Enrichment and analysis of phosphopeptides under different experimental conditions using titanium dioxide affinity chromatography and mass spectrometry

Titanium dioxide metal oxide affinity chromatography (TiO₂‐MOAC) is widely regarded as being more selective than immobilized metal‐ion affinity chromatography (IMAC) for phosphopeptide enrichment. However, the widespread application of TiO₂‐MOAC to biological samples is hampered by conflicting reports as to which experimental conditions are optimal. We have evaluated the performance of TiO₂‐MOAC under a wide range of loading and elution conditions. Loading and stringent washing of peptides with strongly acidic solutions ensured highly selective enrichment for phosphopeptides, with minimal carryover of non‐phosphorylated peptides. Contrary to previous reports, the addition of glycolic acid to the loading solution was found to reduce specificity towards phosphopeptides. Base elution in ammonium hydroxide or ammonium phosphate provided optimal specificity and recovery of phosphorylated peptides. In contrast, elution with phosphoric acid gave incomplete recovery of phosphopeptides, whereas inclusion of 2,5‐dihydroxybenzoic acid in the eluant introduced a bias against the recovery of multiply phosphorylated peptides. TiO₂‐MOAC was also found to be intolerant of many reagents commonly used as phosphatase inhibitors during protein purification. However, TiO₂‐MOAC showed higher specificity than immobilized gallium (Ga³⁺), immobilized iron (Fe³⁺), or zirconium dioxide (ZrO₂) affinity chromatography for phosphopeptide enrichment. Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) was more effective in detecting larger, multiply phosphorylated peptides than liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS), which was more efficient for smaller, singly phosphorylated peptides. Copyright © 2009 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.     

Interactions between polymer-grafted particles and bare particles for biocompatibility applications

We use self-consistent field theory (SCFT) to study the interactions between a polymer-grafted spherical particle and a bare spherical particle and explore how these interaction energies depend on the radii of the two particles and the grafting density. We find that the magnitude of the interaction energies increases with the radii of both the grafted and bare particles and with increasing grafting density. We also find a universal scaling law for the interaction potential which exhibits a power-law dependence on both particle sizes, a linear dependence on grafting density, and a logarithmic dependence on interparticle distance with a range of interaction that scales with brush height. We compare our numerical results to those obtained using the Derjaguin approximation. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 2566–2577, 2009     

SPE and purification of DNA using magnetic particles

Superparamagnetic particles have been attractive for molecular diagnostics and analytical chemistry applications due to their unique magnetic properties and their ability to interact with various biomolecules of interest. This paper presents a critical overview of magnetic nano ‐ and microparticles used as a solid phase for extraction and purification of DNAs. The mechanisms of DNA binding to the surface of functionalised magnetic particles are described. The most widely used materials including silica supports, organic polymers and other materials, mostly containing magnetite or paramagnetic metallic elements are reviewed. The main application areas of magnetic particles for DNA separation are briefly described.     

Electrokinetic properties of bare and particles containing textile

Functional, reactive and smart textiles are nowadays of great interest in the fields of both cosmetic and pharmaceutical industries. Textile functionalization according to demands of the consumers can only be achieved with better understanding of the properties of the textile surface as well as sound knowledge about the technique to be used to functionalize the textiles. The aim of this work was to investigate the zeta potential of polyamide textile and prepared sponge like particles as a function of pH and salinity of the electrolyte. Special attention has been dedicated to the electrokinetic properties of textile as a function of sponge like particles amount present during adsorption process. As a general tendency, streaming potential measurement showed the changes in surface charge density of textile because of the changes in pH, salinity and adsorbed particles amount. All presented results were discussed in terms of zeta potential. Copyright © 2016 John Wiley & Sons, Ltd.     

Isolation of phosphopeptides using solid phase enrichment

Protein phosphorylations are post-translational protein modifications that are crucial for intercellular signal transduction and the regulation of many cellular events. We describe herein a novel technology utilizing α-diazo functionalized solid phase resins to isolate phosphorylated peptides from non-phosphorylated substrates.     

Programmable assembly of colloidal particles using magnetic microwell templates

A substrate of thin micromagnets covered by a template of microwells is used to direct the assembly of superparamagnetic colloidal beads into two-dimensional arrays. It is confirmed that the magnetization of the micromagnets can direct beads to programmed locations on the substrate with assistance of externally applied magnetic fields. Empirical investigations on this topic were guided by mathematical models with the intent to elucidate the conditions that promote a single bead to be assembled in the desired microwells. To demonstrate that this technique is programmable, heterogeneous arrays of colored beads are produced.     

多金属氧酸盐/壳聚糖磁性复合材料的制备及其用于磷酸化肽的富集

建立了一种基于多金属氧酸盐磁性材料富集磷酸化肽的方法。采用层层自组装技术制备多金属氧酸盐/壳聚糖磁性材料,结合基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）检测手段,用于磷酸化肽的富集。该磁性材料具有快速磁响应、亲水性、正电性等优点,对磷酸化肽具有高的富集选择性。实验用β-酪蛋白作为模型蛋白质,通过富集后,方法的检出限为0.02 fmol,说明合成的磁性材料对微量蛋白样品分析具有很高的应用潜力。     

Isolation of phosphopeptides using zirconium-chlorophosphonazo chelate-modified silica nanoparticles

Due to the low abundance of phosphoproteins and substoichiometry of phosphorylation, the elucidation of protein phosphorylation requires highly specific materials for isolation of phosphopeptides from biological samples prior to mass spectrometric analysis. In this study, chlorophosphonazo type derivatives of chromotropic acid including p-hydroxychlorophosphonazo (HCPA) and chlorophosphonazo I (CPA I), traditionally used in the photometric determination of transition metal ions, have been employed as chelating ligands in the preparation of novel affinity materials for phosphopeptide enrichment. The chromogenic reagents of HCPA and CPA I were chemically modified on the surface of silica nanoparticles, and the functionalized materials were charged with zirconium ions through the strong complexation between chelating ligands and Zr(4+). The obtained zirconium-chlorophosphonazo chelate-modified silica nanoparticles (Zr-HCPA-SNPs and Zr-CPA I-SNPs) were applied to the selective enrichment of phosphopeptides, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The purification procedures were optimized using α-casein digest at first, and then the performance of these two affinity materials for efficient and specific enrichment of phosphopeptides was evaluated with the tryptic digests of standard proteins (α-casein, β-casein, ovalbumin and bovine serum albumin). It is found that Zr-HCPA-SNPs are superior to Zr-CPA I-SNPs in phosphopeptide enrichment. Using Zr-HCPA-SNPs to trap phosphopeptides in α-casein digest, the detection limit was close to 50fmol based on MALDI-TOF MS analysis. Finally, Zr-HCPA-SNPs were used to directly isolate phosphopeptides from diluted human serum of healthy, diabetes and hypertension persons, respectively. Our results show that the constitution and level of phosphopeptides are remarkably different among the three groups, which indicate the powerful potentials of Zr-HCPA-SNPs in disease diagnosis and biomarker screening.     

Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling

Reversible phosphorylation of proteins represents an important component of cellular signaling pathways. The isolation of phosphoproteins in complex mixtures and the determination of the level of phosphorylation have been and remain a major challenge. It has prompted the development of several strategies, including immobilized metal affinity capture to enrich for phosphorylated peptides. An improved methodology was published (Ficarro, et al., Nature Biotechnology 2002, 20, 301-305) that showed increased selectivity through esterification of amino acid side chain carboxylic groups of enzymatically digested peptides. This method was applied for relative quantitation of phosphopeptides in conjunction with the use of stable isotope labeling. The merits and limits of the approach are discussed and its application to the analysis of the effects of serum starvation on in vitro cultured human lung cells is presented.     

Preparation of magnetic hydroxyapatite clusters and their application in the enrichment of phosphopeptides

A novel strategy for the effective enrichment of phosphopeptides based on magnetic hydro‐xyapatite (HAp) clusters was developed in the current study. The structure of HAp ensures its probable separation capability, including cation exchange with P‐sites (negatively charged pairs of crystal phosphates), calcium coordination, anion exchange with C‐sites (positively charged pairs of crystal calcium ions). The prepared magnetic HAp clusters showed good performance on the efficient enrichment of phosphopeptides from the digestion mixture of β‐casein and BSA. Compared to commercial HAp particles, the magnetic HAp clusters exhibited better selectivity toward phosphopeptides. In addition, the use of magnetic material greatly simplified the enrichment procedure, which avoided the tedious centrifugation steps in a typical phosphopeptides enrichment protocol. Finally, the material was successfully applied in the enrichment of phosphopeptides from human serum. Taken together, the efficient enrichment of the phosphopeptides by the easily prepared magnetic HAp clusters demonstrated a rapid and convenient strategy for the purification of phosphopeptides from complex samples, which may facilitate protein phosphorylation studies.     

伴刀豆凝集素修饰磁性纳米粒子富集人血清中糖蛋白及质谱鉴定

发展了一种新型的磁性纳米粒子应用于人血清中特异性糖蛋白的亲和富集。制备的磁性纳米粒子具有核/壳/壳结构,即由Fe₃O₄磁性粒子/硅胶层/有机聚合物外层构成。伴刀豆凝集素A（Con A）以共价键合的形式通过短链聚乙二醇固定在粒子表面,实现了人血清中特异性糖蛋白的高效富集。富集的蛋白经过胰蛋白酶酶解后,所得的肽段经离线的二维色谱分离,用高分辨质谱共鉴定出80种蛋白。通过NetNGlyc等搜索软件分析确定其中76种为糖蛋白,分析发现在血清中质量浓度仅为0.00001 g/L的 β -2-glycoprotein 1也得到了鉴定,表明我们发展的磁性纳米粒子与凝集素相结合的方式,可以高效地富集复杂体系中与主要蛋白成分含量相差12个数量级的低丰度糖蛋白。     

Enzyme shadowing: using antibody-enzyme dually-labeled magnetic particles for fast bacterial detection

Using magnetic particles and immunoseparation for target recovery and detection has been reported to improve the performance and detection limits of traditional analytical methods. For example, magnetic immunocapture can be coupled to detection in a sandwich format using an antibody (Ab) labeled with a reporter molecule or enzyme. In this work we demonstrate that simultaneous incorporation of capture and reporter biocomponents onto the sensing surface is possible and provides assays that are extremely fast and easy to carry out. As a proof of concept, we have produced dually-labeled magnetic particles, simultaneously functionalized with antibody and reporter enzyme. Subsequent capture of Escherichia coli generates a shadowing effect on the particle surface and interferes with the activity of a number of enzyme units. The decrease in signal recorded is proportional to the bacterial concentration and is specific for the target microorganism, with a detection limit of 10(3)-10(4) cell mL(-1) in an assay of about one hour.     

Tailoring of carboxyl‐decorated magnetic latex particles using seeded emulsion polymerization

In this research, submicron and carboxyl‐functionalized magnetic latex particles were elaborated by using seeded emulsion polymerization technique in presence of oil‐in‐water (o/w) magnetic emulsion as seed. The polymerization conditions were optimized in order to get well‐defined latex particles with magnetic core and polymer shell bearing carboxylic (–COOH) functionality. Starting from (o/w) magnetic emulsion as seed, synthesis process was performed by copolymerization of styrene (St) monomer with the cross‐linker divinylbenzene (DVB) in presence of 4,4′‐azobis(4‐cyanopentanoic acid) (ACPA) as a carboxyl‐bearing initiator. The prepared magnetic latex particles were first characterized in terms of particle size, chemical composition, morphology, magnetic properties, magnetic content, and colloidal stability using various techniques, e.g. particle size analyzer using dynamic light scattering (DLS) technique, Fourier transform infrared, transmission electron microscopy, vibrating sample magnetometer, thermogravimetric analysis, and zeta potential measurements as a function of pH of the dispersion media, respectively. The prepared magnetic latex particles were then used as second seed for further functionalization with methacrylic acid (MAA) in order to enhance carboxylic groups on the magnetic particle's surface. The results showed that final magnetic latex particles possessed spherical morphology with core‐shell structure and enriched carboxylic acid functionality. More importantly, they exhibited superparamagnetism with high magnetic content (58.42 wt%) and high colloidal stability, which considered as the main requirements for their application in the biomedical diagnostic domains. Copyright © 2017 John Wiley & Sons, Ltd.     

Preparation of fritless capillary using avidin immobilized magnetic particles for electrochromatographic chiral separation

In capillary electrochromatography (CEC), magnetic particles (MPs) were packed in a fused silica capillary by using the magnetic field to be retained without frits. For a chiral CEC separation, avidin was immobilized onto the surface of the MPs (AVI-MPs) as a stationary phase by using the physical adsorption technique. The injected AVI-MPs into the capillary were stably captured with the magnet (surface magnetic flux density, 250 mT) under the separation voltage of 10 kV (190 V/cm). By employing the fritless AVI-MPs packed capillary, the chiral separation of ketoprofen was successfully attained with the packing length of only 5 cm. Effects of the modification condition of avidin, pH of background solution, and the packing length on the enantioseparation were also investigated. Under the optimal condition, furthermore, the repeatability for the retention time of ketoprofen was better than 1.5% in the relative standard deviation and the capillary-to-capillary reproducibility was also acceptable in the prepared fritless capillaries.     

Phosphate-functionalized magnetic microspheres for immobilization of Zr ions for selective enrichment of the phosphopeptides

In this work, we developed phosphate functionalized magnetic Fe₃O₄@C microspheres to immobilize Zr⁴⁺ ions for selective extraction and concentration of phosphopeptides for mass spectrometry analysis. Firstly, we synthesized Fe₃O₄@C magnetic microspheres as our previous work reported. Then, the microspheres were functionalized with phosphate groups through a simple hydrolysis reaction using 3-(trihydroxysilyl)propyl methylphosphate. And the Zr⁴⁺ ions were immobilized on phosphate-functionalized magnetic microspheres by using phosphate chelator. Finally, we successfully employed Zr⁴⁺-phosphate functionalized magnetic microspheres to selectively isolate the phosphopeptides from tryptic digests of standard protein and real samples including rat brain. All the experimental results demonstrate the enrichment efficiency and selectivity of the method we reported here.     

The highly selective capture of phosphopeptides by zirconium phosphonate-modified magnetic nanoparticles for phosphoproteome analysis

The highly selective capture of phosphopeptides from proteolytic digests is a great challenge for the identification of phosphoproteins by mass spectrometry. In this work, the zirconium phosphonate-modified magnetic Fe₃O₄/SiO₂ core/shell nanoparticles have been synthesized and successfully applied for the selective capture of phosphopeptides from complex tryptic digests of proteins before the analysis of MALDI-TOF mass spectrometry with the desired convenience of sample handling. The ratio of magnetic nanoparticle to protein and the incubation time for capturing phosphopeptides from complex proteolytic digests were investigated, and the optimized nanoparticle-to-protein ratio and incubation time were between 15:1 to 30:1 and 30 min, respectively. The excellent detection limit of 0.5 fmol β-casein has been achieved by MALDI-TOF mass spectrometry with the specific capture of zirconium phosphonate-modified magnetic Fe₃O₄ nanoparticles. The great specificity of zirconium phosphonate-modified magnetic Fe₃O₄ nanoparticles to phosphopeptides was demonstrated by the selective capture of phosphopeptides from a complex tryptic digest of the mixture of α-casein and bovine serum albumin at molar ratio of 1 to 100 in MALDI-TOF-MS analysis. An application of the magnetic nanoparticles to selective capture phosphopeptides from a tryptic digest of mouse liver lysate was further carried out by combining with nano-LC-MS/MS and MS/MS/MS analyses, and a total of 194 unique phosphopeptides were successfully identified.     

Analysis of effect of casein phosphopeptides on zinc binding using mass spectrometry

Phosphorylation is one of the key events in signal transduction and zinc plays an important catalytic and/or structural role in many biological systems. The binding of Zn to a phosphopeptide will alter the physiological functions of a peptide. The binding of casein phosphopeptides (CPPs) to Zn has been analyzed using nanospray mass spectrometry. Electrospray ionization (ESI) spectra of peptides produced by tryptic digestion of alpha-casein incubated with Zn show both free and Zn-bound phosphopeptides. The interaction of CPPs and the corresponding dephosphorylated peptides with zinc is compared. This study demonstrates that the phosphorylation state of a peptide dramatically affects Zn binding, with the decrease in Zn-bound forms of peptide paralleling the decrease in phosphorylation as casein is chemically dephosphorylated, although, in some cases, a small amount of residual Zn-binding capacity remains in the completely dephosphorylated peptide. The observed fragmentation patterns of the Zn-bound CPPs support the thesis that nonphosphorylated residues are involved in the metal binding.     

Use of polyethylenimine-modified magnetic nanoparticles for highly specific enrichment of phosphopeptides for mass spectrometric analysis

Phosphopeptides have been isolated and concentrated by use of polyethyleneimine (PEI)-modified magnetic nanoparticles as an extremely specific affinity probe. The particles specifically captured phosphopeptides from a tryptic digest of a protein mixture that contained 0.07% (mole/mole) phosphoproteins, which is the highest specificity obtained to date. The time required for enrichment of the phosphopeptides was 1 min only. PEI-modified magnetic nanoparticles carry positive charges over a wide range of pH—between 3 and 11. This feature means the particles are effectively dispersed in solution during phosphopeptide capture. Mass spectrometric analysis revealed the very high efficiency of enrichment of phosphopeptides that contain both single and multiply-phosphorylated sites. The detection limit in the analysis of phosphopeptides obtained from both bovine α-casein and β-casein by matrix-assisted laser desorption/ionization mass spectrometry was 5 fmol. This approach was also used to enrich the phosphopeptides in a protein digest obtained from non-fat milk.     

Highly efficient enrichment of phosphopeptides by magnetic nanoparticles coated with zirconium phosphonate for phosphoproteome analysis

The location of phosphorylation plays a vital role for the elucidation of biological processes. The challenge of low stoichiometry of phosphoproteins and signal suppression of phosphopeptides by nonphosphopeptides in mass spectrometry (MS) analysis makes the selective enrichment of phosphopeptides prior to MS analysis necessary. Besides the immobilized metal affinity chromatography (IMAC) method, some affinity methods based on nanoparticles displayed a higher enrichment efficiency for phosphopeptides such as Fe(3)O(4)/TiO2 and Fe(3)O(4)/ZrO(2) nanoparticles. To further improve the selectivity and compatibility of the affinity methods, a novel strategy based on magnetic nanoparticles coated with zirconium phosphonate for the enrichment of phosphopeptides has been developed in this study. Under optimized experimental conditions, 1 x 10(-9) M phosphopeptides in 50 microL tryptic digest of beta-casein could be enriched and identified successfully. Reliable results were also obtained for 1 x 10(-8) M phosphopeptides in 50 microL tryptic digest of beta-casein in the presence of nonphosphopeptides from a tryptic digest of bovine serum albumin (BSA) over 20 times in concentration. The performance of nanoparticles for use in a real sample was further demonstrated by employing the strong cation-exchange chromatography (SCX) fraction of a tryptic digest of a protein extract from Chang liver cells as a model sample. Experimental results show that the nanoparticles can be easily and effectively used for enrichment of phosphopeptides in low concentration. Most importantly, our approach is more compatible with commonly used SCX strategies than Fe(3+)-IMAC. The proposed method thus has great potential for future studies of large-scale phosphoproteomes.