Phosphoprotein Analysis by MALDI-TOF Mass Spectrometry using On-Probe Tandem Proteolysis and Dephosphorylation

In this investigation, methods based on on-probe enzymatic cleavage matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF-MS) analyses have been developed, allowing the rapid assignment of phosphorylation sites within phosphoproteins. The procedures involved robotic sample deposition of a phosphoprotein, such as intact bovine β-casein, on stainless steel or gold MALDI plates, on-probe proteolysis with trypsin for 10–180?s at 37°C, on-probe dephosphorylation for 1–10?min at 37°C with alkaline phosphatase, followed by differential mass spectrometry with peptide mass mapping. The dephosphorylation conditions were initially optimized using in-solution tryptic digestion of the phosphoprotein performed in the presence of MS-compatible anionic surfactant sodium 3-[(2-methyl-2-undecyl-1,3-dioxolan-4-yl)methoxy]-1-propanesulfonate. Two methods of trypsin deactivation were investigated, cooling and quenching by acidification, which resulted in the surfactant either staying intact or becoming cleaved, respectively. Since the surfactant had no detrimental effects on dephosphorylation of phosphopeptides, the acidification and neutralization steps were not included in the final analytical method. A protocol, comprising on-probe tandem, surfactant-aided proteolysis for 3?min followed by on-probe dephosphorylation for 10?min was thus established, allowing the rapid identification of location and sequence of phosphopeptides within a phosphoprotein by these procedures.     

Phosphate-Rich Biomimetic Peptides Shed Light on High-Affinity Hyperphosphorylated Uranyl Binding Sites in Phosphoproteins

Some phosphoproteins such as osteopontin (OPN) have been identified as high-affinity uranyl targets. However, the binding sites required for interaction with uranyl and therefore involved in its toxicity have not been identified in the whole protein. The biomimetic approach proposed here aimed to decipher the nature of these sites and should help to understand the role of the multiple phosphorylations in UO₂²⁺ binding. Two hyperphosphorylated cyclic peptides, pS₁₆₈ and pS₁₃₆₈ containing up to four phosphoserine (pSer) residues over the ten amino acids present in the sequences, were synthesized with all reactions performed in the solid phase, including post-phosphorylation. These β-sheet-structured peptides present four coordinating residues from four amino acid side chains pointing to the metal ion, either three pSer and one glutamate in pS₁₆₈ or four pSer in pS₁₃₆₈ . Significantly, increasing the number of pSer residues up to four in the cyclodecapeptide scaffolds produced molecules with an affinity constant for UO₂²⁺ that is as large as that reported for osteopontin at physiological pH. The phosphate-rich pS₁₃₆₈ can thus be considered a relevant model of UO₂²⁺ coordination in this intrinsically disordered protein, which wraps around the metal ion to gather four phosphate groups in the UO₂²⁺ coordination sphere. These model hyperphosphorylated peptides are highly selective for UO₂²⁺ with respect to endogenous Ca²⁺, which makes them good starting structures for selective UO₂²⁺ complexation.     

Facile synthesis of Ti4+‐immobilized affinity silica nanoparticles for the highly selective enrichment of intact phosphoproteins

Currently, great challenges to top‐down phosphoproteomics lie in the selective enrichment of intact phosphoproteins from complex biological samples. Herein, we developed a facile approach for synthesis of Ti⁴⁺‐immobilized affinity silica nanoparticles and applied them to the selective separation and enrichment of intact phosphoproteins based upon the principle of metal(IV) phosphate/phosphonate chemistry. The as‐prepared affinity materials exhibited high selectivity and adsorption capacities for model phosphoproteins (328.9 mg/g for β‐casein, 280.5 mg/g for ovalbumin, and 225.8 mg/g for α‐casein), compared with nonphosphoproteins (79.28 mg/g for horseradish peroxidase, 72.70 mg/g for BSA, and 27.28 mg/g for lysozyme). In addition, the resuability of the affinity silica nanoparticles was evaluated, and the results demonstrated a less than 10% loss of adsorption capacity after six adsorption–regeneration cycles. The practicability of the affinity materials was demonstrated by separating phosphoproteins from protein mixtures and drinking milk samples, and the satisfactory results indicated its potential in phosphoproteomics analysis.     

Application of polydopamine-coated nylon capillary-channeled polymer fibers as a stationary phase for mass spectrometric phosphopeptide analysis

Capillary-channeled polymer (C-CP) fibers are demonstrated as a selective stationary phase for phosphopeptide analysis via LC–MS. Taking advantage of the oxidative self-polymerization of dopamine under alkaline conditions, a simple system involving a dilute aqueous solution of 0.2% w/v dopamine hydrochloride in 0.15% w/v TRIS buffer, pH 8.5 was utilized to coat polydopamine onto nylon 6 C-CP fibers. Confirmation of the polydopamine coating on the fibers (nylon-PDA) was made through attenuated total reflection-FTIR (ATR-FTIR) analysis. Imaging using SEM was also performed to examine the morphology and topography of the nylon-PDA. Subsequent loading of Fe³⁺ to the nylon-PDA matrix was confirmed by SEM/energy dispersive X-ray spectroscopy (SEM/EDX). The Fe³⁺-bound nylon-PDA fibers packed in a microbore column format were tested in the off-line preconcentration of phosphopeptides from a 1:100 mixture of β-casein/BSA digests for MALDI-TOF analysis. The packed column was also installed onto an HPLC system as a platform for the online sample clean-up and enrichment of phosphopeptides from a 1:1000 mixture of β-casein/BSA protein digests that were determined by subsequent ESI–MS analysis.     

Phosphoproteomic analysis identifies activated MET-axis PI3K/AKT and MAPK/ERK in lapatinib-resistant cancer cell line

Lapatinib, a dual inhibitor of epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) tyrosine kinases, has shown promising results as a growth inhibitor of HER2-positive cancer cells in vitro. However, similar to other EGFR-targeting drugs, acquired resistance to lapatinib by HER2-positive cancer cells remains a major clinical challenge. To elucidate resistance mechanisms to EGFR/HER2-targeting agents, we performed a systematic quantitative comparison of the phosphoproteome of lapatinib-resistant (LR) human gastric cancer cells (SNU216-LR) versus parental cells (SNU216) using a titanium dioxide (TiO₂) phosphopeptide enrichment method and analysis with a Q-Exactive hybrid quadrupole-Orbitrap mass spectrometer. Biological network analysis of differentially expressed phosphoproteins revealed apparent constitutive activation of the MET-axis phosphatidylinositide 3-kinase (PI3K)/α-serine/threonine-protein kinase (AKT) and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling pathways in SNU216-LR. Inhibition of the PI3K/AKT and MAPK/ERK signaling pathways in SNU216-LR also leads to cell cycle arrest, confirming the biological network analysis. Lapatinib sensitivity was restored when cells were treated with several molecular targeting agents in combination with lapatinib. Thus, by integrating phosphoproteomic data, protein networks and effects of signaling pathway modulation on cell proliferation, we found that SNU216-LR maintains constitutive activation of the PI3K/AKT and MAPK/ERK pathways in a MET-dependent manner. These findings suggest that pathway activation is a key compensatory intracellular phospho-signaling event that may govern gastric cancer cell resistance to drug treatment.