Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

Bioactivity fingerprint analysis of cyclooxygenase-2 ligands from radix Aconiti by ultrafiltration–UPLC–MSn

A novel fingerprinting method, bioactivity fingerprint analysis, based on an ultrafiltration–ultraperformance liquid chromatography–multistage tandem mass spectrometry (UPLC–MS ⁿ ) method is proposed for the quality control of herbal medicines from the bioactivity viewpoint concerning the efficacy of herbal medicines. The bioactivity fingerprints reflecting the anti-inflammatory activities of radix Aconiti and radix Aconiti preparata were established. With use of ultrafiltration UPLC–MS ⁿ , 11 cyclooxygenase-2 ligands from radix Aconiti preparata and 14 cyclooxygenase-2 ligands from radix Aconiti were found after incubation with cyclooxygenase-2. Twelve of the cyclooxygenase-2 ligands were identified by the ultraperformance UPLC–MS ⁿ method. The enrichment factor of each peak in the bioactivity fingerprint was calculated and was demonstrated to be characteristic, which makes bioactivity fingerprint analysis for the quality control of herbal medicines possible from the viewpoint of their bioactivities.

Preparation of a boronate-functionalized affinity hybrid monolith for specific capture of glycoproteins

A novel strategy for preparation of a boronate affinity hybrid monolith was developed using a Cu(I)-catalyzed 1,3-dipolar azide–alkyne cycloaddition (CuAAC) reaction of an alkyne–boronate ligand with an azide-functionalized monolithic intermediate. An azide-functionalized hybrid monolith was first synthesized via a single-step procedure to provide reactive sites for click chemistry; then the alkyne–boronate ligands were covalently immobilized on the azide-functionalized hybrid monolith via an in-column CuAAC reaction to form a boronate affinity hybrid monolith under mild conditions. The boronate affinity monolith was characterized and evaluated by means of elemental analysis, Fourier transform infrared spectroscopy, and scanning electron microscopy. The boronate affinity hybrid monolith exhibited excellent specificity toward nucleosides and glycoproteins, which were chosen as test cis-diol-containing compounds under neutral conditions. The binding capacity of the monolith for the glycoprotein ovalbumin was 2.36 mg?·?g^-1 at pH 7.0. The practicability of the boronate affinity hybrid monolithic material was demonstrated by specific capture of the glycoproteins ovalbumin and ovotransferrin from an egg sample.

Absolute Quantitation of Glycosylation Site Occupancy Using Isotopically Labeled Standards and LC-MS

N-linked glycans are required to maintain appropriate biological functions on proteins. Underglycosylation leads to many diseases in plants and animals; therefore, characterizing the extent of glycosylation on proteins is an important step in understanding, diagnosing, and treating diseases. To determine the glycosylation site occupancy, protein N-glycosidase F (PNGase F) is typically used to detach the glycan from the protein, during which the formerly glycosylated asparagine undergoes deamidation to become an aspartic acid. By comparing the abundance of the resulting peptide containing aspartic acid against the one containing non-glycosylated asparagine, the glycosylation site occupancy can be evaluated. However, this approach can give inaccurate results when spontaneous chemical deamidation of the non-glycosylated asparagine occurs. To overcome this limitation, we developed a new method to measure the glycosylation site occupancy that does not rely on converting glycosylated peptides to their deglycosylated forms. Specifically, the overall protein concentration and the non-glycosylated portion of the protein are quantified simultaneously by using heavy isotope-labeled internal standards coupled with LC-MS analysis, and the extent of site occupancy is accurately determined. The efficacy of the method was demonstrated by quantifying the occupancy of a glycosylation site on bovine fetuin. The developed method is the first work that measures the glycosylation site occupancy without using PNGase F, and it can be done in parallel with glycopeptide analysis because the glycan remains intact throughout the workflow.

Determination of Se(IV) using solidified floating organic drop microextraction coupled to ultrasound-assisted back-extraction and hydride generation atomic fluorescence spectrometry

A method is presented for matrix separation, preconcentration and determination by hydride generation atomic fluorescence spectrometry of trace amounts of Se(IV). It is based on solidified floating drops of 1-undecanol that are capable of extracting the target analyte after chelation with a water soluble ligand and subsequent ultrasound-assisted back-extraction into a aqueous solution. Hydride generation was then accomplished by reaction with a solution of sodium borohydride. Under optimized conditions, an enrichment factor of 15 and a linear calibration plot in the range from 0.01 to 5.0 μg L^?1 were achieved using a 10.0 mL sample. The detection limit (3σ) is 7.0 ng L^?1, and the relative standard deviation (RSD) is 2.1% at 1.0 μg L^?1 (n?=?11). The method was applied to determination of Se(IV) in different real water samples through recovery experiments and subsequently validated against two certified reference materials.

Single-drop microextraction for the determination of manganese in seafood and water samples

We describe a method for single drop microextraction of manganese from fish, mollusk, and from natural waters using the reagent 1-(2-pyridylazo)-2-naphthol as the complexing agent and chloroform as the fluid extractor. After extraction, the analyte was directly submitted to graphite furnace electrothermal atomic absorption spectrometry. Once optimized, the method has a detection limit of 30 ng L^?1, a limit of quantification of 100 ng L^?1, and an enrichment factor of 16. Its accuracy was verified by applying the procedure to the following certified reference materials: apple leaves, spinach leaves, bovine liver, and mussel tissue. The procedure was also successfully applied to the determination of manganese in seafood and natural waters.

Solid-phase extraction of lead(II) ions using multiwalled carbon nanotubes grafted with tris(2-aminoethyl)amine

Multiwalled carbon nanotubes were grafted with tris(2-aminoethyl)amine (MWCNTs-TAA) and employed for solid phase extraction and preconcentration of trace lead ions prior to its determination by inductively coupled plasma optical emission spectrometry. The material was characterized by FT-IR and Raman spectroscopy, thermosgravimetric and elemental analysis. The effects of pH value, shaking time, sample volume, elution conditions and potentially interfering ions were investigated. Under the optimum conditions, the maximum adsorption capacity is 38?mg?g^?1 of Pb(II), the detection limit is 0.32?ng?mL^?1, the enrichment factor is 60, and the relative standard deviation is 3.5% (n?=?6). The method has been applied to the preconcentration of trace amounts of Pb(II) in environmental water samples with satisfactory results.

Multiwalled carbon nanotubes modified with 2-aminobenzothiazole modified for uniquely selective solid-phase extraction and determination of Pb(II) ion in water samples

A solid phase extraction method is presented for the selective preconcentration and/or separation of trace Pb(II) on multiwalled carbon nanotubes modified with 2-aminobenzothiazole. Inductively coupled plasma optical emission spectrometry was used for detection. The effects of pH, shaking time, sample flow rate and volume, elution condition and interfering ions were examined using batch and column procedures. An enrichment factor of 100 was accomplished. Common other ions do not interfere in both the separation and determination. The maximum adsorption capacity of the sorbent at optimum conditions is 60.3?mg?g^?1 of Pb(II), the detection limit (3??) is 0.27?ng?mL^?1, and the relative standard deviation is 1.6% (n?=?8). The method was validated using a certified reference material, and has been applied to the determination of trace Pb(II) in water samples with satisfactory results.

Simultaneous determination of multi-class antibiotic residues in water using carrier-mediated hollow-fiber liquid-phase microextraction coupled with ultra-high performance liquid chromatography tandem mass spectrometry

A method has been developed for carrier-mediated hollow-fiber liquid-phase microextraction (HF-LPME) and enrichment of multiple classes of antibiotics in water samples. Eleven compounds (erythromycin, spiramycin, tilmicosin, sulfathiazole, sulfamethazine, sulfamerazine, oxytetracycline, tetracycline, ciprofloxacin, danofloxacin and enrofloxacin) from four important classes of antibiotics (of the macrolide, sulfonamide, tetracycline and quinolone type) have been simultaneously preconcentrated with one set of HF-LPME conditions, followed by determination by ultra-HPLC combined with electrospray ionization tandem mass spectrometry (UHPLC-MS/MS). Antibiotics can be determined at ng L^?1 levels using this highly sensitive and selective method. Parameters including immersion time, liquid membrane composition, sample pH, acceptor composition and extraction time were optimized to finally give detection limits in the 10?C250?ng?L^?1 range. Good linearity was achieved, with up to 156 times enrichment over the four classes of antibiotics. This multi-residue method enabled the simultaneous enrichment of all 11 multi-class antibiotics from spiked river water samples, with relative recovery between 79 and 118%.

Solid-phase preconcentration of cadmium(II) using amino-functionalized magnetic-core silica-shell nanoparticles, and its determination by hydride generation atomic fluorescence spectrometry

We report on the synthesis and evaluation of aminated-CoFe₂O₄/SiO₂ nanoparticles that can serve as a selective solid-phase sorbent for the extraction of cadmium ion. The nanoparticles consist of a magnetic CoFe₂O₄ core and an amino-modified silica shell. They can efficiently extract cadmium(II) ion and then can be isolated from the sample solution due to the magnetic nature of the core. The effects of the experimental conditions on the extraction process were optimized. Cadmium was then quantified by hydride generation atomic fluorescence spectrometry. The resulting calibration curve is linear in the concentration range of 0.01–10 μg?L^?1, the instrumental detection limits (3σ) is 3.15 ng?L^?1 and the relative standard deviation is 4.9 % at the 1.0 μg?L^?1 level (for n?=?11). The enrichment factor is 50 (for 50 mL samples), and the adsorbent can be used for at least 45 cycles of preconcentration and elution. The method was applied to the determination of cadmium in environmental water samples, and successfully validated by analyzing two certified reference materials.

Differential pulse anodic stripping voltammetric determination of Cd and Pb at a bismuth glassy carbon electrode modified with Nafion, poly(2,5-dimercapto-1,3,4-thiadiazole) and multiwalled carbon nanotubes

A simple, cheap, and nonpolluting method was developed for the cloud point extraction of gold (Au) and palladium (Pd). It is based on the complexation reaction of Au and Pd with 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone (PMBP) and micelle mediated extraction of the complex using the non-ionic surfactant poly(ethylene glycol) mono-p-nonylphenyl ether (PONPE 7.5). Under the optimized experimental conditions, the enrichment factors are 16 and 17 for Au and Pd, respectively, for 15?mL of preconcentrated solution. The limits of detection are 3.8???g?L^?1 and 1.8???g?L^?1 for Au and Pd, respectively. The relative standard deviations are 1.4% for Au and 0.6% for Pd (n?=?11). The method was successfully applied to the determination of Au and Pd in certified reference materials and mine samples.

Determination of phenolic compounds in water samples by HPLC following ionic liquid dispersive liquid-liquid microextraction and cold-induced aggregation

We report on the determination of bisphenol A and 2-naphthol in water samples using ionic liquid cold-induced aggregation dispersive liquid-liquid microextraction combined with HPLC. Parameters governing the extraction efficiency (disperser solvent, volume of extraction and disperser solvent, pH, temperature, extraction time) were optimized and resulted in enrichment factors of 112 for bisphenol A and of 186 for 2-naphthol. The calibration curve was linear with correlation coefficients of 0.9995 and 0.9998, respectively, in the concentration range from 1.5 to 200?ng?mL^?1. The relative standard deviations are 2.3% and 4.1% (for n?=?5), the limits of detection are 0.58 and 0.86?ng?mL^?1, and relative recoveries in tap, lake and river water samples range between 100.1 and 108.1%, 99.4 and 106.2%, and 97.1 and 103.8%, respectively.

Extraction of phthalate esters from water and beverages using a graphene-based magnetic nanocomposite prior to their determination by HPLC

We have developed a highly sensitive microextraction method for the preconcentration of some phthalate esters such as diethyl phthalate, di-n-propylphthalate, di-n-butyl-phthalate, dicyclohexyl-phthalate, and diethyl-hexyl phthalate prior to their determination by HPLC. It is based on a magnetic graphene nanocomposite as an effective adsorbent. The effects of the amount of the extractant composite employed, extraction time, pH values, salt concentration and desorption conditions were investigated. Under the optimum conditions, the enrichment factors range from 1574 to 2880. Response is linear in the concentration range from 0.1 to 50?ng?mL^?1. The limits of detection (at S/N?=?3) were between 0.01 and 0.04?ng?mL^?1. The method was successfully applied to the determination of five phthalate esters in water and beverage samples.

Ultrasound- assisted emulsification microextraction for separation of trace amounts of antimony prior to FAAS determination

We describe a simple and rapid method for the ultrasound-assisted microextraction of antimony using the solidified floating organic drop method. The effects of pH, type and volume of the extractant, time of sonication, amount of chelating agent, type and amount of surfactant were investigated and optimized. Bromopyrogollol red is acting as the chelating agent. Antimony(III) ion was extracted into finely dispersed droplets of undecanol after ion-pair formation with the water soluble chelator and the cationic detergent benzyldimethyltetradecylammonium chloride. Flame atomic absorption spectrometry was used for the detection. The resulting calibration is linear in the concentration range from 4.0 to 900?ng?mL^-1 of Sb(III) with a correlation coefficient of 0.9981. The enrichment factor is 67, the detection limit is 0.62?ng?mL^-1, and the relative standard deviation is?±?3.6% (at 100?ng?mL^-1; for n?=?10). The method was successfully applied to the determination of antimony in water samples.

Ionic liquid-based hollow fiber supported liquid membrane extraction combined with thermospray flame furnace AAS for the determination of cadmium

We have developed a simple and effective method for hollow fiber liquid-phase microextraction of cadmium. It is based on the use of a room temperature ionic liquid (RTIL) and was coupled to thermospray flame furnace AAS. The RTIL was placed in the pores of a polypropylene hollow fiber (acting as a liquid membrane) and also used as the acceptor solution. Ammonium pyrrolidinedithiocarbamate (APDC) was used as the chelating agent. The effects of the concentration of APDC, the pH of samples, stirring rates, extraction time, and potential interferences were optimized to result in a detection limit of 9?ng?L^?1 and an enrichment factor of 90. The relative standard deviation is 4.7% (at 0.5?ng?mL^?1, for n?=?5). The method was successfully applied to the determination of cadmium.

Elimination of Benzene from Protonated N-Benzylindoline: Benzyl Cation/Proton Transfer or Direct Proton Transfer?

Collision-induced dissociation (CID) of protonated N-benzylindoline and its derivatives was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Elimination of benzene was observed besides hydride transfer and electron transfer reactions. D-labeling experiments and accurate mass determinations of the product ions confirm that the external proton is retained in the fragment ion, and the elimination reaction was proposed to be initiated by benzyl cation transfer rather than proton transfer. Benzyl cation transfer from the nitrogen atom to one of the sp²-hybridized carbon atoms in the indoline core is the key step, and subsequent proton transfer reaction leads to the elimination of benzene. Density functional theory (DFT)-based calculations were performed and the computational results also support the benzyl cation/proton transfer mechanism.

Dual cloud point extraction coupled with hydrodynamic-electrokinetic two-step injection followed by micellar electrokinetic chromatography for simultaneous determination of trace phenolic estrogens in water samples

A dual cloud point extraction (dCPE) off-line enrichment procedure coupled with a hydrodynamic–electrokinetic two-step injection online enrichment technique was successfully developed for simultaneous preconcentration of trace phenolic estrogens (hexestrol, dienestrol, and diethylstilbestrol) in water samples followed by micellar electrokinetic chromatography (MEKC) analysis. Several parameters affecting the extraction and online injection conditions were optimized. Under optimal dCPE–two-step injection–MEKC conditions, detection limits of 7.9–8.9 ng/mL and good linearity in the range from 0.05 to 5 μg/mL with correlation coefficients R ²?≥?0.9990 were achieved. Satisfactory recoveries ranging from 83 to 108 % were obtained with lake and tap water spiked at 0.1 and 0.5 μg/mL, respectively, with relative standard deviations (n?=?6) of 1.3–3.1 %. This method was demonstrated to be convenient, rapid, cost-effective, and environmentally benign, and could be used as an alternative to existing methods for analyzing trace residues of phenolic estrogens in water samples.

Structural Analysis of Guanylyl Cyclase-Activating Protein-2 (GCAP-2) Homodimer by Stable Isotope-Labeling, Chemical Cross-Linking, and Mass Spectrometry

The topology of the GCAP-2 homodimer was investigated by chemical cross-linking and high resolution mass spectrometry. Complementary conducted size-exclusion chromatography and analytical ultracentrifugation studies indicated that GCAP-2 forms a homodimer both in the absence and in the presence of Ca²⁺. In-depth MS and MS/MS analysis of the cross-linked products was aided by ¹⁵ ? N-labeled GCAP-2. The use of isotope-labeled protein delivered reliable structural information on the GCAP-2 homodimer, enabling an unambiguous discrimination between cross-links within one monomer (intramolecular) or between two subunits (intermolecular). The limited number of cross-links obtained in the Ca²⁺-bound state allowed us to deduce a defined homodimeric GCAP-2 structure by a docking and molecular dynamics approach. In the Ca²⁺-free state, GCAP-2 is more flexible as indicated by the higher number of cross-links. We consider stable isotope-labeling to be indispensable for deriving reliable structural information from chemical cross-linking data of multi-subunit protein assemblies.

Determination of trace total inorganic arsenic by hydride generation atomic fluorescence spectrometry after solid phase extraction-preconcentration on aluminium hydroxide gel

We describe a simple, effective, inexpensive and rapid method for the determination of trace amounts of total inorganic arsenic in water samples by means of a modified solid phase preconcentration procedure using an aluminium hydroxide gel sorbent and hydride generation atomic fluorescence spectrometry (HGAFS). This method avoids the traditional extraction procedures that are time- and solvent-consuming. The effects of quantity of adsorbent, solution pH, adsorption time and potentially interfering ions were studied. Under the optimal conditions, the detection limit is 3 ng?L^?1, and the enrichment factor is 167. The calibration plot is linear in the range from 0.05 to 10 μg?L^?1, with a correlation coefficient of 0.9992. The relative standard deviation (RSD) was less than 6.1 % (n?=?5) and recoveries in spiked environmental water were >100 %. The method was successfully applied to the determination of total inorganic arsenic in natural water samples.

Preconcentration of erbium(III) ions from environmental samples using activated carbon modified with benzoyl hydrazine

A method was established for the preconcentration of trace concentrations of Er(III) ion using activated carbon modified with benzoyl hydrazine. Parameters affecting solid-phase extraction such as pH value, shaking time, flow rate, sample volume were systematically studied. At a pH of 3.0, the maximum static adsorption capacity of the sorbent is 59.8?mg?g^?1 for Er(III), and the time for quantitative adsorption (>95%) is as short as 2?min. The adsorbed Er(III) was quantitatively eluted with 2?mL of 1.0?M hydrochloric acid and then determined by inductively coupled plasma optical emission spectrometry. The limit of detection (3??) is 73?ng?g^?1, and the relative standard deviation is <2.0% (n?=?8). The method was validated by analyzing certified reference materials and successfully applied to the determination of trace Er(III) in environmental samples.