Rapid enrichment of phosphopeptides by BaTiO3 nanoparticles after microwave-assisted tryptic digest of phosphoproteins, and their identification by MALDI-MS

We show that BaTiO₃ nanoparticles (NPs) can be used as a novel substrate for the rapid enrichment of phosphopeptides from microwave tryptic digests of α-casein and non-fat milk prior to their identification by MALDI-MS. Protein digestion is achieved by microwave tryptic digest for 50?s, and the resulting phosphopeptides can be effectively adsorbed on the surfaces of the NPs. The phosphopeptides were selectively detected via MALDI-MS. Digestion, enrichment and detection are accomplished within ～60?min. The method was applied to the indentification of 24 phosphopeptides from α-casein and of 21 phosphopeptides (of the α-casein type) from nonfat milk.

Recent developments in nanoparticle-based MALDI mass spectrometric analysis of phosphoproteomes

Mass spectrometry-based strategies are widely used for mapping of post-translational modifications of phosphoproteins. However, the presence of large amounts of non-phosphopeptides seriously interferes by suppressing the intensities of signals for phosphopeptides in direct MALDI-MS techniques due to the low stoichiometry of protein phosphorylation. Several MALDI-MS approaches are known which use either nanoparticles (NPs) as affinity probes, or NPs as microwave heat absorbers. They assist in the enrichment of trace levels of phosphopeptides from complex protein digests and require minimal sample pretreatment, digestion times, and sample volume. This leads to enhance sensitivity and selectivity in the analysis of the phosphoproteomes. This review (with 89 refs.) summarizes and discusses recent developments in the field, with a particular focus on the potential use of nanomaterials such as metal oxides, metal NPs, NPs-coated target plates, and as core-shell nanocomposites acting as affinity probes and as heat absorbers in MALDI-MS analysis of phosphoproteomes.

Ti-SBA-15介孔材料用于磷酸化肽的高效富集

结合基质辅助激光解吸飞行时间质谱(MALDI-TOF MS)检测技术,考察了Ti-SBA-15介孔材料对β-酪蛋白酶解产物中磷酸化肽的选择性富集性能。实验结果显示,含Ti和Si物质的量比为0.08的Ti-SBA-15介孔材料可选择性地对β-酪蛋白酶解产物中的磷酸化肽进行选择性富集;对于β-酪蛋白和牛血清白蛋白物质的量比为1:100的蛋白质酶解混合液,Ti-SBA-15仍能实现对其磷酸化肽的有效富集。上述结果表明,作为一种多孔、高比表面积的磷酸化多肽的选择性吸附材料,Ti-SBA-15有望在磷酸化蛋白质组的分析中得到广泛的应用。     

A capillary column packed with a zirconium(IV)-based organic framework for enrichment of endogenous phosphopeptides

A zirconium(IV)-based metal organic framework (Zr-MOF) was deposited on polydopamine-coated silica microspheres to form microspheres of type SiO₂@PDA@Zr-MOF. These were packed into capillary columns for enrichment of phosphopeptides. The column was off-line coupled to both matrix-assisted laser desorption/ionization time of flight mass spectrometry and LC-ESI-MS/MS. The method has a detection limit as low as 4 fmol of β-casein digest and a selectivity as high as 1:1000 (molar ratio of β-casein and BSA digest). It was applied to the analysis of human saliva. In total, 240 endogenous phosphopeptides were identified in only 25 μL human saliva.

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Graphical abstract A zirconium-based metal organic framework (Zr-MOF) was modified outside of polydopamine-coated silica microspheres to form microspheres named SiO₂@PDA@Zr-MOF. Then they were packed in capillary columns for selective enrichment of phosphopeptides via interaction between Zr-O clusters and phosphate groups. The pre-concentration resulted in a better detection of phosphopeptides by mass spectrometry. Tris: Tris(hydroxymethyl)aminomethane; DMF: Dimethyl Formamide; Zr-MOF: Zirconium(IV)-organic framework; MOAC: Metal oxide affinity chromatography.

     

Fully automated isotopic dimethyl labeling and phosphopeptide enrichment using a microfluidic HPLC phosphochip

Quantitative detection of phosphorylation levels is challenging and requires an expertise in both stable isotope labeling as well as enrichment of phosphorylated peptides. Recently, a microfluidic device incorporating a nanoliter flow rate reversed phase column as well as a titania (TiO₂) enrichment column was released. This HPLC phosphochip allows excellent recovery and separation of phosphorylated peptides in a robust and reproducible manner with little user intervention. In this work, we have extended the abilities of this chip by defining the conditions required for on-chip stable isotope dimethyl labeling allowing for automated quantitation. The resulting approach will make quantitative phosphoproteomics more accessible.

Preparation of monodisperse immobilized Ti affinity chromatography microspheres for specific enrichment of phosphopeptides

This study presented an approach to prepare monodisperse immobilized Ti⁴⁺ affinity chromatography (Ti⁴⁺-IMAC) microspheres for specific enrichment of phosphopeptides in phosphoproteome analysis. Monodisperse polystyrene seed microspheres with a diameter of ca. 4.8 μm were first prepared by a dispersion polymerization method. Monodisperse microspheres with a diameter of ca. 13 μm were prepared using the seed microspheres by a single-step swelling and polymerization method. Ti⁴⁺ ion was immobilized after chemical modification of the microspheres with phosphonate groups. The specificity of the Ti⁴⁺-IMAC microspheres to phosphopeptides was demonstrated by selective enrichment of phosphopeptides from mixture of tryptic digests of α-casein and bovine serum albumin (BSA) at molar ratio of 1 to 500 by MALDI-TOF MS analysis. The sensitivity of detection for phosphopeptides determined by MALDI-TOF MS was as low as 5 fmol for standard tryptic digest of β-casein. The Ti⁴⁺-IMAC microspheres were compared with commercial Fe³⁺-IMAC adsorbent and homemade Zr⁴⁺-IMAC microspheres for enrichment of phosphopeptides. The phosphopeptides and non-phosphopeptides identified by Fe³⁺-IMAC, Zr⁴⁺-IMAC and Ti⁴⁺-IMAC methods were 26, 114, 127 and 181, 11, 11 respectively for the same tryptic digest samples. The results indicated that the Ti⁴⁺-IMAC had the best performance for enrichment of phosphopeptides.     

Novel nanomaterials used for sample preparation for protein analysis

Sample preparation is of vital importance for proteomic analysis because of the high complexity of biological samples. The rapid development of novel nanomaterials with various compositions, morphologies, and proper surface modifications provides a category of powerful tools for the sample preparation for protein analysis. In this paper, we have summarized recent progresses for the applications of novel nanomaterials in sample preparation for the analysis of proteomes, especially for phosphoproteomes, glycoproteomes, and peptidoms. Several kinds of novel nanomaterials were also discussed for their use in other kinds of proteomics analysis.

Specific biotinylation and sensitive enrichment of citrullinated peptides

Protein citrullination is a posttranslational modification where peptidylarginine is enzymatically deiminated to form peptidylcitrulline. Although the role of protein citrullination in both health and disease is being increasingly recognised, techniques available to identify citrullinated proteins and to map their citrullination site(s) are rare and often show poor sensitivity. Here, we present a sensitive technique for specific modification and selective enrichment of citrullinated peptides from complex biological samples. The technique is based on highly specific in-solution biotinylation of citrulline residues followed by selective enrichment of modified peptides using streptavidin beads. We demonstrate that a synthetic citrulline-containing peptide can be selectively enriched when less than 0.5 pmol is spiked into a highly heterogeneous peptide mixture. After enrichment, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of an aliquot of the streptavidin eluate corresponding to theoretically 50 fmol of the spiked-in peptide showed a prominent signal. We further demonstrate the sensitivity of our technique by enrichment of citrullinated peptides from enzymatically deiminated myelin basic protein (MBP), when 10 pmol was spiked into a heterogeneous biological digest. In MALDI-TOF MS analysis, six MBP-derived citrullinated peptides were observed, showing the efficiency of this enrichment strategy. The high sensitivity combined with the remarkable specificity of the described technique makes it a valuable tool for elucidating citrullination in various biological processes.

Direct multielement determination of trace elements in boron carbide powders by direct current arc atomic emission spectrometry using a CCD spectrometer

The use of direct current arc atomic emission spectrometry (DC-arc-AES) with a CCD spectrometer for the direct determination of the trace impurities Al, Ca, Cr, Cu, Fe, Mg, Mn, Na, Ni, Si, Ti, and Zr in three well characterized boron carbide powders is described. The detection limits obtained by the procedure were found to be between 0.2 (Mg) and 25 (Na) ??g?g^?1 for the above elements. Three boron carbide powder samples with trace element concentrations between 0.9 (Cu) and 934 (Si) ??g?g^?1 for Al, Ca, Cr, Cu, Fe, Mg, Mn, Na, Ni, Si, Ti, and Zr ?? including the standard reference material ERM?-ED102 ?? were analyzed by DC-arc-AES. The relative standard deviations for 9 measurements when using 5.0?±?0.3?mg of the respective samples were found to vary from 6.2 to 27% for Al and Cu, respectively. The trace elements Al, Ca, Cr, Cu, Fe, Mn, Ni, Si, Ti and Zr could be determined in the standard reference material and their concentrations determined by DC-arc AES were found to be between 89 and 116% of the accepted values. Fe and Ti were determined by DC-arc AES in the three boron carbide samples as well as in Al₂O₃, BN, SiC, coal fly ash, graphite and obsidian rock. The correlation coefficients of the plots of the net intensities versus the accepted values over the concentration ranges from 18 to 1750 and from 6 to 8000???g?g^?1 are 0.999 and 0.990 for Fe and Ti, respectively.

A two-dimensional HPLC separation for the enantioselective determination of hexabromocyclododecane (HBCD) isomers in biota samples

A new method for enantioselective analysis of isomers of hexabromocyclododecane (HBCD) is described, using a two-dimensional high-performance liquid chromatography (HPLC) approach to avoid coelution, in particular between (+) α-HBCD, (+) β-HBCD, or (+) γ-HBCD. After isomer separation on a conventional column, the single isomers are transferred to an enantioselective HPLC column using heart cuts. Two enantioseparations are conducted in two separate partial chromatograms: one for α-HBCD and one for β- and γ-HBCD. The result is a completely undisturbed enantioselective separation for α-HBCD at a resolution of 4.11. A peak capacity of 107 was achieved. This peak capacity is utilized by the six peaks of the three isomers with two enantiomers each by 6 %. This method was applied to samples of sand eel oil, glaucous gull, and ringed seal. The calibration was performed by treating each enantiomer as a single analyte using a multilevel internal standard calibration. Enantiomeric fractions of 0.495–0.501 with standard deviations (SDs) of 0.056–0.071 were determined for racemic standards of α-HBCD, while the values for fish oil were 0.548–0.562 with SD of 0.018–0.041, depending on the respective mass spectrometric transition.

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

The strategy to concentrate phosphopeptides has become a critical issue for mapping protein phosphorylation sites, which are well known as posttranslational modifications in proteomics. In this study, we propose a simple and highly sensitive method for phosphopeptide enrichment on NiO nanoparticles (NPs) from a trypsin predigested phosphoprotein complex solution in a microwave oven. Furthermore, this technique was combined with centrifugation on-particle ionization/enrichment of phosphopeptides and phosphopeptides were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Weak magnetism of these NPs and a positive surface charge effect at low pH accomplished rapid and selective phosphopeptide enrichment within 30s. Trypsin-digested products of phosphoproteins such as α-casein and β-casein, human blood serum, nonfat milk, and egg white were also investigated to explore their phosphopeptide enrichment from complex samples by this approach. The results demonstrate that NiO NPs exhibit good affinity to trace the phosphopeptides even in the presence of 30 times higher molar concentration of complex solution of non-phosphopeptide proteolytic predigested bovine serum albumin. The detection limits of NiO NPs for α-casein and β-casein were 2.0?×?10(-9) M, with good signal-to-noise ratio in the mass spectrum. NiO NPs were found to be effective and selective for enrichment of singly and multiply phosphorylated peptides at a trace level in complex samples in a microwave oven. The cost of preparing NiO NPs is low, the NiO NPs are thermally stable, and therefore, they hold great promise for use in phosphopeptide enrichment.     

Comparison of different extraction methods for simultaneous determination of B complex vitamins in nutritional yeast using LC/MS-TOF and stable isotope dilution assay

The application of LC/MS-TOF method combined with stable isotope dilution assay was studied for determination of thiamine, riboflavin, nicotinamide, nicotinic acid, pantothenic acid, pyridoxal, and pyridoxine in food. Nutritional yeast powder was used as a model food matrix. Acid extraction was compared with various enzymatic treatments in ammonium formate buffer to find a suitable method for the conversion of more complex vitamers into the same forms as the used isotope-labeled internal standards. The enzyme preparations α-amylase, takadiastase, β-glucosidase, and acid phosphatase were all able to liberate thiamine and riboflavin. The diastatic enzyme preparations α-amylase and takadiastase also expressed proteolytic side activities resulting in the formation of small peptides which interfered with the mass spectra of thiamine and riboflavin. Liberation of nicotinamide and pantothenic acid from NAD⁺ and CoA, respectively, could not be achieved with any of the studied enzyme preparations. Hydrochloric acid extraction at 121 °C for 30 min was found to be destructive to pantothenic acid, but increased the liberation of pyridoxal.

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.     

Study of an Unusual Advanced Glycation End-Product (AGE) Derived from Glyoxal Using Mass Spectrometry

Glycation is a post-translational modification (PTM) that affects the physiological properties of peptides and proteins. In particular, during hyperglycaemia, glycation by α-dicarbonyl compounds generate α-dicarbonyl-derived glycation products also called α-dicarbonyl-derived advanced glycation end products. Glycation by the α-dicarbonyl compound known as glyoxal was studied in model peptides by MS/MS using a Fourier transform ion cyclotron resonance mass spectrometer. An unusual type of glyoxal-derived AGE with a mass addition of 21.98436 Da is reported in peptides containing combinations of two arginine-two lysine, and one arginine-three lysine amino acid residues. Electron capture dissociation and collisionally activated dissociation results supported that the unusual glyoxal-derived AGE is formed at the guanidino group of arginine, and a possible structure is proposed to illustrate the 21.9843 Da mass addition.

Distribution of surfactant ions near the surface of non-aqueous solution gained by angular resolved X-ray photoelectron spectroscopy

Angular resolved X-ray photoelectron spectroscopy (ARXPS) has been applied to obtain the distribution of chemical elements near the surface of non-aqueous solutions containing surfactants. However, such profiles can only yield a quantitative relation between those constituents near the surface regime of sample. With the knowledge of the molar volumes of surfactant and solvent, we have obtained the molar concentration-depth profiles via the molar fraction-depth profiles that were reconstructed by ARXPS with the help of a generic algorithm. The concentration profiles show detailed distributions of the surfactant ions near the surface, which provide a direct insight into the surface picture of the surfactant solution.

Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO₂ laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety’s high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.

Direct high-performance liquid chromatographic enantioseparation of free α-, β- and γ-aminophosphonic acids employing cinchona-based chiral zwitterionic ion exchangers

We report a chiral high-performance liquid chromatographic enantioseparation method for free α-aminophosphonic, β-aminophosphonic, and γ-aminophosphonic acids, aminohydroxyphosphonic acids, and aromatic aminophosphinic acids with different substitution patterns. Enantioseparation of these synthons was achieved by means of high-performance liquid chromatography on CHIRALPAK ZWIX(+) and ZWIX(-) (cinchona-based chiral zwitterionic ion exchangers) under polar organic chromatographic elution conditions. Mobile phase characteristics such as acid-to-base ratio, type of counterion, and solvent composition were systematically varied in order to investigate their effect on the separation performance and to achieve optimal separation conditions for the set of analytes. Under the optimized conditions, 32 of 37 racemic aminophosphonic acids studied reached baseline separation when we employed a single generic mass-spectrometry-compatible mobile phase, with reversal of the elution order when we used (+) and (-) versions of the chiral stationary phase.

Spectral Reproducibility and Quantification of Peptides in MALDI of Samples Prepared by Micro-Spotting

Previously, we reported that MALDI spectra of peptides became reproducible when temperature was kept constant. Linear calibration curves derived from such spectral data could be used for quantification. Homogeneity of samples was one of the requirements. Among the three popular matrices used in peptide MALDI [i.e., α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), and sinapinic acid (SA)], homogeneous samples could be prepared by conventional means only for CHCA. In this work, we showed that sample preparation by micro-spotting improved the homogeneity for all three cases.

Method development and inter-laboratory comparison about the determination of titanium from titanium dioxide nanoparticles in tissues by inductively coupled plasma mass spectrometry

Nanosized titanium dioxide (TiO₂) is one of the most interesting and valuable nanomaterials for the construction industry but also in health care applications, food, and consumer goods, e.g., cosmetics. Therefore, the properties associated with this material are described in detail. Despite its widespread use, the analytical determination and characterization of nanosized metal oxides is not as straightforward as the comparatively easy-to-detect metallic nanoparticles (e.g., silver or gold). This study presents the method development and the results of the determination of tissue titanium (Ti) levels after treatment of rats with the nanosized TiO₂. Total Ti levels were chosen to evaluate the presence and distribution of TiO₂ nanoparticles. A procedure consisting of incubation with a mixture of nitric acid (HNO₃) and hydrofluoric acid (HF), and heating was developed to digest tissues and TiO₂ nanomaterials in order to determine the total Ti content by inductively coupled plasma mass spectrometry (ICPMS). For the inter-laboratory comparison, altogether four laboratories analyzed the same samples upon digestion using the available ICPMS equipment. A major premise for any toxicokinetic study is the possibility to detect the chemical under investigation in biological samples (tissues). So, the study has to be performed with a dose high enough to allow for subsequent tissue level measurement of the chemical under investigation. On the other hand, dose of the chemical applied should not induce over toxicity in the animal as this may affect its absorption, distribution, metabolism, and excretion. To determine a non-toxic TiO₂ dosage, an acute toxicity study in rats was performed, and the organs obtained were evaluated for the presence of Ti by ICPMS. Despite the differences in methodology and independent of the sample preparation and the ICPMS equipment used, the results obtained for samples with Ti concentrations >4 μg Ti/g tissue agreed well.

Microchip-based strategy for enrichment of acetylated proteins

We have developed a simple microchip-based method for the separation and enrichment of acetylated proteins and peptides using a microchip technique. Poly (dimethylsiloxane) (PDMS) microfluidic channels were modified by passing an acidic solution of hydrogen peroxide through them. This resulted in hydrophilic silanol-covered surfaces onto which poly (diallyldimethylammonium chloride) (PDDA) can be coated. Protein A/G beads were then captured by the PDDA layer and antibodies can then be immobilized via the protein A/G. This technique enables efficient capture of antigens due to the optimal spacing and orientation of surface molecules. Two solutions, one containing 72.5 fmol?μL^?1 of acetylated bovine serum albumin (BSA-Ac), the other 72.5 fmol?μL^?1 of tryptic BSA-Ac digest were then enriched. High selectivities were obtained, and a 82.4 % recovery of the acetylated proteins was attained. This on-chip platform was then coupled to MALDI-MS to provide information on the acetylation sites of proteins and peptides. Additional peaks were observed in the mass spectra after enrichment and were assigned to acetylated peptides. This is significant with respect to understanding the mechanism and function of acetylation. In our opinion, this microchip-based technique has a large potential for detecting acetylated proteins and peptides in complex biological mixtures, and in acetylomics in general.