Highly Specific Enrichment of Multi-phosphopeptides by the Diphosphorylated Fructose-Modified Dual-Metal-Centered Zirconium–Organic Framework

Abstract

Multisite phosphorylation of a protein, generally occurring in biological processes, plays important roles in the regulation of cellular functions. However, the identification of multi-phosphopeptides especially at low abundance is a big challenge as the extreme hydrophilicity and poor ionization efficiency of the multiphosphorylated peptides restrict the deep inspection of multisite phosphorylation processes. In this study, the highly specific enrichment of multiphosphorylated peptides was achieved via the modification of the dual-metal-centered zirconium-organic framework with the diphosphorylated fructose. The diphosphorylated fructose-modified dual-metal-centered zirconium-organic framework (DZMOF-FDP) demonstrated the highly specific affinity to the multiple phosphorylated peptides, with the density functional theory calculations explaining the plausible mechanism for multi-phosphopeptides on the DZMOF-FDP. The selective capture of multi-phosphopeptides from mimic samples confirmed the superior performance of the DZMOF-FDP, with comprehensive comparisons to other modification agents, such as orthophosphate and pyrophosphate. A number of 1871 multiphosphorylated peptides captured by DZMOF-FDP from tryptic digests of HeLa cell lysate could be identified, significantly higher than that by the pristine DZMOF. The deliberately designed modification with diphosphorylated fructose for the dual-zirconium-centered metal-organic framework materials suggests an efficient strategy to develop new enrichment methods in the selective capture of target analytes by judiciously optimizing specific modifiers for adsorbents.

Nanomaterials in Proteomics

“…Peng et al immobilized Zr(IV) ions onto UiO‐66–NH 2 by using POCl 3 as linker (dubbed DZMOF, Figure D), and identified 17 phosphopeptides (5 mono‐ and 12 multiphosphopeptides) from 5 µL human saliva . They furtherly modified diphosphorylated fructose on the DZMOF, which was endowed with the ability to deny the binding of monophosphopeptids . Altogether 1871 multiphosphopeptides were identified from HeLa cell extracts, presenting the dramatically improvement than pristine DZMOF.…”

Design of a Spiropyran-Based Smart Adsorbent with Dual Response: Focusing on Highly Efficient Enrichment of Phosphopeptides

“…Therefore, it is necessary to design effective strategies to enrich phosphoproteins before performing MS detection. Commonly used enrichment protocols for phosphoproteins include immobilized metal ion affinity chromatography, − metal oxide affinity chromatography, , and ion-exchange chromatography. , Generally, an ideal phosphoprotein enrichment material often has the following characteristics: the material has strong affinity with phosphoproteins and can distinguish the subtle differences between phosphoproteins and nonphosphoproteins; its binding with phosphoproteins should be adjustable and reversible. Undoubtedly, the introduction of smart responsive materials to the phosphoprotein enrichment field has enticing prospects.…”

Optical chemosensors for the detection of proximally phosphorylated peptides and proteins

“…40 Several techniques enabling enrichment of proximally phosphorylated peptides have recently emerged, which dramatically aids MS/MS analysis in the separation of complex mixtures and/or increasing signal-to-noise of low abundant multi-phosphorylated peptides. [41][42][43][44] In recent years, the introduction of highly sensitive MS hardware that is suitable for single-cell phosphoproteomics can overcome several of the challenges related to sample quality. However, researchers still incorporate complex protocols with enrichment steps to access these deep levels of the proteome.…”