={INTERNATIONAL JOURNAL OF MASS SPECTROMETRY}, author={Dixon, R. Brent and Bereman, Michael S. and Petitte, James N. and Hawkridge, Adam M. and Muddiman, David C.}, year={2011}, month={Aug}, pages={79–86} }
 @article{hawkridge_wysocky_petitte_anderson_mozdziak_fletcher_horowitz_muddiman_2010, title={Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma}, volume={398}, ISSN={["1618-2650"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957867631&partnerID=MN8TOARS}, DOI={10.1007/s00216-010-3979-y}, abstractNote={The domestic chicken (Gallus domesticus) has emerged as a powerful experimental model for studying the onset and progression of spontaneous epithelial ovarian cancer (EOC) with a disease prevalence that can exceed 35% between 2 and 7 years of age. An experimental strategy for biomarker discovery is reported herein that combines the chicken model of EOC, longitudinal plasma sample collection with matched tissues, advanced mass spectrometry-based proteomics, and concepts derived from the index of individuality (Harris, Clin Chem 20: 1535-1542, 1974). Blood was drawn from 148 age-matched chickens starting at 2.5 years of age every 3 months for 1 year. At the conclusion of the 1 year sample collection period, the 73 birds that remained alive were euthanized, necropsied, and tissues were collected. Pathological assessment of resected tissues from these 73 birds confirmed that five birds (6.8%) developed EOC. A proteomics workflow including in-gel digestion, nanoLC coupled to high-performance mass spectrometry, and label-free (spectral counting) quantification was used to measure the biological intra-individual variability (CV(W)) of the chicken plasma proteome. Longitudinal plasma sample sets from two birds within the 73-bird biorepository were selected for this study; one bird was considered "healthy" and the second bird developed late-stage EOC. A total of 116 proteins from un-depleted plasma were identified with 80 proteins shared among all sample sets. Analytical variability (CV(A)) of the label-free proteomics workflow was measured using a single plasma sample analyzed five times and was found to be ≥CV(W) in both birds for 16 proteins (20%) and in either bird for 25 proteins (31%). Ovomacroglobulin (ovostatin) was found to increase (p < 0.001) over a 6 month period in the late-stage EOC bird providing an initial candidate protein for further investigation.}, number={2}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Hawkridge, Adam M. and Wysocky, Rebecca B. and Petitte, James N. and Anderson, Kenneth E. and Mozdziak, Paul E. and Fletcher, Oscar J. and Horowitz, Jonathan M. and Muddiman, David C.}, year={2010}, month={Sep}, pages={737–749} }
 @article{hawkridge_wysocky_petitte_anderson_mozdziak_fletcher_horowitz_muddiman_2010, title={Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma (vol 398, pg 737, 2010)}, volume={398}, ISSN={["1618-2642"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957848897&partnerID=MN8TOARS}, DOI={10.1007/s00216-010-4107-8}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Hawkridge, Adam M. and Wysocky, Rebecca B. and Petitte, James N. and Anderson, Kenneth E. and Mozdziak, Paul E. and Fletcher, Oscar J. and Horowitz, Jonathan M. and Muddiman, David C.}, year={2010}, month={Oct}, pages={1835–1835} }
 @article{shuford_hawkridge_burnett_muddiman_2010, title={Utilizing Spectral Counting To Quantitatively Characterize Tandem Removal of Abundant Proteins (TRAP) in Human Plasma}, volume={82}, ISSN={["0003-2700"]}, DOI={10.1021/ac102248d}, abstractNote={Biomarker discovery efforts in serum and plasma are greatly hindered by the presence of high abundance proteins that prevent the detection and quantification of less abundant, yet biologically significant, proteins. The most common method for addressing this problem is to specifically remove the few abundant proteins through immunoaffinity depletion/subtraction. Herein, we improved upon this method by utilizing multiple depletion columns in series, so as to increase the efficiency of the abundant protein removal and augment the detection/identification of less abundant plasma proteins. Spectral counting was utilized to make quantitative comparisons between undepleted plasma, plasma depleted with a single depletion column, and plasma depleted using two or three depletion columns in tandem. In the undepleted plasma only 29 lower abundance protein groups were identified with the top-scoring protein from each group having a median spectral count of 3, while in the plasma processed using a single HSA depletion column 61 such protein groups were identified with a median spectral count of 8. In comparison, 76 lesser abundant protein groups were identified with a median spectral count of 11.5 in the two column setup (i.e., HSA followed by MARS Hu14). However, in the ultimate depleted plasma sample, which was created using three depletion columns in tandem, the number of less abundant protein groups identified increase to 81 and the median spectral count for the top-scoring proteins from each group increased to 15 counts per protein. Moreover, exogenous B-type natriuretic peptide-32, which was added to the plasma as a detection benchmark at 12 μg/mL, was only detected in the plasma sample depleted using three depletion columns in tandem. Collectively, these data demonstrate that this method, tandem removal of abundant proteins or TRAP, provides superior removal efficiency compared to traditional applications and improves the depth of proteome coverage in plasma.}, number={24}, journal={ANALYTICAL CHEMISTRY}, author={Shuford, Christopher M. and Hawkridge, Adam M. and Burnett, John C., Jr. and Muddiman, David C.}, year={2010}, month={Dec}, pages={10179–10185} }
 @article{andrews_shuford_burnett_hawkridge_muddiman_2009, title={Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides}, volume={877}, ISSN={1570-0232}, url={http://dx.doi.org/10.1016/j.jchromb.2009.02.040}, DOI={10.1016/j.jchromb.2009.02.040}, abstractNote={The circulating concentration of a biomarker for congestive heart failure, Brain (B-type) Natriuretic Peptide (BNP-32), is measured using ELISA based assays in order to rapidly diagnose and monitor disease progression. The lack of molecular specificity afforded by these assays has recently come into question as emerging studies indicate there are potentially multiple heterogeneous forms of BNP in circulation with immunoreactive capabilities. In order to better understand the molecular biology of BNP-32 as it relates to congestive heart failure, it would thus be advantageous to use a detection platform such as Fourier transform ion cyclotron resonance mass spectrometry. This high resolving power mass spectrometer can provide unparalleled molecular specificity and can facilitate identification and characterization of the various molecular forms across all disease states. Unfortunately, BNP circulates at low concentrations (as low as 3fmol/mL). Thus, it will require a collaborative effort from a number of orthogonal front-end technologies to overcome the disconnect between the practical detection limits of this instrument platform and the physiological levels of BNP-32 and its alternative molecular forms. Herein, we begin optimization of these front-end techniques by first enhancing the conditions for online nanoLC-ESI-MS separations of BNP-32 and its proteolytic fragments. Through extensive analysis of various chromatographic parameters we determined that Michrom Magic C8 stationary phase used in conjunction with a continuous, vented column configuration provided advanced chromatographic performance for the nano-flow separations involving intact BNP-32 and its associated tryptic peptides. Furthermore, conditions for the tryptic digestion of BNP-32 were also studied. We demonstrate that the use of free cysteine as an alkylation quenching agent and a secondary digestion within the digestion scheme can provide targeted tryptic peptides with increased abundances. Combined, these data will serve to further augment the detection of BNP-32 by LC-MS.}, number={10}, journal={Journal of Chromatography B}, publisher={Elsevier BV}, author={Andrews, Genna L. and Shuford, Christopher M. and Burnett, John C., Jr. and Hawkridge, Adam M. and Muddiman, David C.}, year={2009}, month={Apr}, pages={948–954} }
 @article{hawkridge_muddiman_2009, title={Mass Spectrometry-Based Biomarker Discovery: Toward a Global Proteome Index of Individuality}, volume={2}, ISSN={["1936-1327"]}, DOI={10.1146/annurev.anchem.1.031207.112942}, abstractNote={Biomarker discovery and proteomics have become synonymous with mass spectrometry in recent years. Although this conflation is an injustice to the many essential biomolecular techniques widely used in biomarker-discovery platforms, it underscores the power and potential of contemporary mass spectrometry. Numerous novel and powerful technologies have been developed around mass spectrometry, proteomics, and biomarker discovery over the past 20 years to globally study complex proteomes (e.g., plasma). However, very few large-scale longitudinal studies have been carried out using these platforms to establish the analytical variability relative to true biological variability. The purpose of this review is not to cover exhaustively the applications of mass spectrometry to biomarker discovery, but rather to discuss the analytical methods and strategies that have been developed for mass spectrometry–based biomarker-discovery platforms and to place them in the context of the many challenges and opportunities yet to be addressed.}, journal={ANNUAL REVIEW OF ANALYTICAL CHEMISTRY}, author={Hawkridge, Adam M. and Muddiman, David C.}, year={2009}, pages={265–277} }
 @article{alcazar_hawkridge_collier_cousins_bhattacharya_muddiman_marin-castano_2009, title={Proteomics Characterization of Cell Membrane Blebs in Human Retinal Pigment Epithelium Cells}, volume={8}, ISSN={["1535-9484"]}, DOI={10.1074/mcp.M900203-MCP200}, abstractNote={Age-related macular degeneration (AMD) is the leading cause of legal blindness among the elderly population in the industrialized world, affecting about 14 million people in the United States alone. Smoking is a major environmental risk factor for AMD, and hydroquinone is a major component in cigarette smoke. Hydroquinone induces the formation of cell membrane blebs in human retinal pigment epithelium (RPE). Blebs may accumulate and eventually contribute first to sub-RPE deposits and then drusen formation, which is a prominent histopathologic feature in eyes with AMD. As an attempt to better understand the mechanisms involved in early AMD, we sought to investigate the proteomic profile of RPE blebs. Isolated blebs were subjected to SDS-PAGE fractionation, and in-gel trypsin-digested peptides were analyzed by LC-MS/MS that lead to the identification of a total of 314 proteins. Identified proteins were predominantly involved in oxidative phosphorylation, cell junction, focal adhesion, cytoskeleton regulation, and immunogenic processes. Importantly basigin and matrix metalloproteinase-14, key proteins involved in extracellular matrix remodeling, were identified in RPE blebs and shown to be more prevalent in AMD patients. Altogether our findings suggest, for the first time, the potential involvement of RPE blebs in eye disease and shed light on the implication of cell-derived microvesicles in human pathology.}, number={10}, journal={MOLECULAR & CELLULAR PROTEOMICS}, author={Alcazar, Oscar and Hawkridge, Adam M. and Collier, Timothy S. and Cousins, Scott W. and Bhattacharya, Sanjoy K. and Muddiman, David C. and Marin-Castano, Maria E.}, year={2009}, month={Oct}, pages={2201–2211} }
 @article{dixon_sampson_hawkridge_muddiman_2008, title={Ambient aerodynamic ionization source for remote analyte sampling and mass spectrometric analysis}, volume={80}, ISSN={["1520-6882"]}, DOI={10.1021/ac800289f}, abstractNote={The use of aerodynamic devices in ambient ionization source development has become increasingly prevalent in the field of mass spectrometry. In this study, an air ejector has been constructed from inexpensive, commercially available components to incorporate an electrospray ionization emitter within the exhaust jet of the device. This novel aerodynamic device, herein termed remote analyte sampling, transport, and ionization relay (RASTIR) was used to remotely sample neutral species in the ambient and entrain them into an electrospray plume where they were subsequently ionized and detected using a linear ion trap Fourier transform mass spectrometer. Two sets of experiments were performed in the ambient environment to demonstrate the device's utility. The first involved the remote (approximately 1 ft) vacuum collection of pure sample particulates (i.e., dry powder) from a glass slide, entrainment and ionization at the ESI emitter, and mass spectrometric detection. The second experiment involved the capture (vacuum collection) of matrix-assisted laser desorbed proteins followed by entrainment in the ESI emitter plume, multiple charging, and mass spectrometric detection. This approach is in principle a RASTIR-assisted matrix-assisted laser desorption electrospray ionization source (Sampson, J. S.; Hawkridge, A. M.; Muddiman, D. C. J. Am. Soc. Mass Spectrom. 2006, 17, 1712-1716; Rapid Commun. Mass Spectrom. 2007, 21, 1150-1154.). A detailed description of the device construction, operational parameters, and preliminary small molecule and protein data are presented.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Dixon, R. Brent and Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2008}, month={Jul}, pages={5266–5271} }
 @article{sampson_hawkridge_muddiman_2008, title={Construction of a versatile high precision ambient Ionization source for direct analysis and imaging}, volume={19}, DOI={10.1016/j.jasms.2008.06.013}, abstractNote={The design and construction of a high precision ambient ionization source matrix-assisted laser desorption electrospray ionization (MALDESI) are described in full detail, including a complete parts list. The computer controlled high precision motion control system and high repetition rate Explorer laser are demonstrated during MALDESI-FT-ICR analysis of peptides and proteins ranging from 1 to 17 kDa. The high stability ionization source platform described herein demonstrates both the advantages of the new MALDESI source and versatility for application to numerous desorption and ionization techniques.}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, author={Sampson, J. S. and Hawkridge, A. M. and Muddiman, David}, year={2008}, pages={1527–1534} }
 @article{caskey_yamamoto_addicott_shoemaker_vacek_hawkridge_muddiman_kottas_michl_stang_2008, title={Coordination-driven face-directed self-assembly of trigonal prisms. Face-based conformational chirality}, volume={130}, ISSN={["1520-5126"]}, DOI={10.1021/ja710715e}, abstractNote={The coordination-driven self-assembly of four different trigonal prisms from 3 equiv of one of four different tetrapyridyl star connectors and 6 equiv of a platinum linker dication in nitromethane is presented. This face-directed approach affords high yields without template assistance. The prisms have been characterized by multinuclear and DOSY NMR and dual ESI-FT-ICR mass spectrometry. The use of a conformationally chiral star connector leads to a conformationally chiral prism when connector arm ends attached to a vertex have a strongly correlated twist sense and chirality is communicated across polyhedral faces, edges, and vertices. Molecular mechanics results suggest that in the smallest prism 3d collective effects dominate and the all-P and all-M conformers are strongly favored. NMR data prove that the two edges of the pyridine rings in the triflate salts of 3a-3d are distinct. An Eyring plot of rates obtained from line-shape analysis and 1-D EXCHSY NMR yields an activation enthalpy DeltaH(double dagger) of approximately 12 kcal/mol and activation entropy DeltaS(double dagger) of approximately -15 cal/mol x K for the edge interconversion process, compatible with pyridine rotation around the Pt-N bond. For 3c, this behavior is observed only up to approximately 318 K. At higher temperatures, the Eyring plot is again linear but follows a very different straight line, with a DeltaH(double dagger) of approximately 35 kcal/mol and DeltaS(double dagger) of approximately 60 cal/mol x K. This highly unusual result is further investigated and discussed in the following companion paper.}, number={24}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Caskey, Douglas C. and Yamamoto, Takuya and Addicott, Chris and Shoemaker, Richard K. and Vacek, Jaroslav and Hawkridge, Adam M. and Muddiman, David C. and Kottas, Gregg S. and Michl, Josef and Stang, Peter J.}, year={2008}, month={Jun}, pages={7620–7628} }
 @article{sampson_hawkridge_muddiman_2008, title={Development and characterization of an ionization technique for analysis of biological macromolecules: Liquid matrix-assisted laser desorption electrospray ionization}, volume={80}, ISSN={["0003-2700"]}, DOI={10.1021/ac8001935}, abstractNote={We have developed an atmospheric pressure ionization technique called liquid matrix-assisted laser desorption electrospray ionization (liq-MALDESI) for the generation of multiply charged ions by laser desorption from liquid samples deposited onto a stainless steel sample target biased at a high potential. This variant of our previously reported MALDESI source does not utilize an ESI emitter to postionize neutrals. Conversely, we report desorption and ionization from a macroscopic charged droplet. We demonstrate high mass resolving power single-acquisition FT-ICR-MS analysis of peptides and proteins ranging from 1 to 8.6 kDa at atmospheric pressure. The liquid sample acts as a macroscopic charged droplet similar to those generated by electrospray ionization, whereby laser irradiation desorbs analyte from organic matrix containing charged droplets generating multiply charged ions. We have observed a singly charged radical cation of an electrochemically active species indicating oxidation occurs for analytes and therefore water; the latter would play a key role in the mechanism of ionization. Moreover, we demonstrate an increase in ion abundance and a concurrent decrease in surface tension with an increase in the applied potential.}, number={17}, journal={ANALYTICAL CHEMISTRY}, author={Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2008}, month={Sep}, pages={6773–6778} }
 @misc{hawkridge_muddiman_helmlein_cataliotti_burnett_2008, title={Effect of plasma protein depletion on BNP-32 recovery}, volume={54}, ISSN={["0009-9147"]}, DOI={10.1373/clinchem.2007.098038}, abstractNote={Depletion of abundant proteins from plasma and serum is an important initial step in many biomarker discovery platforms(1). Decreasing the concentrations of highly abundant proteins (e.g., albumin, IgG, and antitrypsin) facilitates the use of contemporary proteomics technologies, such as gel electrophoresis and mass spectrometry, for detection and identification of low-abundant proteins. Furthermore, decreasing abundant protein concentrations may also improve immunoprecipitation recovery efficiencies for targeted low-abundant species by decreasing nonspecific binding (i.e., shielding the antigen-binding domain) to the antibody and/or solid supports. A notable pitfall to depletion strategies is the potential for unintentionally removing low-abundant plasma or serum proteins. These low-abundant species may be bound specifically or nonspecifically to the depletion ligand, depletion target protein (e.g., carrier proteins), or the solid support(s). Thus, it is important to critically evaluate the effectiveness of abundant plasma protein depletion for enhancing the study of low-abundant protein biomarker(s).

We have been actively developing a targeted biomarker discovery platform for characterizing the circulating forms of B-type natriuretic peptide (BNP) that includes protein depletion strategies, immunoprecipitation, gel electrophoresis, isotope dilution (absolute quantification), and nanoflow liquid chromatography coupled to high-performance hybrid Fourier transform mass …}, number={5}, journal={CLINICAL CHEMISTRY}, author={Hawkridge, Adam M. and Muddiman, David C. and Helmlein, Denise M. and Cataliotti, Alessandro and Burnett, John C., Jr.}, year={2008}, month={May}, pages={933–934} }
 @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{georgianna_hawkridge_muddiman_payne_2008, title={Temperature-dependent regulation of proteins in Aspergillus flavus: Whole organism stable isotope labeling by amino acids}, volume={7}, ISSN={["1535-3907"]}, DOI={10.1021/pr8001047}, abstractNote={Stable isotope labeling by amino acids in cell culture (SILAC) has been used in many different organisms including yeast, mammalian cells, and Arabidopsis cell culture. We present an adaptation of this method to quickly quantify protein changes in response to environmental stimuli regulating biosynthesis of the carcinogen aflatoxin in the fungus Aspergillus flavus. Changes in relative protein concentrations in response to temperature were quantified and compared to changes in aflatoxin biosynthesis and the transcription of the aflatoxin biosynthetic genes. In a comparison between conducive (28 degrees C) and nonconducive (37 degrees C) temperatures for aflatoxin biosynthesis, 31 proteins were found to be more abundant at 37 degrees C and 18 more abundant at 28 degrees C. The change in expression of the aflatoxin pathway enzymes closely followed the strong repression of both aflatoxin biosynthesis and transcription of the aflatoxin pathway genes observed at 37 degrees C. Transcripts corresponding to the 379 proteins quantified by SILAC were analyzed using microarrays, but their expression did not always correlate well with transcript levels of encoding genes. This is the first reported labeling of a multicellular free-living prototroph using the SILAC procedure to compare (13)C(6)-arginine-labeled samples to (12)C(6)-arginine-labeled samples for quantitative proteomics. The data presented shows the utility of this procedure in quantifying changes in protein expression in response to environmental stimuli.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Georgianna, D. Ryan and Hawkridge, Adam M. and Muddiman, David C. and Payne, Gary A.}, year={2008}, month={Jul}, pages={2973–2979} }
 @article{collier_hawkridge_georgianna_payne_muddiman_2008, title={Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer}, volume={80}, ISSN={["1520-6882"]}, DOI={10.1021/ac800254z}, abstractNote={Online liquid chromatography-mass spectrometric (LC-MS) analysis of intact proteins (i.e., top-down proteomics) is a growing area of research in the mass spectrometry community. A major advantage of top-down MS characterization of proteins is that the information of the intact protein is retained over the vastly more common bottom-up approach that uses protease-generated peptides to search genomic databases for protein identification. Concurrent to the emergence of top-down MS characterization of proteins has been the development and implementation of the stable isotope labeling of amino acids in cell culture (SILAC) method for relative quantification of proteins by LC-MS. Herein we describe the qualitative and quantitative top-down characterization of proteins derived from SILAC-labeled Aspergillus flavus using nanoflow reversed-phase liquid chromatography directly coupled to a linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FTICR-MS). A. flavus is a toxic filamentous fungus that significantly impacts the agricultural economy and human health. SILAC labeling improved the confidence of protein identification, and we observed 1318 unique protein masses corresponding to 659 SILAC pairs, of which 22 were confidently identified. However, we have observed some limiting issues with regard to protein quantification using top-down MS/MS analyses of SILAC-labeled proteins. The role of SILAC labeling in the presence of competing endogenously produced amino acid residues and its impact on quantification of intact species are discussed in detail.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Collier, Timothy S. and Hawkridge, Adam M. and Georgianna, D. Ryan and Payne, Gary A. and Muddiman, David C.}, year={2008}, month={Jul}, pages={4994–5001} }
 @article{frahm_bori_comins_hawkridge_muddiman_2007, title={Achieving augmented limits of detection for peptides with hydrophobic alkyl tags}, volume={79}, ISSN={["0003-2700"]}, DOI={10.1021/ac070558q}, abstractNote={The wide range of protein concentrations found in biological matrixes presents a formidable analytical challenge in proteomics experiments. It is predicted that low-abundance proteins are the likely clinically relevant targets in disease-based proteomics analyses. To effectively analyze low-abundance proteins by electrospray ionization mass spectrometry, limits of detection must be improved upon. Previous studies have demonstrated hydrophobicity is a main determinant of the electrospray ionization response. One would expect to improve the electrospray ionization response of a hydrophilic peptide by making it more hydrophobic, thus increasing the molecule's affinity for the surface of the electrospray droplet, thereby allowing the molecule to more effectively compete for charge. In this report, we demonstrate a strategy to increase the electrospray ionization response of cysteine-containing peptides with the addition of an octylcarboxyamidomethyl modification via alkylation chemistry, which we name the ALiPHAT strategy (augmented limits of detection for peptides with hydrophobic alkyl tags). We demonstrate the relative increase in electrospray ionization response of peptides with an octylcarboxyamidomethyl modification compared to carboxyamidomethyl-modified peptides upon LC-MS analysis. Furthermore, we show the octylcarboxyamidomethyl group does not fragment or undergo neutral loss during collision-induced dissociation. Collectively, our results demonstrate the feasibility of the octylcarboxyamidomethyl modification to improve limits of detection for cysteine-containing peptides.}, number={11}, journal={ANALYTICAL CHEMISTRY}, author={Frahm, Jennifer L. and Bori, Ibrahim D. and Comins, Daniel L. and Hawkridge, Adam M. and Muddiman, David C.}, year={2007}, month={Jun}, pages={3989–3995} }
 @article{sampson_hawkridge_muddiman_2007, title={Direct characterization of intact polypeptides by matrix-assisted laser desorption electrospray ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometry}, volume={21}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.2947}, abstractNote={Abstract}, number={7}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2007}, pages={1150–1154} }
 @article{yang_hawkridge_huang_das_bunge_muddiman_stang_2007, title={New cavity rules}, volume={6}, ISSN={["1476-1122"]}, DOI={10.1021/ja066804h}, abstractNote={The design and self-assembly of novel cavity-cored metallodendrimers via noncovalent interactions are described. By employing [G0]-[G3] 120 degrees ditopic donor linkers substituted with Fréchet-type dendrons and appropriate rigid di-Pt(II) acceptor subunits, [G0]-[G3]-rhomboidal metallodendrimers and [G0]-[G3]-hexagonal, "snowflake-shaped" metallodendrimers with well-defined shape and size were prepared under mild conditions in high yields. The assemblies were characterized with multinuclear NMR ((1)H and (31)P), mass spectrometry (ESI-MS and ESI-FT-ICR-MS), and elemental analysis. Isotopically resolved mass spectrometry data support the existence of the metallodendrimers with rhomboidal and hexagonal cavities, and NMR data are consistent with the formation of all ensembles. The structures of [G0]- and [G1]-rhomboidal metallodendrimers were unambiguously confirmed via single-crystal X-ray crystallography. The shape and size of two [G3]-hexagonal metallodendrimers were investigated with MM2 force-field modeling.}, number={3}, journal={NATURE MATERIALS}, author={Yang, H. B. and Hawkridge, A. M. and Huang, S. P. D. and Das, N. and Bunge, S. D. and Muddiman, David and Stang, P. J.}, year={2007}, month={Mar}, pages={171–171} }
 @article{dixon_muddiman_hawkridge_fedorov_2007, title={Probing the mechanisms of an air amplifier using a LTQ-FT-ICR-MS and fluorescence spectroscopy}, volume={18}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2007.08.006}, abstractNote={We report the first quantitative assessment of electrosprayed droplet/ion focusing enabled by the use of a voltage-assisted air amplifier between an electrospray ionization emitter and a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (ESI-LTQ-FT-ICR-MS). A solution of fluorescent dye was electrosprayed with a stainless steel mesh screen placed in front of the MS inlet capillary acting as a gas-permeable imaging plate for fluorescence spectroscopy. Without use of the air amplifier, no detectable FT-ICR signal was observed, as well as no detectable fluorescence on the screen upon imaging using a fluorescence scanner. When the air amplifier was turned ON while electrospraying the fluorescent dye, FT-ICR mass spectra with high signal to noise ratio were obtained with an average ion injection time of 21 ms for an AGC target value of 5 x 10(5). Imaging of the screen using a fluorescence scanner produced a distinct spot of cross-sectional area approximately 33.5 mm(2) in front of the MS inlet capillary. These experimental results provide direct evidence of aerodynamic focusing of electrosprayed droplets/ions enabled by an air amplifier, resulting in improved electrospray droplet/ion capture efficiency and reduced ion injection time. A second set of experiments was carried out to explore whether the air amplifier assists in desolvation. By electrospraying a mix of quaternary amines, ratios of increasingly hydrophobic molecules were obtained. Observation of the solvophobic effect associated with electrospray ionization resulted in a higher abundance of the hydrophobic molecule. This bias was eliminated when the air amplifier was turned ON and a response indicative of the respective component concentrations of the molecules in the bulk solution was observed.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Dixon, R. Brent and Muddiman, David C. and Hawkridge, Adam M. and Fedorov, A. G.}, year={2007}, month={Nov}, pages={1909–1913} }
 @article{dixon_bereman_muddiman_hawkridge_2007, title={Remote mass spectrometric sampling of electrospray- and desorption electrospra-generated ions using an air ejector}, volume={18}, DOI={10.1016/i.jasms.2007.07.024}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, author={Dixon, R. B. and Bereman, M. S. and Muddiman, David and Hawkridge, A. M.}, year={2007}, pages={1844–1847} }
 @article{williams_hawkridge_muddiman_2007, 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}, ISSN={["1044-0305"]}, 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, Keith, Jr. and Hawkridge, Adam M. and Muddiman, David C.}, year={2007}, month={Jan}, pages={1–7} }
 @article{sampson_hawkridge_muddiman_2006, title={Generation and detection of multiply-charged peptides and proteins by matrix-assisted laser desorption electrospray ionization (MALDESI) Fourier transform ion cyclotron resonance mass spectrometry}, volume={17}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2006.08.003}, abstractNote={We report the coupling of a hybrid ionization source, matrix-assisted laser desorption electrospray ionization (MALDESI), to a Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR MS). The details of the source design and initial data are presented. Analysis of peptides and proteins ranging from 1 to 8.6 kDa resulted in high resolving power single-acquisition FT-ICR mass spectra with average charge-states highly correlated to those obtained by nanoESI, thus, providing strong evidence that the ESI process dictates the observed charge-state distribution. Importantly, unlike the recently introduced electrospray assisted laser desorption ionization (ELDI) source reported by Shiea and coworkers [1, 2], the data we have obtained to date rely on the use of an organic acid matrix. The results presented herein provide insight into the charging mechanism of this emerging ionization approach, while also expanding the utility of FT-ICR MS for top-down protein and complex mixture analysis.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2006}, month={Dec}, pages={1712–1716} }
 @article{yang_das_huang_hawkridge_diaz_arif_finn_muddiman_stang_2006, title={Incorporation of 2,6-di(4,4 '-dipyridyl)-9-thiabicyclo[3.3.1] nonane into discrete 2D supramolecules via coordination-driven self-assembly}, volume={71}, ISSN={["0022-3263"]}, DOI={10.1021/jo0608117}, abstractNote={The synthesis and characterization of three new supramolecular complexes 6-8 (a rhomboid and two hexagons) via coordination-driven self-assembly are reported in excellent yields (>90%). These assemblies have 2,6-di(4,4'-dipyridyl)-9-thiabicyclo[3.3.1]nonane 2 as the bridging tecton. All assemblies were characterized by multinuclear NMR (1H and 31P), mass spectrometry (ESI-MS and ESI-FT-ICR), and elemental analysis. The X-ray structure of the 120 degrees tecton 2 is also discussed.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Yang, Hai-Bo and Das, Neeladri and Huang, Feihe and Hawkridge, Adam M. and Diaz, David D. and Arif, Atta M. and Finn, M. G. and Muddiman, David C. and Stang, Peter J.}, year={2006}, month={Aug}, pages={6644–6647} }
 @article{yang_das_huang_hawkridge_muddiman_stang_2006, title={Molecular Architecture via Coordination:  Self-Assembly of Nanoscale Hexagonal Metallodendrimers with Designed Building Blocks}, volume={128}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja063377z}, DOI={10.1021/ja063377z}, abstractNote={The first self-assembly of nanoscale metallodendrimers that have a hexagonal cavity as a core via the directional-bonding approach is reported. All metallodendrimers were characterized by multinuclear NMR (1H and 31P), mass spectrometry (ESI-MS and ESI-FT-ICR), and elemental analysis.}, number={31}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Yang, Hai-Bo and Das, Neeladri and Huang, Feihe and Hawkridge, Adam M. and Muddiman, David C. and Stang, Peter J.}, year={2006}, month={Aug}, pages={10014–10015} }