Phytic acid functionalized Fe3O4 nanoparticles loaded with Ti(IV) ions for phosphopeptide enrichment in mass spectrometric analysis

Enrichment of Phosphopeptides Based on Zirconium Phthalocyanine-Modified Magnetic Nanoparticles

Highly selective extraction of phosphopeptides is necessary before mass spectrometry (MS) analysis. Herein, zirconium phthalocyanine-modified magnetic nanoparticles were prepared through a simple method. The Fe-O groups on Fe3O4 and the zirconium ions on phthalocyanine had a strong affinity for phosphopeptides based on immobilized metal ion affinity chromatography (IMAC). The enrichment platform exhibited low detection limit (0.01 fmol), high selectivity (α-/β-casein/bovine serum albumin, 1/1/5000), good reusability (10 circles), and recovery (91.1 ± 1.1%) toward phosphopeptides. Nonfat milk, human serum, saliva, and A549 cell lysate were employed as actual samples to assess the applicability of the enrichment protocol. Metallo-phthalocyanine will be a competitive compound for designing highly efficient adsorbents and offers a new approach to phosphopeptide analysis.

Preparation of high-efficiency titanium ion immobilized magnetic graphite nitride nanocomposite for phosphopeptide enrichment

BACKGROUND

Protein phosphorylation has been implicated in life processes including molecular interaction, protein structure transformation, and malignant disease. An in-depth study of protein phosphorylation may provide vital information for the discovery of early biomarkers. Mass spectrometry (MS)-based techniques have become an important method for phosphopeptide identification. Nevertheless, direct detection remains challenging because of the low ionization efficiency of phosphopeptides and serious interference from non-phosphopeptides. There is a great need for an efficient enrichment strategy to analyze protein phosphorylation prior to MS analysis.

RESULTS

In this study, a novel nanocomposite was prepared by introducing titanium ions into two-dimensional magnetic graphite nitride. The nanocomposite was combined with immobilized metal ion affinity chromatography (IMAC) and anion-exchange chromatography mechanisms for phosphoproteome research. The nanocomposite had the advantages of a large specific surface (412.9 m2 g-1), positive electricity (175.44 mV), and excellent magnetic property (35.7 emu g-1). Moreover, it presented satisfactory selectivity (α-casein:β-casein:bovine serum albumin = 1:1:5000), a low detection limit (0.02 fmol), great recyclability (10 cycles), and high recovery (92.8%). The nanocomposite demonstrated great practicability for phosphopeptides from non-fat milk, human serum, and saliva. Further, the nanocomposite was applied to enrich phosphopeptides from a more complicated specimen, A549 cell lysate. A total of 890 phosphopeptides mapping to 564 phosphoproteins were successfully detected with nano LC-MS.

SIGNIFICANCE

We successfully designed and developed an efficient analysis platform for phosphopeptides, which includes protein digestion, phosphopeptide enrichment, and MS detection. The MS-based enrichment platform was further used to analyze phosphopeptides from complicated bio-samples. This work paves the way for the design and preparation of graphite nitride-based IMAC materials for phosphoproteome analysis.

Cerium ions immobilized magnetic graphite nitride decorated with L-Alanyl-L-Glutamine as new chelator for enrichment of phosphopeptides

Cerium ions immobilized magnetic graphite nitride material have been prepared using L-Alanyl-L-Glutamine as the new chelator. The resulting Fe3O4/g-C3N4-L-Ala-L-Gln-Ce4+, as an immobilized metal ion affinity chromatography (IMAC) sorbent, was reusable. This is due to the strong coordination interaction between L-Alanyl-L-Glutamine and cerium ions. After a series of characterizations, the magnetic nanocomposite showed high surface area, good hydrophilicity, positive electricity, and magnetic response. Fe3O4/g-C3N4-L-Ala-L-Gln-Ce4+ had high sensitivity (0.1 fmol), selectivity (α-/β-casein/bovine serum albumin, 1:1:5000), and good recyclability (10 cycles). A total of 647 unique phosphopeptides mapped to 491 phosphoproteins were identified from A549 cell lysate by nano LC-MS analysis.

Bifunctional Ti4+-modified paper for selective extraction or removal of phospholipids and paper spray mass spectrometry for bioanalysis in urine and plasma

BACKGROUND

Phospholipids (PLs) are major constituents of cell membranes, play important roles in cell proliferation and death, as well as in signal transduction, and therefore are relevant biomarkers for different pathologies. On the other hand, when the analysis of small compounds, such as therapeutics in blood is desired, then phospholipids are part of the matrix and cause serious interference during analysis. Currently, both the analysis and removal of PLs from biological samples are limited by extensive sample preparation and instrumental separation.

RESULTS

A fast and simple quantitative Ti4+-modified paper spray tandem mass spectrometric (TiPS-MS/MS) method was established in urine, where the enrichment of phospholipids was achieved, as well as reduction of matrix effects (primarily caused by high salt content) that ultimately led to improved sensitivity and selectivity. The method could achieve a physiologically relevant limit of detection (0.01-0.03 μg mL-1). Also, the usefulness of the Ti4+-modified paper was investigated in the opposite mode, namely for the selective removal of phospholipids from matrices such as plasma. Clonidine is used as model compound, as the detection of this compound is known to suffer from ion suppression by phospholipids. Compared with blank paper spray tandem mass spectrometry, the limit of detection could be improved from 0.3 μg mL-1 to 0.03 μg mL-1 by employing a Ti4+-modified paper on top of the spray tip to capture phospholipids from the sample.

SIGNIFICANCE AND NOVELTY

A novel Ti4+-modified paper was developed to allow for rapid solid-phase extraction of phospholipids from urine or selective removal from plasma, followed by direct paper spray mass spectrometric detection as a fast and convenient sample preparation and analysis combination. The paper properties are based on the Ti4+ metal ion, which can selectively bind phosphate-containing compounds under acidic conditions, and its applicability was demonstrated in relevant biological matrices.

ATP-Coated Dual-Functionalized Titanium(IV) IMAC Material for Simultaneous Enrichment and Separation of Glycopeptides and Phosphopeptides

Protein glycosylation and phosphorylation are two of the most common post-translational modifications (PTMs), which play an important role in many biological processes. However, low abundance and poor ionization efficiency of phosphopeptides and glycopeptides make direct MS analysis challenging. In this study, we developed a hydrophilicity-enhanced bifunctional Ti-IMAC (IMAC: immobilized metal affinity chromatography) material with grafted adenosine triphosphate (denoted as epoxy-ATP-Ti4+) to enable simultaneous enrichment and separation of common N-glycopeptides, phosphopeptides, and M6P glycopeptides from tissue/cells. The enrichment was achieved through a dual-mode mechanism based on the electrostatic and hydrophilic properties of the material. The epoxy-ATP-Ti4+ IMAC material was prepared from epoxy-functionalized silica particles via a convenient two-step process. The ATP molecule provided strong and active phosphate sites for binding phosphopeptides in the conventional IMAC mode and also contributed significantly to the hydrophilicity, which permitted the enrichment of glycopeptides via hydrophilic interaction chromatography. The two modes could be implemented simultaneously, allowing glycopeptides and phosphopeptides to be collected sequentially in a single experiment from the same sample. In addition to standard protein samples, the material was further applied to glycopeptide and phosphopeptide enrichment and characterization from HeLa cell digests and mouse lung tissue samples. In total, 2928 glycopeptides and 3051 phosphopeptides were identified from the mouse lung tissue sample, supporting the utility of this material for large-scale PTM analysis of complex biological samples. Overall, the newly developed epoxy-ATP-Ti4+ IMAC material and associated fractionation method enable simple and effective enrichment and separation of glycopeptides and phosphopeptides, offering a useful tool to study potential crosstalk between these two important PTMs in biological systems. The MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029775.

A nitrogen-doped graphene tube composite based on immobilized metal affinity chromatography for the capture of phosphopeptides

A novel immobilized metal affinity chromatography (IMAC) functional composite, mNi@N-GrT@PDA@Ti⁴⁺, was fabricated based on ultrathin magnetic nitrogen-doped graphene tube (mNi@N-GrT) after chelated Ti⁴⁺ with polydopamine, following as a magnetic solid-phase extraction sorbent for rapidly selective enrichment and mass spectrometry identification of phosphorylated peptides. After optimized, the composite exhibited high specificity in the enrichment of phosphopeptides from the digest mixture of β-casein and bovine serum albumin (BSA). The robust method presented the low detection limits (1 fmol, 200 μL) and excellent selectivity (1:100) in the molar ration mixture of β-casein and BSA digests. Furthermore, the selective enrichment of phosphopeptides in the complex bio-samples, was successfully carried out. The results showed that 28 phosphopeptides were finally detected in mouse brain, and 2087 phosphorylated peptides were identified in the HeLa cells extracts with specific selectivity of 95.6%. The enrichment performance of mNi@N-GrT@PDA@Ti⁴⁺ was satisfactory, suggesting that the functional composite provided a potential application in the enrichment of trace phosphorylated peptides from the complex biological matrix.

A Ti/Nb-functionalized COF material based on IMAC strategy for efficient separation of phosphopeptides and phosphorylated exosomes

In this work, on the basis of an immobilized metal ion affinity chromatography enrichment strategy, a new kind of covalent organic framework (COF) material for enrichment of phosphorylated peptides and exosomes was successfully prepared in a facile method, and Ti⁴⁺ and Nb⁵⁺ were used as dual-functional ions (denoted as COF-S-S-COOH-Ti⁴⁺/Nb⁵⁺). With the advantage of unbiased enrichment towards phosphopeptides, COF-S-S-COOH-Ti⁴⁺/Nb⁵⁺ shows ultra-high selectivity (maximum molar ratio of β-casein: BSA is 1:20,000) and low limit of detection (0.2 fmol). In addition, the material has an excellent phosphopeptide loading capacity (100 μg/mg) and reusability (at least seven times). Furthermore, applying the material to the actual sample, 4 phosphopeptides were selectively extracted from the serum of renal carcinoma patients. At the same time, exosomes with an intact structure in the serum of renal carcinoma patients were successfully isolated rapidly using this strategy. All experiments have shown that COF-S-S-COOH-Ti⁴⁺/Nb⁵⁺ exhibits exciting potential in practical applications.

Addition of Organic Acids during PEO of Titanium in Alkaline Solution

This research study describes recent advances in understanding the effects of the addition of organic acids, such as acetic, lactic, citric and phytic acids, on the process of plasma electrolytic oxidation (PEO) on Ti using an alkaline bath. As the plasma developed over the workpiece is central to determine the particular morphological and structural features of the growing oxide, the focus is then on the inter-relationships between the electrolyte and the resultant plasma regime established. In situ optical emission spectroscopy (OES) allowed us to verify a marked plasma suppression when adding low-molecular-weight anions such as acetates, resulting in short-lived and well-distributed discharges. Conversely, when more bulky anions, such as lactates, citrates and phytates, were considered, a less efficient shielding of the electrode caused the build-up of long-lasting and destructive sparks responsible for the formation of thicker coatings, even >30 µm, at the expense of a higher roughness and loss of compactness. Corrosion resistance was tested electrochemically, according to electrochemical impedance spectroscopy (EIS), and weight losses evidenced the coatings produced in the solution containing acetates to be more suitable for service in H2SO4.

Facile synthesis of Ti4+-immobilized magnetic covalent organic frameworks for enhanced phosphopeptide enrichment

In this work, core-shell structured Ti⁴⁺-immobilized magnetic covalent organic frameworks (denoted as Fe₃O₄@TAPTDHTA-Ti⁴⁺ composites) were prepared for enhanced phosphopeptide enrichment by one-pot synthesis of COFs shell with inherent bifunctional groups on Fe₃O₄ NPs and further Ti⁴⁺ immobilization. The widely distributed bifunctional groups could provide abundant chelating sites for Ti⁴⁺ immobilizing. Combining with the high specific surface area and mesoporous structure, the Fe₃O₄@TAPTDHTA-Ti⁴⁺ composites exhibited excellent enrichment efficiency for phosphopeptides, such as low detection limit (0.05 fmol μL^-1), high selectivity (1:5000 of molar ratio of β-casein/bovine serum albumin (BSA) tryptic digests), high adsorption capacity (62.9 μg mg^-1) and strong size-exclusive effect (1:250:250 of molar ratio of β-casein tryptic digest/β-casein/BSA). In addition, this method was general for immobilizing other metal ions (Zr⁴⁺ and Fe³⁺). Notably, the Fe₃O₄@TAPTDHTA-Fe³⁺ composites exhibited controllable affinity towards mono-phosphopeptides and multi-phosphopeptides. Furthermore, the Fe₃O₄@TAPTDHTA-Ti⁴⁺ composites were successfully applied to selectively capture phosphopeptides from complex biological samples including the tryptic digest of nonfat milk, human serum and human saliva. More significantly, 3333 phosphopeptides derived from 1409 phosphoproteins with 3492 phosphorylation sites were clearly identified from the tryptic digest of HeLa cell lysate. In addition to providing a potential excellent enrichment probe for comprehensive phosphoproteomic analysis, this study also offers a new perspective for the functionalization of COFs.

Development of dual-ligand titanium (IV) hydrophilic network sorbent for highly selective enrichment of phosphopeptides

A hydrophilic metal-organic network based on Ti⁴⁺ and dual natural ligand, tannic acid (TA) and phytic acid (PA), has been developed to enrich phosphopeptides from complex bio-samples prior to liquid chromatography-mass spectrometric analysis. Due to the strong chelation ability of TA and PA, abundant Ti⁴⁺ can be immobilized in the material, forming hydrophilic network by one-step coordination-driven self-assembly approach. The sorbent, TA-Ti-PA@Fe₃O₄, exhibited satisfactory selectivity for the phosphopeptides in the tryptic digest of β-casein, and can eliminate the interference components in 1000-fold excess of bovine serum albumin. The adsorption capacity of the sorbents for phosphopeptides was up to 35.2 mg g^-1 and the adsorbing equilibrium can be reached in 5 min. The adsorbing mechanism has been investigated and the results indicated that the Ti⁴⁺ in forms of [Ti(f-TA)(H₂O)₄]²⁺, [Ti(f-PA)(H₂O)₄]²⁺ and Ti(f-PA)₂(H₂O)₂ may play an important role in the adsorption process. The sorbent of the TA-Ti-PA@Fe₃O₄ has been applied to enrichment of the phosphopeptides in tryptic digest of rat liver lysate, and 3408 phosphopeptides have been identified, while the numbers of the identified phosphopeptides were 2730 and 1217 when the sample was enriched by the commercial TiO₂ and Fe³⁺-IMAC kit, respectively. This work provides a strategy to enrich phosphopeptides from complex samples and shows great potential application in phosphoproteome research.

Recent trends in sorbents for bioaffinity chromatography

Isolation or enrichment of biological molecules from complex biological samples is mostly a prerequisite in proteomics, genomics, and glycomics. Different techniques have been used to advance the efficiency of the purification of biological molecules. Bioaffinity chromatography is one of the most powerful technique that plays an important role in the isolation of target biological molecules by the specific interactions with ligands that are immobilized on different support materials. This review examines the recent developments in bioaffinity chromatography particularly over the past 5 years in the literature. Also properties of supports, immobilization techniques, types of binding agents, and methods used in bioaffinity chromatography applications are summarized.

In situ synthesis of a novel metal oxide affinity chromatography affinity probe for the selective enrichment of low-abundance phosphopeptides

RATIONALE

Due to the dynamic nature of phosphorylation states and the low stoichiometry of phosphopeptides, it is still a challenge to efficiently capture phosphopeptides from complex biological samples before mass spectrometry analysis. Among the enrichment strategies, metal oxide affinity chromatography (MOAC) is one of the most widely used and the one with the most potential. It is based on reversible Lewis acid-base interactions between the metal oxides and the negatively charged phosphate groups to achieve the specific selection of phosphopeptides.

METHODS

A novel MOAC affinity probe, denoted as G@PDA@ZrO₂ , was successfully synthesized by in situ grafting ZrO₂ onto the surface of graphene (G) modified with polydopamine (PDA). The novel MOAC probe thus obtained was used for phosphopeptide enrichment.

RESULTS

This novel MOAC affinity probe when used to selectively enrich phosphopeptides from standard protein digest solutions exhibited a high selectivity (β-casein:bovine serum albumin = 1:1000), a low detection limit (4 fmol), and a high loading capacity (400 mg/g). At the same time, the experimental results proved that G@PDA@ZrO₂ had great recyclability (five cycles), stability, and reproducibility. Subsequently, G@PDA@ZrO₂ was applied to enrich phosphopeptides from human saliva and human serum, in which 25 and 4 phosphopeptide peaks, respectively, were detected.

CONCLUSIONS

This novel MOAC affinity probe (G@PDA@ZrO₂ ) showed good performance in enriching phosphopeptides. Thus, G@PDA@ZrO₂ has good potential in phosphopeptidomics analysis.

Targeted immobilization of titanium (IV) on magnetic mesoporous nanomaterials derived from metal-organic frameworks for high-efficiency phosphopeptide enrichment in biological samples

A selectively modified porous metal/carbon nanocomposite was fabricated to enhance the enrichment of low-abundance phosphopeptides from biological samples. The carbon matrix derived from the metal-organic framework provides a suitable pore size to allow the diffusion of peptides, while the deliberately modified metal nanoparticles within the pores enhance their interaction with the phosphopeptides. This nanocomposite shows extremely high enrichment selectivity for phosphopeptides in the MALDI-TOF MS detection, even when the molar ratio of α-casein digests versus bovine serum albumin digests was up to about 1:20,000. By combining such nanocomposite with nano-LC-MS/MS, 4556 unique phosphopeptides were identified with high selectivity (95.2%) from HeLa cell extracts. Furthermore, phosphopeptides from prostate tissue digests were also determined. A total of 277 and 1242 phosphopeptides were identified from normal and tumor tissues of a patient with prostate cancer, respectively. This indicates that phosphorylation and prostate cancer can be related to each other.

Magnetic metal phenolic networks: expanding the application of a promising nanoprobe to phosphoproteomics research

Ti–tannic acid modified Fe₃O₄ was prepared through a facile, mild and eco-friendly synthesis procedure and can be applied to identify phosphopeptides from HeLa cell extracts with high efficiency.

A polymer monolith composed of a perovskite and cucurbit[6]uril hybrid for highly selective enrichment of phosphopeptides prior to mass spectrometric analysis

A hybrid monolith was prepared from perovskite and cucurbit[6]uril [poly(hydroxyethyl methacrylate-pentaerythritol triacrylate) monolith] for the enrichment of phosphopeptides. By coupling with mass spectrometry, three goals were simultaneously realized, viz. (a) selective enrichment of phosphopeptides from non-phosphopeptides, (b) identification of mono- and multi-phosphopeptides, and (c) recognition of tyrosine phosphopeptides. The perovskite introduced into the monolith warrants high selectivity for phosphopeptides even at a high (10,000:1) ratio of non-phosphopeptides to phosphopeptides, and and enables identification of eight mono- and multi-phosphopeptides from standard β-casein tryptic digests. Tyrosine phosphopeptides were specifically detected via the recognition capability of cucurbit[6]uril integrated into the monolith. The method has remarkably specific enrichment capacity for phosphopeptides from samples including human serum, nonfat milk, and human acute myelocytic leukemia cell lysate. Graphical abstractSchematic representation of a monolith integrated with perovskite and cucurbit[6]uril. The monolithic column was coupled with mass spectrometry and applied to the enrichment of phosphopeptides. The method has remarkably specific enrichment capacity for phosphopeptides from complex biological samples.

Titanium(IV)-functionalized zirconium-organic frameworks as dual-metal affinity probe for recognition of endogenous phosphopeptides prior to mass spectrometric quantification

A zirconium-organic framework was modified with titanium(IV) ions to obtain a modified framework that is shown to be a viable sorbent for selective capture of phosphopeptides. This dual-metal affinity probe exhibits 0.1 fM limits of detection and excellent size-exclusion effect (the mass ratio of β-casein digests/BSA/intact β-casein is 1:1000:1000). This is attributed to abundant Ti(IV) and Zr(IV) coordination sites and high porosity. The performance of the sorbent for extracting endogenous phosphopeptides from human serum and saliva was investigated. Especially, 105 endogenous phosphopeptides from saliva were captured specifically. In addition, the amino acid frequency of the enriched phosphopeptides was analyzed. Conservation of sequence around the identified phosphorylated sites from saliva confirmed that phosphorylation took place in the proline-directed motifs. Graphical abstractSchematic representation of a method for the specific enrichment of phosphopeptides by a modified metal-organic framework. Following size-exclusion elution, the phosphopeptides are quantified by mass spectrometry.