Dataset related to the design of a novel rhodamine B-based pH-responsive magnetic adsorbent and its application in phosphopeptidomics.

[Background]: Protein phosphorylation is one of the key post-translational modifications, but due to the low abundance and poor ionization efficiency of phosphopeptides in biological samples, direct analysis by mass spectrometry faces significant challenges. Therefore, the development of novel adsorption materials that can efficiently and selectively enrich phosphopeptides is of great significance for phosphoproteomics research. [Purpose]: This study aims to design and synthesize a pH responsive magnetic adsorbent (Fe ∝ O ₄ @ NH ₂ @ Rb) based on Rhodamine B, and systematically evaluate its enrichment performance for phosphopeptides in complex biological samples such as skim milk, human serum, and saliva, in order to promote its application in phosphoproteomics. [Methods]: Fe-O ₄ magnetic nanoparticles were synthesized by hydrothermal method, and surface modified with bis (2-hydroxyethyl) -3-aminopropyltriethoxysilane (Bis) and rhodamine B (Rb) in sequence to construct Fe-O ₄ @ NH ₂ @ Rb adsorbent. The material was characterized using Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS), Zeta potential analysis, X-ray diffraction (XRD), fluorescence, and UV visible spectroscopy. Evaluate the enrichment sensitivity, selectivity, and repeatability of phosphopeptides in standard β - casein hydrolysate and actual biological samples using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). [Results]: The characterization results confirm the successful synthesis of Fe-O ₄ @ NH ₂ @ Rb and its excellent pH response characteristics. Under acidic conditions, Bis protonation and Rb ring opening form a zwitterionic structure, enhancing the electrostatic adsorption capacity for phosphopeptides; Under alkaline conditions, mild elution is achieved. The detection limit of this material for phosphopeptides in β - casein hydrolysate is as low as 0.4 fmol/μ L, and it can effectively enrich phosphopeptides even in complex systems with a BSA to β - casein mass ratio of up to 1000:1. In actual samples (skim milk, human serum, saliva), 27, 6, and 68 phosphopeptides were identified, respectively, which were significantly better than direct mass spectrometry analysis and some commercial materials (such as Fe ∝ O ₄ @ TiO ₂). [Conclusions]: This study has successfully developed a novel Rhodamine B-based pH responsive magnetic adsorbent Fe ∝ O ₄ @ NH ₂ @ Rb. The material has a simple synthesis method, low cost, good stability, and exhibits excellent phosphopeptide enrichment performance. The successful application of this material in various complex biological samples demonstrates its broad prospects in phosphopeptide omics research, providing new ideas for the design of highly selective phosphopeptide enrichment materials based on electrostatic interactions.