Immobilized zirconium ion affinity chromatography for specific enrichment of phosphopeptides in phosphoproteome analysis

In-Tip Nanoreactors for Simultaneous Proteolysis and Enrichment of Phosphorylated Peptides

Protein phosphorylation introduces negative charges on the hydroxyl groups of serine, threonine, and tyrosine residues, reducing the ionization efficiency of phosphorylated peptides. The low abundance of phosphorylated peptides often diminishes their detection using mass spectrometry. To enhance the identification of the low-abundance peptides, an enrichment step was often used, which complicated the high-throughput analysis of phosphorylated proteomes. In this study, we developed a titanium dioxide surface-modified macroporous silicon encapsulated micropipette tips, loaded with trypsin, to integrate rapid enzymatic protein hydrolysis with selective enrichment and extraction of phosphorylated peptides within a microfluidic enzyme reactor. This streamlined approach simplified the protein sample preparation process, combining enzymatic hydrolysis, selective enrichment and separation while maintaining high efficiency. The method enabled comprehensive analysis of complex cancer cell line samples in 1-2 h. Successful detection of phosphorylated peptides from protein mixtures was achieved using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry. This application may provide the potential for high-throughput phosphoproteomics and advance the study of protein modifications.

Immobilized metal ion affinity chromatography: waltz of metal ions and biomacromolecules

INTRODUCTION

Immobilized metal ion affinity chromatography (IMAC) is an effective method developed in the 1980s for the separation and purification of proteins. The system consists of a solid-phase matrix, a linking ligand, and a metal ion. The method is based on the ability of metal ions to bind specifically to certain specific amino acid residues of proteins, thereby selectively enriching and purifying proteins.

AREAS COVERED

This review aims to describe current knowledge of fundamental principle of IMAC and summarize the supports, chelating ligands, and metal ions of IMAC. In addition, how IMAC technology is used in proteomics and nucleic acids research are highlighted.

EXPERT OPINION

Over the past decades, IMAC has been extensively utilized as a predominant technique for protein enrichment in a variety of biological and medical research, such as disease diagnosis, tumor biomarker identification, protein purification, and nucleic acids research. In the future, IMAC should be integrated with other emerging proteomics technologies to promote the applications of metalloproteomes in disease diagnosis, metallodrug development, and clinical translation.

Hierarchical Mesoporous Metal-Organic Frameworks with Boric Acid Sites on the Inner Surface of Small Mesopores for the Extraction of Nucleotides in Human Plasma Samples

In this work, a boronate affinity-functionalized hierarchical mesoporous metal-organic framework adsorbent with boronate sites only in the small mesopore has been structured based on UiO-66@Fe₃O₄. The introduction of large mesopores in the adsorbent can promote the diffusion of small cis-diol-containing compounds (cis-diols) into small mesopore channels, and the removal of the adsorption sites on the external surface of materials and in large mesopores can enhance the size-exclusion effect of the adsorbent. In addition, the adsorbent has faster adsorption kinetics and excellent selectivity to small cis-diols. Finally, a magnetic dispersive solid-phase extraction coupled with high-performance liquid chromatography was established for the enrichment and detection of nucleotides in plasma. Four nucleotides achieve the recoveries from 93.25 to 118.79%, the limits of detection from 0.35 to 1.26 ng·mL^-1, and the intra-day and inter-day relative standard deviations of less than 10.2%. In conclusion, this method can be directly used for the detection of small cis-diol targets in complex biological samples without protein precipitation prior to the extraction.

Bioinertization of nanoLC/MS/MS systems by depleting metal ions from the mobile phases for phosphoproteomics

We have successfully developed a bioinertized nanoflow liquid chromatography/tandem mass spectrometry (nanoLC/MS/MS) system for the highly sensitive analysis of phosphopeptides by depleting metal ions from the mobile phase. We found that not only direct contact of phosphopeptides with metal components, but also indirect contact with nanoLC pumps through the mobile phase causes significant losses during the recovery of phosphopeptides. Moreover, electrospray ionization was adversely affected by the mobile phase containing multiple metal ions as well as by the sample solvents contaminated with metal ions used in immobilized metal ion affinity chromatography for phosphopeptide enrichment. To solve these problems, metal ions were depleted by inserting an on-line metal ion removal device containing metal-chelating membranes between the gradient mixer and the autosampler. As a result, the peak areas of the identified phosphopeptides increased an average of 9.9-fold overall and 77-fold for multiply phosphorylated peptides with the insertion of the on-line metal ion removal system. This strategy would be applicable to highly sensitive analysis of other phosphorylated biomolecules by microscale-LC/MS/MS.

Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways

Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.

Advances in phosphoproteomics and its application to COPD

INTRODUCTION

Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities.

AREAS COVERED

In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease.

EXPERT OPINION

The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.

Proteomics of Cryptococcus neoformans: From the Lab to the Clinic

Fungal pathogens cause an array of diseases by targeting both immunocompromised and immunocompetent hosts. Fungi overcome our current arsenal of antifungals through the emergence and evolution of resistance. In particular, the human fungal pathogen, Cryptococcus neoformans is found ubiquitously within the environment and causes severe disease in immunocompromised individuals around the globe with limited treatment options available. To uncover fundamental knowledge about this fungal pathogen, as well as investigate new detection and treatment strategies, mass spectrometry-based proteomics provides a plethora of tools and applications, as well as bioinformatics platforms. In this review, we highlight proteomics approaches within the laboratory to investigate changes in the cellular proteome, secretome, and extracellular vesicles. We also explore regulation by post-translational modifications and the impact of protein-protein interactions. Further, we present the development and comprehensive assessment of murine models of cryptococcal infection, which provide valuable tools to define the dynamic relationship between the host and pathogen during disease. Finally, we explore recent quantitative proteomics studies that begin to extrapolate the findings from the bench to the clinic for improved methods of fungal detection and monitoring. Such studies support a framework for personalized medical approaches to eradicate diseases caused by C. neoformans.

WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT

Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.

Post-translational modification control of viral DNA sensors and innate immune signaling

The vertebrate innate immune system confers host cells with mechanisms to protect against both evolutionarily ancient pathogens and newly emerging pathogenic strains. Innate immunity relies on the host cell's ability to distinguish between self and pathogen-derived molecules. To achieve this, the innate immune system uses germline encoded receptors called pattern recognition receptors (PRRs), which recognize various molecular signatures, including nucleic acids, proteins, lipids, glycans and glycolipids. Among these molecules, the recognition of pathogenic, mislocalized, or damaged DNA by cellular protein receptors, commonly called DNA sensors, represents a major surveillance pathway for initiating immune signaling. The ability of cells to temporally regulate DNA sensor activation and subsequent signal termination is critical for effective immune signaling. These same mechanisms are also co-opted by pathogens to promote their replication. Therefore, there is significant interest in understanding DNA sensor regulatory networks during microbial infections and autoimmune disease. One emerging aspect of DNA sensor regulation is through post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, ADP-ribosylation, SUMOylation, methylation, deamidation, glutamylation. In this chapter, we discuss how PTMs have been shown to positively or negatively impact DNA sensor functions via diverse mechanisms, including direct regulation of enzymatic activity, protein-protein and protein-DNA interactions, protein translocations and protein turnover. In addition, we highlight the ability of virus-induced PTMs to promote immune evasion. We also discuss the recent evidence linking PTMs on DNA sensors with human diseases and more broadly, highlight promising directions for future research on PTM-mediated regulation of DNA sensor-dependent immune signaling.

Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment

Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO₂ magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO₂-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO₂ as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.

Profiling of post-translational modifications by chemical and computational proteomics

Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potential. Classical biochemical methods are suitable for studying PTMs on individual proteins; however, global profiling of PTMs in proteomes remains a challenging task. In this feature article, we start with a brief review of the traditional affinity-based strategies and shift the emphasis to summarizing recent progress in the development and application of chemical and computational proteomic strategies to delineate the global landscapes of functional PTMs. Finally, we discuss current challenges in PTM detection and provide future perspectives on how the field can be further advanced.

Iron-chelated thermoresponsive polymer brushes on bismuth titanate nanosheets for metal affinity separation of phosphoproteins

Separation of phosphoproteins plays an important role for identification of biomarkers in life science. In this work, bismuth titanate supported, iron-chelated thermoresponsive polymer brushes were prepared for selective separation of phosphoproteins. The iron-chelated thermoresponsive polymer brushes were synthesized by surface-initiated atom transfer radical polymerization of N-isopropylacrylamide and glycidyl methacrylate, followed by a ring opening reaction of epoxy group, and chelation of the obtained cis-diols with Fe³⁺ ions. The composite material was characterized to determine the size and thickness, the content of the organic polymer and the metal loading. The bismuth titanate supported, iron-chelated thermoresponsive polymer brushes showed selective binding for phosphoproteins in the presence of abundant interfering proteins, and a high binding capacity for phosphoproteins by virtue of the metal affinity between the metal ions on the polymer brushes and the phosphate groups in the phosphoproteins (664 mg β-Casein per g sorbent). The thermoresponsive property of the polymer brushes made it possible to adjust phosphoprotein binding by changing temperature. Finally, separation of phosphoproteins from a complex biological sample (i.e. milk) was demonstrated using the nanosheet-supported thermoresponsive polymer brushes.

Core–shell magnetic microporous covalent organic framework with functionalized Ti(iv) for selective enrichment of phosphopeptides

We fabricated a core-shell magnetic Ti⁴⁺-functionalized covalent organic framework composite to selectively capture phosphopeptides in biosamples. This method is applicable to achieve rapid, selective and efficient phosphopeptide analysis.

Synthesis of biscarboxylic acid functionalised EDTA mimicking polymers and their ability to form Zr(iv) chelation mediated nanostructures

We present a new biscarboxylic acid acrylate, which is used for the synthesis of double hydrophilic EDTA-mimicking block copolymers capable of self-assembly upon zirconium complexation.

Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment of N-Glyco and Phosphopeptides

Simultaneous enrichment of glyco- and phosphopeptides will benefit the studies of biological processes regulated by these posttranslational modifications (PTMs). It will also reveal potential crosstalk between these two ubiquitous PTMs. Unlike custom-designed multifunctional solid phase extraction (SPE) materials, operating strong anion exchange (SAX) resin in electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) mode provides a readily available strategy to analytical labs for enrichment of these PTMs for subsequent mass spectrometry (MS)-based characterization. However, the choice of mobile phase has largely relied on empirical rules from hydrophilic interaction chromatography (HILIC) or ion-exchange chromatography (IEX) without further optimization and adjustments. In this study, ten mobile phase compositions of ERLIC were systematically compared; the impact of multiple factors including organic phase proportion, ion pairing reagent, pH, and salt on the retention of glycosylated and phosphorylated peptides was evaluated. This study demonstrated good enrichment of glyco- and phosphopeptides from the nonmodified peptides in a complex tryptic digest. Moreover, the enriched glyco- and phosphopeptides elute in different fractions by orthogonal retention mechanisms of hydrophilic interaction and electrostatic interaction in ERLIC, maximizing the LC-MS identification of each PTM. The optimized mobile phase can be adapted to the ERLIC HPLC system, where the high resolution in separating multiple PTMs will benefit large-scale MS-based PTM profiling and in-depth characterization.

Proteomic analysis showing the signaling pathways involved in the rhizome enlargement process in Nelumbo nucifera

Background

Rhizome is the storage underground stem of lotus (Nelumbo nucifera), which is enlarged before winter season and could be used for asexual propagation. In addition, the enlarged rhizome is a nutritional vegetable with abundant starch, proteins, and vitamins. Enlargement of lotus rhizome is not only significance for itself to survive from the cold winter, but also important for its economic value.

Results

To explore the mechanism underlying its enlargement, integrative analyses of morphology, physiology and proteomics were conducted on the rhizome at stolon, middle, and enlarged stages. Morphological observation and physiological analyses showed that rhizomes were gradually enlarged during this process, in which the starch accumulation was also initiated. Quantitative proteomic analysis on the rhizomes at these three stages identified 302 stage-specific proteins (SSPs) and 172 differently expressed proteins (DEPs), based on which GO and KEGG enrichment analyses were conducted. The results indicated that light and auxin signal might be transduced through secondary messenger Ca²⁺, and play important roles in lotus rhizome enlargement.

Conclusion

These results will provide new insights into understanding the mechanism of lotus rhizome enlargement. Meanwhile, some candidate genes might be useful for further studies on this process, as well as breeding of rhizome lotus.

Novel Ti4+-Chelated Polyoxometalate/Polydopamine Composite Microspheres for Highly Selective Isolation and Enrichment of Phosphoproteins

Selective isolation and enrichment of phosphoproteins play critical roles for identification of biomarkers in biological applications. Herein, a kind of polyoxometalate (P₅W₃₀)/polydopamine (PDA) composite microspheres is readily synthesized via an in situ polymerization way, followed by immobilization of Ti⁴⁺ on the surface of the microspheres to obtain P₅W₃₀/PDA-Ti⁴⁺. Due to metal affinity and π stacking interaction, this novel material exhibits high selectivity to β-casein (β-ca), and the theoretical maximum adsorption capacity is as high as 1250 mg g^-1, fitting well with the Langmuir model. The captured β-ca can be collected by using Britton-Robinson (B-R) buffer at pH 7.0, and a recovery of 81.5% is acquired. The enrichment factor is over 150 at a mass ratio of BSA/β-ca = 100:1, indicating that phosphoproteins can be purified by P₅W₃₀/PDA-Ti⁴⁺. Moreover, the application of P₅W₃₀/PDA-Ti⁴⁺ as sorbent in real biological samples has been investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, and the consequences show that this kind of material is able to selectively isolate phosphoproteins from complex samples such as drinking milk and chicken egg white.

A glassy carbon electrode modified with a monolayer of zirconium(IV) phosphonate for sensing of methyl-parathion by square wave voltammetry

A glassy carbon electrode (GCE) was consecutively modified with amino groups and phosphate groups, and then loaded with Zr(IV) ions. Fourier transform infrared spectrophotometry, field-emission scanning electron microscopy, energy dispersive X-ray spectroscopy and cyclic voltammetry were used to characterize the morphologies and electrochemical properties. The sensor was used to detect p-nitrophenyl-substituted organophosphorus pesticides, with methyl-parathion (MP) as the model analyte. Under optimized conditions, the oxidation current of square wave voltammetry (typically measured at around -0.28 V vs. saturated calomel electrode) increases linearly in the 1.0 to 100 ng mL^-1 MP concentration range, and the detection limit is 0.25 ng mL^-1 (at a signal to noise ratio of 3). Average recoveries from (spiked) real water samples are 99.9-102.2%, with relative standard deviations of 0.3-2.6% (n = 3) at three levels. The reliability and accuracy of the method was validated by HPLC. Graphical abstract Zr(IV) modified GCE is prepared via three steps. The electrode shows high specificity and selectivity towards methyl-parathion. And the linear range is 1.0 - 100.0 ng mL-¹ with the detection limit as low as 0.25 ng mL-¹ with SWV.

Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine

Protein phosphorylation is a post-translational modification that is involved in the regulation of all major biological processes in cells. As a rapid and reversible means to modulate protein activity and transduce signals, aberrant protein phosphorylation is implicated in the onset and progression of most cancer types. Therefore, pharmacological inhibitors against protein kinases are highly pursued therapeutic approaches for treating cancer. Phosphoproteomics has become an important approach for investigating protein phosphorylation, and it is a technique that provides measurements of kinase pathway activation and the circuitry of signalling networks with both spatial and temporal resolution. Combined with the recent advances in mass spectrometry and development in biochemical procedures for phosphopeptide enrichment and computational approaches, high-throughput phosphoproteomics enables the investigation of kinase signalling networks with unprecedented depth. Here, we review the recent progresses in phosphoproteomics methodology and how phosphoproteomics profiling could be implemented in translational research to aid cancer therapies, facilitate novel drug target discovery and overcome the therapeutic obstacles caused by drug resistance. SIGNIFICANCE: In this review, we summarized the recent progress in mass spectrometry-based phosphoproteomics and discussed how phosphoproteomics profiling can be implemented in translational research to aid cancer therapies, facilitate novel drug target discovery and overcome the therapeutic obstacles caused by drug resistance due to the rapid remodelling of signalling networks in response to kinase inhibitor treatment. In addition, we addressed the insights and challenges of applying MS phosphoproteomics in clinical routine practice in precision medicine. This review will help readers become more familiar with the recent advancements and applications of phosphoproteomics, especially in the field of kinase-targeted cancer therapy.

Functional Proteomic Analysis to Characterize Signaling Crosstalk

The biological activities of a cell are determined by its response to external stimuli. The signals are transduced from either intracellular or extracellular milieu through networks of multi-protein complexes and post-translational modifications of proteins (PTMs). Most PTMs including phosphorylation, acetylation, ubiquitination, and SUMOylation, among others, modulate activities of proteins and regulate biological processes such as proliferation, differentiation, as well as host pathogen interaction. Conventionally, reverse genetics analysis and single molecule-based studies were employed to identify and characterize the function of PTMs and enzyme-substrate networks regulated by them. With the advent of high-throughput technologies, it is now possible to identify and quantify thousands of PTM sites in a single experiment. Here, we discuss recent advances in enrichment strategies of various PTMs. We also describe a method for the identification and relative quantitation of proteins using a tandem mass tag labeling approach combined with serial enrichment of phosphorylation, acetylation and succinylation using antibody enrichment strategy.

Fly-ash as a low-cost material for isolation of phosphoproteins

Metal oxide affinity chromatography (MOAC) is one of the most commonly used techniques for selective isolation phosphoproteins and phosphopeptides. This technique is capable of capturing the phosphorylated biomolecules through the affinity of the phosphoryl group for metal oxides/hydroxides. Fly-ash (FA), a by-product of coal-combustion power plants, is primarily composed of oxides of silicon and metals, among which iron and titanium. A number of studies have demonstrated the potential of these metal oxides for phosphoprotein and phosphopeptide enrichment. FA is annually produced over hundred million tons worldwide and generally considered as hazardous waste. It is thus of great importance to enhance its utilization. Here we present the first demonstration of the utility of FA as a low-cost MOAC material for the enrichment of phosphoproteins. With an FA-microcolumn, phosphoproteins can be successfully sequestered from other proteins. FA-microcolumns are shown to be simple, cheap and selective devices for phosphoprotein enrichment from a small volume of mixtures.

Investigation of post-translational modifications in type 2 diabetes

The investigation of post-translational modifications (PTMs) plays an important role for the study of type 2 diabetes. The importance of PTMs has been realized with the advancement of analytical techniques. The challenging detection and analysis of post-translational modifications is eased by different enrichment methods and by high throughput mass spectrometry based proteomics studies. This technology along with different quantitation methods provide accurate knowledge about the changes happening in disease conditions as well as in normal conditions. In this review, we have discussed PTMs such as phosphorylation, N-glycosylation, O-GlcNAcylation, acetylation and advanced glycation end products in type 2 diabetes which have been characterized by high throughput mass spectrometry based proteomics analysis.

Dendritic Mesoporous Silica Nanoparticles with Abundant Ti4+ for Phosphopeptide Enrichment from Cancer Cells with 96% Specificity

Selective enrichment and sensitive detection of phosphopeptides are of great significance in many bioapplications. In this work, dendritic mesoporous silica nanoparticles modified with polydopamine and chelated Ti⁴⁺ (denoted DMSNs@PDA-Ti⁴⁺) were developed to improve the enrichment selectivity of phosphopeptides. The unique central-radial pore structures endowed DMSNs@PDA-Ti⁴⁺ with a high surface area (362 m² g^-1), a large pore volume (1.37 cm³ g^-1), and a high amount of chelated Ti⁴⁺ (75 μg mg^-1). Compared with conventional mesoporous silica-based materials with the same functionalization (denoted mSiO₂@PDA-Ti⁴⁺) and commercial TiO₂, DMSNs@PDA-Ti⁴⁺ showed better selectivity and a lower detection limit (0.2 fmol/μL). Moreover, 2422 unique phosphopeptides were identified from HeLa cell extracts with a high specificity (>95%) enabled by DMSNs@PDA-Ti⁴⁺, better than those in previous reports.

Defeating Major Contaminants in Fe3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment

Here we demonstrate that biomolecular contaminants, such as nucleic acid molecules, can seriously interfere with immobilized metal ion affinity chromatography (IMAC)-based phosphopeptide enrichments. We address and largely solve this issue, developing a robust protocol implementing methanol/chloroform protein precipitation and enzymatic digestion using benzonase, which degrades all forms of DNA and RNA, before IMAC-column loading. This simple procedure resulted in a drastic increase of enrichment sensitivity, enabling the identification of around 17,000 unique phosphopeptides and 12,500 unambiguously localized phosphosites in human cell-lines from a single LC-MS/MS run, constituting a 50% increase when compared with the standard protocol. The improved protocol was also applied to bacterial samples, increasing the number of identified bacterial phosphopeptides even more strikingly, by a factor 10, when compared with the standard protocol. For E. coli we detected around 1300 unambiguously localized phosphosites per LC-MS/MS run. The preparation of these ultra-pure phosphopeptide samples only requires marginal extra costs and sample preparation time and should thus be adoptable by every laboratory active in the field of phosphoproteomics.

PAMA–Arg brush-functionalized magnetic composite nanospheres for highly effective enrichment of phosphorylated biomolecules

A novel polymer brush-functionalized magnetic composite nanosphere was successfully prepared, exhibiting large enrichment capacity, extremely high detection sensitivity, and high enrichment recovery in phosphorylated biomolecule enrichment.

Development of immobilized Sn4+ affinity chromatography material for highly selective enrichment of phosphopeptides

In this work, we first immobilized tin(IV) ion on polydopamine-coated magnetic graphene (magG@PDA) to synthesize Sn⁴⁺ -immobilized magG@PDA (magG@PDA-Sn⁴⁺ ) and successfully applied the material to highly selective enrichment of phosphopeptides. The material gathered the advantages of large surface area of graphene, superparamagnetism of Fe₃ O₄ , good hydrophilicity and biocompatibility of polydopamine, and strong interaction between Sn⁴⁺ and phosphopeptides. The enrichment performance of magG@PDA-Sn⁴⁺ toward phosphopeptides from digested β-casein at different concentrations, with and without added digested BSA was investigated and compared with magG@PDA-Ti⁴⁺ . The results showed high selectivity and sensitivity of the Sn⁴⁺ -IMAC material toward phosphopeptides, as good as the Ti⁴⁺ -IMAC material. Finally, magG@PDA-Sn⁴⁺ was applied to the analysis of endogenous phosphopeptides from a real sample, human saliva, with both MALDI-TOF MS and nano-LC-ESI-MS/MS. The results indicated that the as-synthesized Sn⁴⁺ -IMAC material not only has good enrichment performance, but also could serve as a supplement to the Ti⁴⁺ -IMAC material and expand the phosphopeptide coverage enriched by the single Ti⁴⁺ -IMAC material, demonstrating the broad application prospects of magG@PDA-Sn⁴⁺ in phosphoproteome research.

Facile synthesis of Fe3O4@PDA core-shell microspheres functionalized with various metal ions: A systematic comparison of commonly-used metal ions for IMAC enrichment

Metal ions differed greatly in affinity towards phosphopeptides, and thus it is essential to systematically compare the phosphopeptides enrichment ability of different metal ions usually used in the IMAC techniques. In this work, for the first time, eight metal ions, including Nb⁵⁺, Ti⁴⁺, Zr⁴⁺, Ga³⁺, Y³⁺, In³⁺, Ce⁴⁺, Fe³⁺, were immobilized on the polydopamine (PDA)-coated Fe₃O₄ (denoted as Fe₃O₄@PDA-Mⁿ⁺), and systematically compared by the real biosamples, in addition to standard phosphopeptides. Fe₃O₄ microspheres were synthesized via the solvothermal reaction, followed by self-polymerization of dopamine on the surface. Then through taking advantage of the hydroxyl and amino group of PDA, the eight metal ions were easily adhered to the surface of Fe₃O₄@PDA. After characterization, the resultant Fe₃O₄@PDA-Mⁿ⁺ microspheres were applied to phosphopeptides enrichment based on the binding affinity between metal ions and phosphopeptides. According to the results, different metal ions presented diverse phosphopeptides enrichment efficiency in terms of selectivity, sensitivity and the enrichment ability from real complex samples, and Fe₃O₄@PDA-Nb⁵⁺ and Fe₃O₄@PDA-Ti⁴⁺ showed obvious advantages of the phosphopeptides enrichment effect after the comparison. This systematic comparison may provide certain reference for the use and development of IMAC materials in the future.

Preparation of quaternized cellulose/chitosan microspheres for selective enrichment of phosphopeptides

As one of the most important posttranslational modifications, protein phosphorylation plays an important role in vital movement. However, an efficiency enrichment treatment prior to MS detection is still a crucial step to protein phosphorylation analysis. In this work, a novel hybrid microsphere for efficient phosphopeptide enrichment was prepared by reverse-phase suspension polymerization of cellulose derivative and chitosan. The microspheres bore different kinds of amine groups and the main enrichment mechanism was based on anion exchange. This approach exhibited high selectivity for phosphopeptides from β-casein, α-casein, and non-fat milk. Three phosphopeptides could still be detected when the amount of β-casein was as low as 10 fmol. This study demonstrated a new attractive solid-phase support for phosphopeptide enrichment to meet the increasing need of phosphoproteomics analysis.

Metal–organic framework incorporated monolithic capillary for selective enrichment of phosphopeptides

Protein phosphorylation is a major post-translational modification, which plays a central role in the cellular signaling of numerous biological processes.

Dual-Metal Centered Zirconium-Organic Framework: A Metal-Affinity Probe for Highly Specific Interaction with Phosphopeptides

The highly specific affinity between probes and phosphopeptides is the fundamental interaction for selective identification of phosphoproteomes that uncover the mechanisms of signal transduction, cell cycle, enzymatic regulation, and gene expression in biological systems. In this study, a metal-affinity probe possessing both interactions of metal oxide affinity chromatography (MOAC) and immobilized metal ion affinity chromatography (IMAC) was facilely prepared by immobilizing zirconium(IV) on a zirconium-organic framework of UiO-66-NH₂, which holds dual-metal centers of not only the inherent Zr-O cluster but also the immobilized Zr(IV) center. This dual-metal centered zirconium-organic framework (DZMOF) demonstrates as a highly specific metal-affinity probe toward the extraction of phosphopeptides due to the metal-affinity interactions of MOAC and IMAC toward either mono-phosphorylated or multi-phosphorylated peptides. The binding energies of zirconium 3d_5/2 and 3d_3/2 in this DZMOF are 183.07 and 185.47 eV, respectively, which are higher than those of the intact UiO-66-NH₂ (182.84 and 185.17 eV, respectively), confirming the higher metal-affinity interaction between the DZMOF and phosphopeptides. This high metal-affinity probe presents an unprecedented strong performance in anti-nonspecific interference during the capturing of phosphopeptides of β-casein with the molar ratio of β-casein vs bovine serum albumin up to ca. 1:5000. The enrichment of phosphopeptides from a human saliva sample by DZMOF further confirms the great potential of DZMOF in the extraction of low-abundance phosphopeptides for real complex biological samples.

The current state of the art of quantitative phosphoproteomics and its applications to diabetes research

Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.

Proteomic discovery of host kinase signaling in bacterial infections

Protein phosphorylation catalyzed by protein kinases acts as a reversible molecular switch in signal transduction, providing a mechanism for the control of protein function in cellular processes. During microbial infection, cellular signaling essentially contributes to immune control to restrict the dissemination of invading pathogens within the host organism. However, pathogenic microbes compete for the control of host signaling to create a beneficial environment for successful invasion and infection. Although efforts to achieve a better understanding of the host–pathogen interaction and its molecular consequences have been made, there is urgent need for a comprehensive characterization of infection‐related host signaling processes. System‐wide and hypothesis‐free analysis of phosphorylation‐mediated host signaling during host–microbe interactions by mass spectrometry (MS)‐based methods is not only promising in view of a greater understanding of the pathogenesis of the infection but also may result in the identification of novel host targets for preventive or therapeutic intervention. Here, we review state‐of‐the‐art MS‐based techniques for the system‐wide identification and quantitation of protein phosphorylation and compare them to array‐based phosphoprotein analyses. We also provide an overview of how phosphoproteomics and kinomics have contributed to our understanding of protein kinase‐driven phosphorylation networks that operate during host–microbe interactions.