Highly selective and sensitive enrichment of phosphopeptides via NiO nanoparticles using a microwave-assisted centrifugation on-particle ionization/enrichment approach in MALDI-MS

Facile synthesis of titanium(IV) ion-immobilized arsenate-modified poly(glycidyl methacrylate) microparticles and the application to the specific enrichment of phosphoproteins

Selective separation and enrichment of phosphoproteins possess the distinct clinical and biological importance in the diagnosis, treatment, and management of several fatal human diseases. In this study, a facile synthesis of titanium(IV) ion-immobilized arsenate-modified poly(glycidyl methacrylate) microparticles (denoted as Ti⁴⁺-arsenate-PGMA-MPs) was developed for the efficient enrichment of intact phosphoproteins found in biologically complex protein samples. By virtue of the strong interaction between the titanium ions immobilized on the surface of Ti⁴⁺-arsenate-PGMA-MPs and phosphate groups of phosphoproteins, Ti⁴⁺-arsenate-PGMA-MPs had a high saturated adsorption capacity for phosphoproteins (901 mg/g for β-casein), which was much higher than that of non-phosphoproteins (73.5 mg/g for BSA). Ti⁴⁺-arsenate-PGMA-MPs were characterized by SEM, TEM, and FT-IR, and the average particle diameter was about 2.5 μm with good dispersibility. Besides, the application of Ti⁴⁺-arsenate-PGMA-MPs in real biological samples was investigated by SDS-PAGE analysis, and the results showed that Ti⁴⁺-arsenate-PGMA-MPs were able to enrich phosphoproteins efficiently.

Mechanical/Physical Methods of Cell Disruption and Tissue Homogenization

This chapter covers the various methods of mechanical cell disruption and tissue homogenization that are currently commercially available for processing small samples s < 1 mL) to larger multikilogram production quantities. These mechanical methods of lysing do not introduce chemicals or enzymes to the system. However, the energies required when using these "harsh," high mechanical energy methods can be enough to damage the very components being sought.The destruction of cell membranes and walls is effected by subjecting the cells (a) to shearing by liquid flow, (b) to exploding by pressure differences between inside and outside of cell, (c) to collision forces by impact of beads or paddles, or (d) a combination of these forces.Practical suggestions to optimize each method, where to acquire such equipment, and links to reference sources are included. Several novel technologies are presented.

Characterization of glycan isomers using magnetic carbon nanoparticles as a MALDI co-matrix

Matrix-assisted laser desorption ionization-in source decay (MALDI-ISD) analysis is a useful technique in the structural analysis of glycans. Our recent publication demonstrated that magnetic carbon nanoparticles (MCNPs), used as a MALDI co-matrix, significantly enhanced ISD efficiency for glycomic analysis by MALDI-TOF. In this study, MCNPs were used for the structural study of isomeric glycans. Results from the standard glycans confirmed easy distinction of positional and linkage isomers without the need for further derivatization of glycan molecules. Extensive glycosidic and cross-ring fragmented ions provided different fragment patterns for various glycan isomers. Core- and branch-fucosylated isomers were distinguished by several unique ions, and pseudo-MS³ data were used to recognize the fucosylated branch. Although no diagnostic fragment ion was observed for 2,3- and 2,6-linked sialic acid isomers, their MALDI-ISD patterns were found to be significantly different (P < 0.05). Furthermore, the method introduced in this study could not only be used for the identification of glycan isomers but has also proved effective for the isomeric structural confirmation of gangliosides. GD1a and GD1b gangliosides were easily distinguished by the diagnostic ion originated from GD1a, produced by Z_4αZ_2β cleavages. Moreover, liquid chromatography coupled with MALDI-TOF was applied to analyze N-glycan isomers derived from a pooled human blood serum sample, providing an alternative method of isomeric glycomic analysis of biological specimens.

Magnetic carbon nanoparticles as a MALDI co-matrix enable isomeric characterization of glycans in biological samples.

Yolk-shell magnetic mesoporous TiO2 microspheres with flowerlike NiO nanosheets for highly selective enrichment of phosphopeptides

In this work, we fabricated a yolk-shell magnetic composite that contains mesoporous TiO₂ as the inner shell and flowerlike NiO as the outer shell (denoted as Fe₃O₄@H-TiO₂@f-NiO) to reduce the limitations of single-component metal oxides in phosphopeptide enrichment. The NiO nanosheets play a synergistic role in phosphopeptide enrichment. And the unique flowerlike structure of NiO with sufficient space can facilitate the reversible insertion/extraction of peptides, which will have less impact on the enrichment process of the inner TiO₂ shell. The yolk-shell structure and two types of porous nanostructures endowed this composite with a high surface area (156.58 m² g^-1) and a large pore volume (0.37 cm³ g^-1). Owing to the high surface area and combined properties of TiO₂ and NiO, the Fe₃O₄@H-TiO₂@f-NiO microspheres showed a better performance for phosphopeptide enrichment than the same material without NiO nanosheets (Fe₃O₄@H-TiO₂). According to the LC-MS/MS results, 972 unique phosphopeptides were identified from HeLa cell extracts with a high selectivity (91.9%) by Fe₃O₄@H-TiO₂@f-NiO relative to 837 phosphopeptides (selectivity: 60.2%) by Fe₃O₄@H-TiO₂. The results demonstrated that, compared with single-component metal oxides, composite metal oxides could enhance the selectivity and sensitivity for phosphopeptide enrichment.

Insights into chemoselectivity principles in metal oxide affinity chromatography using tailored nanocast metal oxide microspheres and mass spectrometry-based phosphoproteomics

Custom-made nanocast metal oxide materials provide new insights into the mechanisms of metal oxide affinity chromatography, a method widely used to study proteome-wide protein phosphorylation.

Large protein analysis of Staphylococcus aureus and Escherichia coli by MALDI TOF mass spectrometry using amoxicillin functionalized magnetic nanoparticles

Bacteria or their protein and peptide entity enrichment using biomolecules-functionalized magnetic nanoparticles, and analysis by matrix assisted laser desorption/ionization mass spectrometry (MALDI MS) is a promising technique to analyze microorganisms. High and low molecular weight proteins like penicillin-binding proteins are responsible for final step synthesis of peptidoglycan biosynthesis; those are the target of lactam antibiotics. In this paper, we synthesized magnetic nanoparticles (mag-NPs) and further modified them with 3-aminopropyltriethoxysilane, and then the β-lactam antibiotic amoxicillin was covalently linked to their surface. β-Lactam group attributes as penicillin binding proteins (PBPs) in bacteria. Staphylococcus aureus and Escherichia coli were used as model bacteria for enrichment based on the β-lactam affinity of magnetic nanoparticles, and then the bacteria were easily separated by an external magnet. Several high molecular weight penicillin binding proteins (PBPs) were detected by MALDI MS containing 10(4) and 10(3) colony-forming unit (cfu) per milileter (mL) of S. aureus and E. coli, respectively. In the case of E. coli, higher molecular weight PBPs were observed at 20 to 55 kDa in MALDI mass spectra. However, S. aureus bacteria resulted with femAB operon-based proteins, with molecular weight of 49570.4 Da, by MALDI MS after using amoxicillin functionalized-mag-NPs. The current approach provides an effective bacteria detection and preconcentration method that has high potential in the near future for fast and sensitive diagnosis of pathogenic bacteria infection. Graphical Abstract Schematic for large proteins analysis by MALDI TOF MS (a) mag-NPs and bacterial interaction (b) Penicillin binding proteins trapping by Amox-mag-NPs.

CoFe2 O4 -ZnO nanoparticles for rapid microwave-assisted tryptic digestion of phosphoprotein and phosphopeptide analysis by matrix-assisted laser desorption/ionization mass spectrometry

RATIONALE

Phosphorylation is a post-translational modification of proteins that plays very important role in a large number of biological processes. However, despite recent advancements in phosphoproteome research, large-scale detection and characterization of phosphopeptides by mass spectrometry (MS) is still a challenging task due to the low abundance of phosphopeptides and sub-stoichiometric nature of phosphorylation sites. On-particle microwave-assisted trypsin digestion of phosphoproteins and enrichment of phosphopeptides is an effective method for identification/characterization of phosphopeptides. Magnetic nanoparticles typically can absorb microwave radiation and generate heat in order to resolve complex phosphproteins and to enhance the digestion rate and capture the phosphopeptides on their modified surfaces.

METHODS

In this study, we used a cheap and efficient method for rapid microwave-assisted tryptic digestion of phosphoproteins and simultaneous enrichment of phosphopeptides using CoFe2 O4 -ZnO magnetic nanoparticles. Using this technique, the digestion time of phosphoproteins can be reduced and the phosphopeptides can be quickly analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). For the first time, we have applied CoFe2 O4 -ZnO magnetic nanoparticles for enrichment of phosphopeptides from standard phosphoproteins (β-casein and ovalbumin), complex samples (human serum and egg white) and a protein mixture of β-casein and BSA (1:100).

RESULTS

Our results demonstrate that the capture efficiency of CoFe2 O4 -ZnO nanoparticles for β-casein and ovalbumin in MALDI-TOFMS is very high (detection limits 0.2 fmol and 20 fmol, respectively). The CoFe2 O4 -ZnO nanoparticles have high affinity for phosphopeptide enrichment for β-casein in complex mixtures with BSA at 1:10 and 1:100 molar ratios in the microwave within 30 s.

CONCLUSIONS

Compared with other reported magnetic nanoparticles, the CoFe2 O4 -ZnO nanoparticles are easy to prepare and handle, and can save time in the phosphopeptide enrichment procedure, making these nanoparticle a good choice for highly sensitive phosphopeptide enrichment. Copyright © 2016 John Wiley & Sons, Ltd.

Low-cost iron oxide magnetic nanoclusters affinity probe for the enrichment of endogenous phosphopeptides in human saliva

Simple and low cost iron oxide magnetic nanoclusters (Fe₃O₄ MNCs) affinity material has been directly applied for phosphorylated peptides/proteins enrichment.

Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis

Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field.

Enhanced enrichment performance of nickel oxide nanoparticles via fabrication of a nanocomposite with a graphene template

Using graphene as a template after modification with nickel oxide, a nanocomposite with an increased surface area is fabricated and applied to phosphopeptides.

Phosphonate-modified metal oxides for the highly selective enrichment of phosphopeptides

Phosphonate-modified metal oxides display higher selectivity than unmodified ones for the effective enrichment of phosphopeptides.

FOLIC ACID-FUNCTIONALIZED GOLD AND SILVER NANOPARTICLES: THEIR CYTOTOXIC EFFECT ON CANCEROUS MYELOID CELLS WITH MICROWAVE IRRADIATION

Introduction: Metal nanoparticles such as gold and silver nanoparticles have attracted much interest during the last decades for their special chemical and physical properties. Gold and silver nanoparticles can be functionalized with active biologic moieties like antibodies, drugs and chemicals, enabling them to react with specific cells. Furthermore, penetration and cytotoxic effects of nanoparticles can be increased by electromagnetic waves such as infrared, ultraviolet, radiofrequency and microwave. Aim: The aim of this study was to evaluate the rate of cell cytotoxicity induced by folic acid-functionalized gold and silver nanoparticles with and without microwave irradiation on cancer cells from patients with acute myeloid leukemia (AML). Method: Patients with known AML (M1, M2, M3 and M4), all recently diagnosed by histopathology, special stains and immunohistochemistry, and 4 normal persons were enrolled in the study. The blood mononuclear cell fraction was separated, so that the final concentration of neoplastic myeloid cells and normal mononuclear cells in each tube was adjusted to about 400 cells/μL. For preparation of folate-functionalized gold and silver nanoparticles, folic acid was dissolved in deionized water, added to 1 mM HAuCl4 and 1 mM AgNO3 solution, and incubated at 50°C for 8 h. Scanning electron micrographs, ultraviolet-visible spectrophotometer and Fourier transform infrared (FTIR) were used for confirmation of the synthesis of functionalized nanoparticles. After preparation, nanoparticles were added to cancerous and normal cell suspensions, and then incubated at 37°C for 1 h. Another experiment was carried out in the same way but with exposure to microwave irradiation for 10 s so that its temperature reached at 50°C, and then incubated at 37°C for 1 h, after which cell cytotoxicity was evaluated with MTT test. All of the tests were duplicated, and paired t-test was used to compare the mean absorbance read-out in each of the above-mentioned groups of wells. Results: The sizes of functionalized gold and silver nanoparticles were approximately 25 nm to 32 nm. After synthesis of functionalized nanoparticles, the tubes containing HAuCl4 turned to red color, and the peak absorbance for gold nanoparticles was at 520 nm. For AgNo3 , it turned to yellow color with a peak absorbance at 420 nm. FTIR test showed connection of folic acid moieties to gold and silver surfaces. This study showed that functionalized gold nanoparticles were more toxic than functionalized silver nanoparticles on cancer and normal cells. Also, microwave irradiation was more synergic with functionalized gold nanoparticles. Furthermore, the most effectiveness score was 2.87 for functionalized silver nanoparticles without microwave irradiation and the minimum effectiveness score was 2.20 for functionalized silver nanoparticles with microwave. Conclusion: This study clearly demonstrated that although functionalized gold nanoparticles have high toxicity to cells, but silver nanoparticles without microwave irradiation are more effective because of less cytotoxic effect on normal cells.

A comparative study on the mode of interaction of different nanoparticles during MALDI-MS of bacterial cells

We propose the benefits of preincubation during nanoparticle-assisted bacterial analysis, where the bacteria are grown along with the nanoparticles. We were able to obtain a two to ten fold enhancement of bacterial signals in 3 h compared to the generally used methodology followed in previous literature. The previous literature method required a long time (18 h) to obtain such an enhancement. We probe the interactions of two bacteria, Staphylococcus aureus and Pseudomonas aeruginosa, with Ag, NiO, Pt TiO(2) and ZnO nanoparticles via transmission electron microscopy, ultraviolet spectroscopy and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). Based on these results, we propose a mechanism for interaction of these five nanoparticles with bacteria. Two mechanisms were observed for the interactions: (1) Mechanism A is proposed for the Pt and NiO NPs which functioned based on affinity for bacterial cells. (2) Mechanism B was proposed for the bactericidal NPs such as TiO(2), ZnO and Ag NPs. The results indicate that the success of the unmodified NPs in MALDI-MS bacterial studies lies in following the ideal protocol for incubation at the ideal concentrations.

Monitoring the heat stress response of Escherichia coli via NiO nanoparticle assisted MALDI-TOF mass spectrometry

The heat stress response of Escherichia coli at various temperatures has been investigated using NiO nanoparticles assisted MALDI-TOF-MS. Significant numbers of protein peaks were obtained in the presence of NiO NPs when the samples were incubated at various temperatures in comparison with the control E. coli suspension (10(7)cfu/mL). The 10 kDa chaperonin (groES) is the principal protein operating both for the protection of proteins from denaturation and in the assembly of newly synthesized proteins. During the heat stress response with NiO NPs, 10 kDa chaperonin (grosES) proteins were detected using MALDI-TOF MS. The viability of E. coli was checked on LB agar plates at different temperatures and time treatments. In the presence of NiO NPs, viability decreases drastically; this has been explored and correlated with the MALDI-TOF MS results. Further, surface morphological changes of E. coli at different temperatures were investigated with NiO NPs by transmission electron microscopy (TEM). The response of heat stress toward E. coli for generating more stable protein ions can be applied for bacterial detection under high temperature conditions from biological, clinical and environmental samples.

Future perspective of nanoparticle interaction-assisted laser desorption/ionization mass spectrometry for rapid, simple, direct and sensitive detection of microorganisms

The introduction of nanoparticles into mass spectrometric research greatly influenced the applicability of this technique into various omics. Surface-modified or functionalized nanoparticles (NPs) have recently extended the use of mass spectrometry into microorganism research. We survey the application of unmodified NPs, for microorganism research, on the basis of our expertise in this area within the recent years in this decade. The use of unmodified NPs in mass spectrometry, especially with respect to microorganisms, is an untreaded research area, which we have ventured to probe and have been fruitful. On the basis of our experience, we provide an insight into the principle behind the use of unmodified NPs and provide guidelines to be followed to obtain significant results. We also brief the current scenario of nanoparticle interaction-assisted laser desorption/ionization mass spectrometry (NPILDI-MS) for rapid, simple, direct and sensitive detection of microorganisms on the basis of our past and present reports, quoting examples of successful application of this technique. Finally, we address the future of the NPILDI-MS technique and the tools needed to reach those visions.