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1.  Quantitative Profiling of Endogenous Retinoic Acid in Vivo and in Vitro by Tandem Mass Spectrometry 
Analytical chemistry  2008;80(5):1702-1708.
We report an improved tandem mass spectrometric assay for retinoic acid (RA) applicable to in vitro and in vivo biological samples. This liquid chromatography tandem mass spectrometric (LC/MS/MS) assay for direct RA quantification is the most sensitive to date, with a 62.5 attomol lower limit of detection and a linear range spanning greater than 4 orders of magnitude (from 250 attomol to 10 pmol). This assay resolves all-trans-RA (atRA) from its endogenous geometric isomers, is applicable to samples of limited size (10–20 mg of tissue), and functions with complex biological matrixes. Coefficients of variation are as follows: instrumental, ≤2.6%; intraday, 5.2% ± 0.7%; interday, 6.7% ± 0.9%. In vitro capabilities are demonstrated by quantification of endogenous RA and RA production (from retinol) in primary cultured astrocytes. Quantification of endogenous atRA and its geometric isomers in 129SV mouse serum and tissues (liver, kidney, adipose, muscle, spleen, testis, and brain) reveals in vivo utility of the assay. The ability to discriminate spatial concentrations of RA in vivo is illustrated with C57BL/6 mouse brain loci (hippocampus, cortex, olfactory bulb, thalamus, cerebellum, and striatum), as well as with Lewis rat proximal/distal mammary gland regions during various morphological stages: virgin, early pregnancy (e7), late pregnancy (e20), lactating (day 4), involuting day 1, and involuting day 11. This assay provides the sensitivity necessary for direct, endogenous RA quantification necessary to elucidate RA function, e.g., in neurogenesis, morphogenesis, and the contribution of altered RA homeostasis to diseases, such as Alzheimer’s disease, type 2 diabetes, obesity, and cancer.
doi:10.1021/ac702030f
PMCID: PMC4086453  PMID: 18251521
2.  Analysis of Covalent Modifications of Proteins by Oxidized Phospholipids Using a Novel Method of Peptide Enrichment 
Analytical chemistry  2014;86(2):1254-1262.
Free radical-induced oxidation of phospholipids contributes significantly to pathologies associated with inflammation and oxidative stress. Detection of covalent interaction between oxidized phospholipids (oxPL) and proteins by LC-MS/MS could provide valuable information about the molecular mechanisms of oxPL effects. However, such studies are very limited because of significant challenges in detection of the comparatively low levels of oxPL–protein adducts in complex biological systems. Current approaches have several limitations, most important of which is the inability to detect protein modifications by naturally occurring oxPL. We now report, for the first time, an enrichment method that can be applied to the global analysis of protein adducts with various naturally occurring oxPL in relevant biological systems. This method exploits intrinsic properties of peptides modified by oxPL, allowing highly efficient enrichment of oxPL-modified peptides from biological samples. Very low levels of oxPL–protein adducts (<2 ppm) were detected using this enrichment method in combination with LC-MS/MS. We applied the method to several model systems, including oxidation of high density lipoprotein (HDL) and interaction of human platelets with a specific oxPL, and demonstrated its extremely high efficiency and productivity. We report multiple new modifications of apolipoproteins in HDL and proteins in human platelets.
doi:10.1021/ac4035949
PMCID: PMC4084736  PMID: 24350680
3.  An O18-labeling assisted LC-MS method for assignment of aspartyl/isoaspartyl products from Asn deamidation and Asp isomerization in proteins 
Analytical chemistry  2013;85(13):6446-6452.
An O18-labeling assisted LC-MS method was designed for unambiguous assignment of aspartyl/isoaspartyl products produced by Asn deamidation and Asp isomerization. By preparing the acid- and base–catalyzed deamidation standards in H2O18, isomer-specific mass tags were introduced to aspartyl- and isoaspartyl-containing peptides, which could be easily distinguished by mass spectrometry (MS). In contrast to the traditional ways to assign the isomers based on their elution order in reverse phase HPLC, the new method is more reliable and universal. Furthermore, the new method can be applied to the entire protein digest, and is therefore more time- and cost-effective compared with existing methods that use synthetic aspartyl- and isoaspartyl-containing peptide standards. Finally, since the identification of isomers in the new method only relies on LC-MS analysis, it can be easily implemented using the most basic and inexpensive MS instrumentation, thus providing an attractive alternative to tandem MS-based approaches. The feasibility of this new method is demonstrated using a model peptide as well as the entire digest of human serum transferrin.
doi:10.1021/ac400984r
PMCID: PMC3702055  PMID: 23713887
4.  Origins of Nanoscale Damage to Glass-Sealed Platinum Electrodes with Submicrometer and Nanometer Size 
Analytical chemistry  2013;85(13):6198-6202.
Glass-sealed Pt electrodes with submicrometer and nanometer size have been successfully developed and applied for nanoscale electrochemical measurements such as scanning electrochemical microscopy (SECM). These small electrodes, however, are difficult to work with because they often lose a current response or give a low SECM feedback in current–distance curves. Here we report that these problems can be due to the nanometer-scale damage that is readily and unknowingly made to the small tips in air by electrostatic discharge or in electrolyte solution by electrochemical etching. The damaged Pt electrodes are recessed and contaminated with removed electrode materials to lower their current responses. The recession and contamination of damaged Pt UMEs are demonstrated by scanning electron microscopy and X-ray energy dispersive spectroscopy. The recessed geometry is noticeable also by SECM, but is not obvious from a cyclic voltammogram. Characterization of a damaged Pt electrode with recessed geometry only by cyclic voltammetry may underestimate electrode size from a lower limiting current owing to invalid assumption of inlaid disk geometry. Significantly, electrostatic damage can be avoided by grounding a Pt electrode and nearby objects, most importantly, an operator as a source of electrostatic charge. Electrochemical damage can be avoided by maintaining potentiostatic control of a Pt electrode without internally disconnecting the electrode from a potentiostat between voltammetric measurements. Damage-free Pt electrodes with submicrometer and nanometer size are pivotal for reliable and quantitative nanoelectrochemical measurements.
doi:10.1021/ac401316n
PMCID: PMC3727625  PMID: 23763642
5.  Evaluating the Diffusion Coefficient of Dopamine at the Cell Surface During Amperometric Detection: Disk vs. Ring Microelectrodes 
Analytical chemistry  2013;85(13):6421-6428.
During exocytosis, small quantities of neurotransmitters are released by the cell. These neurotransmitters can be detected quantitatively using electrochemical methods, principally with disk carbon fiber microelectrode amperometry. An exocytotic event then results in the recording of a current peak whose characteristic features are directly related to the mechanisms of exocytosis. We have compared two exocytotic peak populations obtained from PC12 cells with a disk carbon fiber microelectrode and with a pyrolyzed carbon ring microelectrode array, with a 500 nm ring thickness. The specific shape of the ring electrode allows for precise analysis of diffusion processes at the vicinity of the cell membrane. Peaks obtained with a ring microelectrode array show a distorted average shape, owing to increased diffusion pathways. This result has been used to evaluate the diffusion coefficient of dopamine at the surface of a cell, which is up to an order of magnitude smaller than that measured in free buffer. The lower rate of diffusion is discussed as resulting from interactions with the glycocalyx.
doi:10.1021/ac400965d
PMCID: PMC3737586  PMID: 23706095
Exocytosis; microelectrodes; glycocalyx; diffusion coefficient of dopamine; amperometric detection
6.  Controlled Generation of Double Emulsions in Air 
Analytical chemistry  2013;85(13):6190-6194.
This communication describes the controlled generation of double emulsions in the gas phase, which was carried out using an integrated emitter in a PDMS (poly(dimethylsiloxane)) microfluidic chip. The integrated emitter was formed using a molding approach, in which metal wires with desirable diameters were used as emitter molds. The generation of double emulsions in air was achieved with electrohydrodynamics actuation, which offers controllable force exerting on the double emulsions. We developed this capability for future integration of droplet microfluidics with mass spectrometry (MS), where each aqueous droplet in the microchannel is introduced into the gas phase as a double emulsion for subsequent ionization and MS analysis.
doi:10.1021/ac400844p
PMCID: PMC3747772  PMID: 23767768
7.  Paper analytical devices for fast field screening of beta lactam antibiotics and anti-tuberculosis pharmaceuticals 
Analytical chemistry  2013;85(13):6453-6460.
Reports of low quality pharmaceuticals have been on the rise in the last decade with the greatest prevalence of substandard medicines in developing countries, where lapses in manufacturing quality control or breaches in the supply chain allow substandard medicines to reach the marketplace. Here, we describe inexpensive test cards for fast field screening of pharmaceutical dosage forms containing beta lactam antibiotics or combinations of the four first-line antituberculosis (TB) drugs. The devices detect the active pharmaceutical ingredients (APIs) ampicillin, amoxicillin, rifampicin, isoniazid, ethambutol, and pyrazinamide, and also screen for substitute pharmaceuticals such as acetaminophen and chloroquine that may be found in counterfeit pharmaceuticals. The tests can detect binders and fillers like chalk, talc, and starch not revealed by traditional chromatographic methods. These paper devices contain twelve lanes, separated by hydrophobic barriers, with different reagents deposited in the lanes. The user rubs some of the solid pharmaceutical across the lanes and dips the edge of the paper into water. As water climbs up the lanes by capillary action, it triggers a library of different chemical tests and a timer to indicate when the tests are completed. The reactions in each lane generate colors to form a “color bar code” which can be analyzed visually by comparison to standard outcomes. While quantification of the APIs is poor compared to conventional analytical methods, the sensitivity and selectivity for the analytes is high enough to pick out suspicious formulations containing no API or a substitute API, as well as formulations containing APIs that have been “cut” with inactive ingredients.
doi:10.1021/ac400989p
PMCID: PMC3800146  PMID: 23725012
pharmaceutical; antiinfective; antibiotic; tuberculosis; substandard; counterfeit; falsified; fake; screening test; field test; colorimetric; paper; paper-based; microfluidic; millifluidic
8.  Label-free DNA Biosensor Based on SERS Molecular Sentinel on Nanowave Chip 
Analytical chemistry  2013;85(13):6378-6383.
Development of a rapid, cost-effective, label-free biosensor for DNA detection is important for many applications in clinical diagnosis, homeland defense, and environment monitoring. A unique label-free DNA biosensor based on Molecular Sentinel (MS) immobilized on a plasmonic ‘Nanowave’ chip, which is also referred to as a metal film over nanosphere (MFON), is presented. Its sensing mechanism is based upon the decrease of the surface-enhanced Raman scattering (SERS) intensity when Raman label tagged at one end of MS is physically separated from the MFON's surface upon DNA hybridization. This method is label-free as the target does not have to be labeled. The MFON fabrication is relatively simple and low-cost with high reproducibility based on depositing a thin shell of gold over close-packed arrays of nanospheres. The sensing process involves a single hybridization step between the DNA target sequences and the complementary MS probes on the Nanowave chip without requiring secondary hybridization or post-hybridization washing, thus resulting in rapid assay time and low reagent usage. The usefulness and potential application of the biosensor for medical diagnostics is demonstrated by detecting the human radical S-adenosyl methionine domain containing 2 (RSAD2) gene, a common inflammation biomarker.
doi:10.1021/ac400763c
PMCID: PMC4022286  PMID: 23718777
DNA Biosensor; Surface-Enhanced Raman Scattering; Molecular Sentinel; Nanowave; Metal Film over Nanosphere
10.  In Situ Electrokinetic Enhancement for Self-Assembled-Monolayer-Based Electrochemical Biosensing 
Analytical chemistry  2012;84(6):2702-2707.
This study reports a multifunctional electrode approach which directly implements electrokinetic enhancement on a self-assembled-monolayer-based electro-chemical sensor for point-of-care diagnostics. Using urinary tract infections as a model system, we demonstrate that electrokinetic enhancement, which involves in situ stirring and heating, can enhance the sensitivity of the strain specific 16S rRNA hybridization assay for 1 order of magnitude and accelerate the time-limiting incubation step with a 6-fold reduction in the incubation time. Since the same electrode platform is used for both electrochemical signal enhancement and electrochemical sensing, the multifunctional electrode approach provides a highly effective strategy toward fully integrated lab-on-a-chip systems for various biomedical applications.
doi:10.1021/ac203245j
PMCID: PMC4069200  PMID: 22397486
11.  Discovery of Undefined Protein Crosslinking Chemistry: A Comprehensive Methodology Utilizing 18O-labeling and Mass Spectrometry 
Analytical chemistry  2013;85(12):5900-5908.
Characterization of protein crosslinking, particularly without prior knowledge of the chemical nature and site of crosslinking, poses a significant challenge due to their intrinsic structural complexity and the lack of a comprehensive analytical approach. Towards this end, we have developed a generally applicable workflow—XChem-Finder that involves four stages. (1) Detection of crosslinked peptides via 18O-labeling at C-termini. (2) Determination of the putative partial sequences of each crosslinked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search. (3) Extension to full sequences based on protease specificity, the unique combination of mass, and other constraints. (4) Deduction of crosslinking chemistry and site. The mass difference between the sum of two putative full-length peptides and the crosslinked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross- linking. Combined with sequence restraint from MS/MS data, plausible crosslinking chemistry and site were inferred, and ultimately, confirmed by matching with all data. Applying our approach to a stressed IgG2 antibody, ten cross-linked peptides were discovered and found to be connected via thioether originating from disulfides at locations that had not been previously recognized. Furthermore, once the crosslink chemistry was revealed, a targeted crosslink search yielded four additional crosslinked peptides that all contain the C-terminus of the light chain.
doi:10.1021/ac400666p
PMCID: PMC3691076  PMID: 23634697
12.  Automated assignments of N- and O-site specific glycosylation with extensive glycan heterogeneity of glycoprotein mixtures 
Analytical chemistry  2013;85(12):5666-5675.
Site-specific glycosylation (SSG) of glycoproteins remains a considerable challenge and limits further progress in the areas of proteomics and glycomics. Effective methods require new approaches in sample preparation, detection, and data analysis. While the field has advanced in sample preparation and detection, automated data analysis remains an important goal. A new bioinformatics approach implemented in software called GP Finder automatically distinguishes correct assignments from random matches and compliments experimental techniques that are optimal for glycopeptides, including non-specific proteolysis and high mass resolution LC/MS/MS. SSG for multiple N- and O-glycosylation sites, including extensive glycan heterogeneity, was annotated for single proteins and protein mixtures with a 5% false-discovery rate, generating hundreds of non-random glycopeptide matches and demonstrating the proof-of-concept for a self-consistency scoring algorithm shown to be compliant with the target-decoy approach (TDA). The approach was further applied to a mixture of N-glycoproteins from unprocessed human milk and O-glycoproteins from very-low-density-lipoprotein (vLDL) particles.
doi:10.1021/ac4006556
PMCID: PMC3692395  PMID: 23662732
Glycoproteomics; site-specific glycosylation; tandem mass spectrometry; false-discovery rate; target-decoy approach
13.  Western Blotting Using Microchip Electrophoresis Interfaced to a Protein Capture Membrane 
Analytical chemistry  2013;85(12):6073-6079.
Western blotting is a commonly used assay for proteins. Despite the utility of the method, it is also characterized by long analysis times, manual operation, and lack of established miniaturized counterpart. We report a new way to Western blot which addresses these limitations. In the method, sodium dodecyl sulfate (SDS)-protein complexes are separated by sieving electrophoresis in a microfluidic device or chip. The chip is interfaced to a moving membrane so that proteins are captured in discrete zones as they migrate from the chip. Separations of SDS-protein complexes in the molecular weight range of 11 to 155 kDa were completed in 2 min with 4 × 104 theoretical plates at 460 V/cm. Migration time and peak area relative standard deviations were 3–6% and 0.2% respectively. Detection limit for actin was 0.7 nM. Assays for actin, AMP-kinase, carbonic anhydrase, and lysozyme are shown to demonstrate versatility of the method. Total analysis time including immunoassay was 22–32 min for a single sample. Because processing membrane for immunoassay is the slow step of the assay, sequential injections from different reservoirs on the chip and capture in different tracks on the same membrane allow increased throughput. As a demonstration, 9 injections were collected on one membrane and analyzed in 43 min (~5 min/sample). Further improvements in throughput are possible with more reservoirs or parallel channels.
doi:10.1021/ac400940x
PMCID: PMC3696989  PMID: 23672369
14.  Measurement of Protein Tyrosine Phosphatase Activity in Single Cells by Capillary Electrophoresis 
Analytical chemistry  2013;85(12):6136-6142.
A fluorescent peptide substrate was used to measure dephosphorylation by protein tyrosine phosphatases (PTP) in cell lysates, and single cells and to investigate the effect of environmental toxins on PTP activity in these systems. Dephosphorylation of the substrate by PTPN1 and PTPN2 obeyed Michaelis-Menten kinetics, with KM values of 770 ± 250 nM and 290 ± 54 nM, respectively. Dose-response curves and IC50 values were determined for the inhibition of these two enzymes by the environmental toxins Zn2+ and 1,2-naphthoquinone, as well as pervanadate. In A431 cell lysates, the reporter was a poor substrate for peptidases (degradation rate of 100 ± 8.2 fmol min−1 mg−1) but an excellent substrate for phosphatases (dephosphorylation rate of 1.4 ± 0.3 nmol min−1 mg−1). Zn2+, 1,2-naphthoquinone and pervanadate inhibited dephosphorylation of the reporter in cell lysates with IC50 values of 470 nM, 35 μM, and 100 nM, respectively. Dephosphorylation of the reporter following loading into living single cells occurred at rates of at least 2 pmol min−1 mg−1. When single cells were exposed to 1,2-naphthoquinone (50 μM), Zn2+ (100 μM), and pervandate (1 mM), dephosphorylation was inhibited with median values and first and third quartile values of 41 (Q1 = 0%, Q3 = 96%), 50 (Q1 = 46%, Q3 = 74%), and 53% (Q1 = 36%, Q3 = 77%), respectively, demonstrating both the impact of these toxic exposures on cell signaling and the heterogeneity of response between cells. This approach will provide a valuable tool for the study of PTP dynamics, particularly in small, heterogeneous populations such as human biopsy specimens.
doi:10.1021/ac401106e
PMCID: PMC3704224  PMID: 23682679
15.  Enabling Quantitative Analysis in Ambient Ionization Mass Spectrometry: Internal Standard Coated Capillary Samplers 
Analytical chemistry  2013;85(12):5632-5636.
We describe a sampling method using glass capillaries for quantitative analysis of trace analytes in small volumes of complex mixtures (~1 μL) using ambient ionization mass spectrometry. The internal surface of a sampling glass capillary was coated with internal standard then used to draw liquid sample and so transfer both the analyte and internal standard in a single fixed volume onto a substrate for analysis. The internal standard was automatically mixed into the sample during this process and the volumes of the internal standard solution and sample are both fixed by the capillary volume. Precision in quantitation is insensitive to variations in length of the capillary, making the preparation of the sampling capillary simple and providing a robust sampling protocol. Significant improvements in quantitation accuracy were obtained for analysis of 1 μL samples using various ambient ionization methods.
doi:10.1021/ac401056q
PMCID: PMC3705643  PMID: 23731380
16.  Microfluidic Amperometric Sensor for Analysis of Nitric Oxide in Whole Blood 
Analytical chemistry  2013;85(12):6066-6072.
Standard photolithographic techniques and a nitric oxide (NO) selective xerogel polymer were utilized to fabricate an amperometric NO microfluidic sensor with low background noise and the ability to analyze NO levels in small sample volumes (~250 μL). The sensor exhibited excellent analytical performance in phosphate buffered saline, including a NO sensitivity of 1.4 pA nM−1, a limit of detection (LOD) of 840 pM, and selectivity over nitrite, ascorbic acid, acetaminophen, uric acid, hydrogen sulfide, ammonium, ammonia, and both protonated and deprotonated peroxynitrite (selectivity coefficients of −5.3, −4.2, −4.0, −5.0, −6.0, −5.8, −3.8, −1.5, and −4.0 respectively). To demonstrate the utility of the microfluidic NO sensor for biomedical analysis, the device was used to monitor changes in blood NO levels during the onset of sepsis in a murine pneumonia model.
doi:10.1021/ac400932s
PMCID: PMC3712765  PMID: 23692300
Nitric oxide; amperometric sensor; microfluidic device; sensor membrane; sepsis
17.  Using Glycinylation, a Chemical Derivatization Technique, for the Quantitation of Ubiquitinated Proteins 
Analytical chemistry  2013;85(12):5827-5834.
The quantitation of lysine post-translational modifications (PTMs) by bottom-up mass spectrometry is convoluted by the need for analogous derivatives and the production of different tryptic peptides from the unmodified and modified versions of a protein. Chemical derivatization of lysines prior to enzymatic digestion circumvents these problems and has proven to be a successful method for lysine PTM quantitation. The most notable example is the use of deuteroacetylation to quantitate lysine acetylation. In this work, levels of lysine ubiquitination were quantitated using a structurally homologous label that is chemically similar to the di-glycine (GlyGly)-tag, which is left at the ubiquitination site upon trypsinolysis. The LC-MS analysis of a chemically equivalent mono-glycine (Gly)-tag that is analogous to the corresponding GlyGly-tag proved that the mono-glycine tag can be used for the quantitation of ubiquitination. A glycinylation protocol was then established for the derivatization of proteins to label unmodified lysine residues with a single glycine tag. Ubiquitin multimers were used to show that after glycinylation and tryptic digestion, the mass spectrometric response from the corresponding analogous tagged peptides could be compared for relative quantitation. For a proof of principle regarding the applicability of this technique to the analysis of ubiquitination in biological samples, the glycinylation technique was used to quantitate the increase in mono-ubiquitinated histone H2B that is observed in yeast which lack the enzyme responsible for deubiquitinating H2B-K123, compared to wild-type yeast.
doi:10.1021/ac400398s
PMCID: PMC3713787  PMID: 23682733
18.  Coupling Supported Lipid Bilayer Electrophoresis with MALDI-MS Imaging 
Analytical chemistry  2013;85(12):6047-6052.
Herein we describe a new analytical platform utilizing advances in heterogeneous supported lipid bilayer (SLB) electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging. This platform allowed for the separation and visualization of both charged and neutral lipid membrane components without the need for extrinsic labels. A heterogeneous SLB was created using vesicles containing monosialoganglioside GM1, disialoganglioside GD1b, POPC, as well as the ortho- and para- isomers of Texas Red-DHPE. These components were then separated electrophoretically into five resolved bands. This represents the most complex separation by SLB electrophoresis performed to date. The SLB samples were flash frozen in liquid ethane and dried under vacuum before imaging with MALDI-MS. Fluorescence microscopy was employed to confirm the position of the Texas Red labeled lipids, which agreed well with the MALDI-MS imaging results. These results clearly demonstrate this platform’s ability to isolate and identify non-labeled membrane components within an SLB.
doi:10.1021/ac4008804
PMCID: PMC3717335  PMID: 23731179
19.  Phosphopeptide Enrichment with TiO2-Modified Membranes and Investigation of Tau Protein Phosphorylation 
Analytical chemistry  2013;85(12):5699-5706.
Selective enrichment of phosphopeptides prior to their analysis by mass spectrometry (MS) is vital for identifying protein phosphorylation sites involved in cellular regulation. This study describes modification of porous nylon substrates with TiO2 nanoparticles to create membranes that rapidly enrich phosphopeptides. Membranes with a 22-mm diameter bind 540 nmol of phosphoangiotensin and recover 70% of the phosphopeptides in mixtures with a 15-fold excess of non-phosphorylated proteins. Recovery is 90% for a pure phosphopeptide. Insertion of small membrane disks into HPLC fittings allows rapid enrichment of 5 mL of 1 fmol/μL phosphoprotein digests and concentration into small-volume (10’s of μL) eluates. The combination of membrane enrichment with tandem mass spectrometry reveals seven phosphorylation sites from in vivo phosphorylated tau (p-tau) protein, which is associated with Alzheimer’s disease.
doi:10.1021/ac400198n
PMCID: PMC3721342  PMID: 23638980
20.  An Approach for Separation and Complete Structural Sequencing of Heparin/Heparan Sulfate-like Oligosaccharides 
Analytical chemistry  2013;85(12):5787-5795.
As members of the glycosaminoglycan (GAG) family, heparin and heparan sulfate (HS) are responsible for mediation of a wide range of essential biological actions, most of which are mediated by specific patterns of modifications of regions of these polysaccharides. To fully understand the regulation of HS modification and the biological function of HS through its interactions with protein ligands, it is essential to know the specific HS sequences present. However, the sequencing of mixtures of HS oligosaccharides presents major challenges due to the lability of the sulfate modifications, as well as difficulties in separating isomeric HS chains. Here, we apply a sequential chemical derivatization strategy involving permethylation, desulfation and trideuteroperacetylation to label original sulfation sites with stable and hydrophobic trideuteroacetyl groups. The derivatization chemistry differentiates between all possible heparin/HS sequences solely by glycosidic bond cleavages, without the need to generate cross-ring cleavages. This derivatization strategy combined with LC-MS/MS analysis has been used to separate and sequence five synthetic HS-like oligosaccharides of sizes up to dodecasaccharide, as well as a highly-sulfated Arixtra-like heptamer. This strategy offers a unique capability for the sequencing of microgram quantities of HS oligosaccharide mixtures by LC-MS/MS.
doi:10.1021/ac400439a
PMCID: PMC3725598  PMID: 23659663
21.  Impact of TiO2 Nanoparticles on Growth, Biofilm Formation, and Flavin Secretion in Shewanella oneidensis 
Analytical chemistry  2013;85(12):5810-5818.
Understanding of nanoparticle impacts on critical bacteria functions allows us to gain a mechanistic understanding of toxicity and guides us towards design rules for creating safe nanomaterials. Herein and using analytical techniques, biofilm formation, a general bacteria function, and riboflavin secretion, a species-specific function, were monitored in Shewanella oneidensis, a metal reducing bacterium, following exposure to a variety of TiO2 nanoparticle types (synthesized, Aeroxide P25, and T-Eco). TEM images show that dosed nanoparticles are in close proximity to the bacteria but they are not internalized. Using quartz crystal microbalance (QCM), it was revealed that S. oneidensis biofilm formation is slowed in the presence of nanoparticles. Though S. oneidensis grows more slowly in the presence of TiO2 nanoparticles, riboflavin secretion, a function related to the S. oneidensis metal reducing capacity, was increased significantly in a nanoparticle dose-dependent manner. Both changes in biofilm formation and riboflavin secretion are supported by changes in gene expression in nanoparticle-exposed S. oneidensis. This broad study of bacterial nanotoxicity, including use of sensitive analytical tools for functional assessments of biofilm formation, riboflavin secretion, and gene expression has implications for total ecosystem health as the use of engineered nanoparticles grows.
doi:10.1021/ac400486u
PMCID: PMC3733218  PMID: 23701037
titanium dioxide; nanoparticle; toxicity; quartz crystal microbalance; high performance liquid chromatography
22.  Method development and analysis of free HS and HS in proteoglycans from pre- and postmenopausal women: Evidence for biosynthetic pathway changes in sulfotransferase and sulfatase enzymes 
Analytical chemistry  2013;85(12):5917-5923.
Heparan sulfate (HS) is one of the most complex and informative biopolymers found on the cell surface or in the extracellular matrix as either free HS fragments or constituents of HS proteoglycans (HSPGs). Analysis of free HS and HSPG sugar chains in human serum at the disaccharide level has great potential for early disease diagnosis and prognosis, however, the low concentration of HS in human serum, together with the complexity of the serum matrix, limits the information on HS. In this study, we present and validate the development of a new sensitive method for in-depth compositional analysis of free HS and HSPG sugar chains. This protocol involved several steps including weak anion exchange chromatography, ultrafiltration and solid phase extraction for enhanced detection prior to LC-MS/MS analysis. Using this protocol, a total of 51 serum samples from 26 premenopausal and 25 postmenopausal women were analyzed. Statistically significant differences in heparin/HS disaccharide profiles were observed. The proportion of N-acetylation and N-sulfation in both free HS and HSPG sugar chains were significantly different between pre- and postmenopausal women, indicating changes in N-deacetylase/N-sulfotransferases (NDSTs), the enzymes involved in the initial step of the biosynthetic pathway. Differences in the proportion of 6-O-sulfation suggest that 6-O-sulfotransferase and/or 6-O-sulfatase enzymes may also be implicated.
doi:10.1021/ac400690g
PMCID: PMC3741352  PMID: 23659730
23.  Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins 
Analytical chemistry  2013;85(12):6080-6088.
In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step allowing direct force measurements of the formation of a peptide bond catalyzed by the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1µm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and non-polar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski’s equality and demonstrated, as expected, that non-equilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair.
doi:10.1021/ac400949t
PMCID: PMC3760192  PMID: 23679912
Hydrazide; MBP; CBD; Split-inteins; Binding forces; Protein Association
24.  Fast top-down intact protein characterization with capillary zone electrophoresis-electrospray ionization tandem mass spectrometry 
Analytical chemistry  2013;85(12):5989-5995.
Capillary zone electrophoresis (CZE)-electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was applied for rapid top-down intact protein characterization. A mixture containing four model proteins (cytochrome c, myoglobin, bovine serum albumin (BSA) and beta casein) was used as the sample. The CZE-ESI-MS system was first evaluated with the mixture. The four model proteins and five impurities were baseline separated within 12 min. The limits of detection (s/n = 3) of the four model proteins ranged from 20 amole (cytochrome c) to 800 amole (BSA). The relative standard deviations of migration time and intensity for the four model proteins were less than 3% and 30%, respectively, in quintuplicate runs. CZE-ESI-MS/MS was then applied for top-down characterization of the mixture. Three of the model proteins (all except BSA) and an impurity (bovine transthyretin) were confidently identified by database searching of the acquired tandem spectra from protein fragmentation. Modifications including phosphorylation, N-terminal acetylation, and heme group binding were identified.
doi:10.1021/ac4008122
PMCID: PMC3770260  PMID: 23692435
CZE-ESI-MS/MS; top-down; intact protein; throughput; sensitivity; reproducibility
25.  Typing of Blood-Group Antigens on Neutral Oligosaccharides by Negative-Ion Electrospray Ionization Tandem Mass Spectrometry 
Analytical chemistry  2013;85(12):10.1021/ac400700e.
Blood-group antigens, such as those containing fucose and bearing the ABO(H)- and Lewis-type determinants expressed on the carbohydrate chains of glycoproteins and glycolipids, and also on unconjugated free oligosaccharides in human milk and other secretions, are associated with various biological functions. We have previously shown the utility of negative-ion electrospay ionization tandem mass spectrometry with collision-induced dissociation (ESI-CID-MS/MS) for typing of Lewis (Le) determinants, e.g. Lea, Lex, Leb, and Ley on neutral and sialylated oligosaccharide chains. In the present report we extended the strategy to characterization of blood-group A-, B- and H-determinants on type 1 and type 2, and also on type 4 globoside chains to provide a high sensitivity method for typing of all the major blood-group antigens, including the A, B, H, Lea, Lex, Leb, and Ley determinants, present in oligosaccharides. Using the principles established we identified two minor unknown oligosaccharide components present in the products of enzymatic synthesis by bacterial fermentation. We also demonstrated that the unique fragmentations derived from the D- and 0,2A-type cleavages observed in ESI-CID-MS/MS, which are important for assigning blood-group and chain types, only occur under the negative-ion conditions for reducing sugars but not for reduced alditols or under positive-ion conditions.
doi:10.1021/ac400700e
PMCID: PMC3856363  PMID: 23692402

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