A magnetic calcium phosphate for selective capture of multi-phosphopeptides

The specific enrichment of multi-phosphopeptides in the presence of non-phosphopeptides and mono-phosphopeptides was still a challenge for phosphoproteomics research. Most of these enrichment materials relied on Zn, Ti, Sn, and other rare precious metals as the bonding center to enrich multi-phosphopeptides while ignoring the use of common metal elements. The addition of rare metals increased the cost of the experiment, which was not conducive to their large-scale application in biomedical proteomics laboratories. In addition, multiple high-speed centrifugation steps also resulted in the loss of low-abundance multi-phosphopeptides in the treatment procedure of biological samples. This study proposed the use of calcium, a common element, as the central bonding agent for synthesizing magnetic calcium phosphate materials (designated as CaP-Fe3O4). These materials aim to capture multi-phosphopeptides and identifying phosphorylation sites. The current results demonstrate that CaP-Fe3O4 exhibited excellent selection specificity, high sensitivity, and stability in the enrichment of multi-phosphopeptides and the identification of phosphorylation sites. Additionally, the introduction of magnetic separation not only reduced the time required for multi-phosphopeptides enrichment but also prevented the loss of these peptides during high-speed centrifugation. These findings contribute to the widespread application and advancement of phosphoproteomics research.

An easy and straightforward synthesized nano calcium phosphate for highly capture of multiply phosphorylated peptides

Multisite phosphorylation of proteins regulates various cellular life activities, however, the capture of low abundance multi-phosphopeptides from biosamples and identification of phosphorylation sites are largely limited due to the limited enrichment materials and their unclear interactions with multi-phosphopeptides. Here we propose using two cheap raw materials (CaCl₂·2H₂O and Na₂HPO₄·12H₂O) in 10 min at room temperature to synthesize the structurally simple Nanometric Calcium Phosphate (CaP) to resolve this challenge. The current results showed that the "simple" CaP has good selection specificity, high sensitivity and stability for multi-phosphopeptides enrichment and the identification of phosphorylation sites, which facilitate the popularization and application of phosphoproteomics research. Further, the interaction of CaP and multi-phosphopeptides were qualitatively characterized at the molecular/atomic level and the high affinity between them was quantified by the isothermal titration microcalorimeter based on the laws of thermodynamics. The results indicated that the interaction was a spontaneous (ΔG < 0) exothermic reaction with enthalpy reduction (ΔH < 0) and driven mainly by hydrogen bond and electrostatic interaction process.

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.

Mono-Sized Anion-Exchange Magnetic Microspheres for Protein Adsorption

In this study, mono-sized anion-exchange microspheres with polyglycidylmethacrylate were engineered and processed to introduce magnetic granules by penetration-deposition approaches. The obtained magnetic microspheres showed a uniform particle diameter of 1.235 μm in average and a good spherical shape with a saturation magnetic intensity of 12.48 emu/g by VSM and 12% magnetite content by TGA. The magnetic microspheres showed no cytotoxicity when the concentration was below 10 μg/mg. The magnetic microspheres possess respective adsorption capacity for three proteins including Bovine albumin, Hemoglobin from bovine blood, and Cytochrome C. These magnetic microspheres are also potential biomaterials as targeting medicine carriers or protein separation carriers at low concentration.

Efficient separation of phosphopeptides employing a Ti/Nb-functionalized core-shell structure solid-phase extraction nanosphere

A strategy for effectively enriching global phosphopeptides was successfully developed by using ammonia methyl phosphate (APA) as a novel chelating ligand and Ti⁴⁺ and Nb⁵⁺ as double functional ions (referred to as Fe₃O₄@mSiO₂@APA@Ti⁴⁺/Nb⁵⁺). With the advantage of large specific surface area (151.1 m²/g), preeminent immobilized ability for metal ions (about 8% of total atoms), and unbiased enrichment towards phosphopeptides, Fe₃O₄@mSiO₂@APA@Ti⁴⁺/Nb⁵⁺ displays high selectivity (maximum mass ratio β-casein to BSA is 1:1500), low limit of detection (LOD, as low as 0.05 fmol), good relative standard deviation (RSD, lower than 7%), recovery rate of 87% (¹⁸O isotope labeling method), outstanding phosphopeptide loading capacity (330 μg/mg), and at least five times re-use abilities. In the examination of the actual sample, 24 phosphopeptides were successfully detected in saliva and 4 phosphopeptides were also selectively extracted from human serum. All experiments have shown that Fe₃O₄@mSiO₂@APA@Ti⁴⁺/Nb⁵⁺ exhibits exciting potential in view of the challenge of low abundance of phosphopeptides. Graphical abstract.

Efficient synthesis of 6,6′-diamido-2,2′-dipicolylamine ligands for potential phosphate anion sensing

Through retrosynthetic analysis, functionalized 6,6′-diamido-2,2′-dipicolylamines (DA-DPAs) have been efficiently synthesized, which may accelerate the development of selective probes towards phosphate anions.

Phosphoproteomic strategies in cancer research: a minireview

Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.

Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials

Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.

Zinc(ii) and copper(ii) complexes as tools to monitor/inhibit protein phosphorylation events

A perspective on the advance of copper(ii) and zinc(ii) complexes of varied ligand architectures as binders of phosphorylated peptides/proteins and as sensors of phosphorylation reactions is presented.

Simultaneous Detection of Phosphoproteins and Total Proteins in SDS-PAGE Using Calcon

A novel fluorescent staining protocol to detect phosphoproteins in sodium dodecyl sulfate-polyacrylamide gels using a fluorescence sensor, 1-(2-hydroxy-1-naphthylazo)-2-naphthol-4-sulfonic acid sodium salt (Calcon), was developed. This method yields results within 135 min, with the sensitivities of 15 ng of α-casein and β-casein, and 62.5 ng of κ-casein, respectively. Since non-phosphoproteins have shown negative signals that are distinctly different from positive signals of phosphoproteins, this detection method allows one to monitor phosphoproteins with high specificity. Furthermore, a total protein profile can be achieved before a destaining step using a scanner with rapid and low-cost without further total protein staining.