Identification of p65-Associated Phosphoproteins by Mass Spectrometry after On-Plate Phosphopeptide Enrichment Using Polymer-oxotitanium Films

New Opportunities and Challenges of Smart Polymers in Post-Translational Modification Proteomics

Protein post-translational modifications (PTMs), which denote covalent additions of various functional groups (e.g., phosphate, glycan, methyl, or ubiquitin) to proteins, significantly increase protein complexity and diversity. PTMs play crucial roles in the regulation of protein functions and numerous cellular processes. However, in a living organism, native PTM proteins are typically present at substoichiometric levels, considerably impeding mass-spectrometry-based analyses and identification. Over the past decade, the demand for in-depth PTM proteomics studies has spawned a variety of selective affinity materials capable of capturing trace amounts of PTM peptides from highly complex biosamples. However, novel design ideas or strategies are urgently required for fulfilling the increasingly complex and accurate requirements of PTM proteomics analysis, which can hardly be met by using conventional enrichment materials. Considering two typical types of protein PTMs, phosphorylation and glycosylation, an overview of polymeric enrichment materials is provided here, with an emphasis on the superiority of smart-polymer-based materials that can function in intelligent modes. Moreover, some smart separation materials are introduced to demonstrate the enticing prospects and the challenges of smart polymers applied in PTM proteomics.

Comparing multistep immobilized metal affinity chromatography and multistep TiO2 methods for phosphopeptide enrichment

Phosphopeptide enrichment from complicated peptide mixtures is an essential step for mass spectrometry-based phosphoproteomic studies to reduce sample complexity and ionization suppression effects. Typical methods for enriching phosphopeptides include immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO2) beads, which have selective affinity and can interact with phosphopeptides. In this study, the IMAC enrichment method was compared with the TiO2 enrichment method, using a multistep enrichment strategy from whole cell lysate, to evaluate their abilities to enrich for different types of phosphopeptides. The peptide-to-beads ratios were optimized for both IMAC and TiO2 beads. Both IMAC and TiO2 enrichments were performed for three rounds to enable the maximum extraction of phosphopeptides from the whole cell lysates. The phosphopeptides that are unique to IMAC enrichment, unique to TiO2 enrichment, and identified with both IMAC and TiO2 enrichment were analyzed for their characteristics. Both IMAC and TiO2 enriched similar amounts of phosphopeptides with comparable enrichment efficiency. However, phosphopeptides that are unique to IMAC enrichment showed a higher percentage of multiphosphopeptides as well as a higher percentage of longer, basic, and hydrophilic phosphopeptides. Also, the IMAC and TiO2 procedures clearly enriched phosphopeptides with different motifs. Finally, further enriching with two rounds of TiO2 from the supernatant after IMAC enrichment or further enriching with two rounds of IMAC from the supernatant TiO2 enrichment does not fully recover the phosphopeptides that are not identified with the corresponding multistep enrichment.

Functionalizing Microporous Membranes for Protein Purification and Protein Digestion

This review examines advances in the functionalization of microporous membranes for protein purification and the development of protease-containing membranes for controlled protein digestion prior to mass spectrometry analysis. Recent studies confirm that membranes are superior to bead-based columns for rapid protein capture, presumably because convective mass transport in membrane pores rapidly brings proteins to binding sites. Modification of porous membranes with functional polymeric films or TiO₂ nanoparticles yields materials that selectively capture species ranging from phosphopeptides to His-tagged proteins, and protein-binding capacities often exceed those of commercial beads. Thin membranes also provide a convenient framework for creating enzyme-containing reactors that afford control over residence times. With millisecond residence times, reactors with immobilized proteases limit protein digestion to increase sequence coverage in mass spectrometry analysis and facilitate elucidation of protein structures. This review emphasizes the advantages of membrane-based techniques and concludes with some challenges for their practical application.

Phosphopeptide enrichment with TiO2-modified membranes and investigation of tau protein phosphorylation

Selective enrichment of phosphopeptides prior to their analysis by mass spectrometry (MS) is vital for identifying protein phosphorylation sites involved in cellular regulation. This study describes modification of porous nylon substrates with TiO2 nanoparticles to create membranes that rapidly enrich phosphopeptides. Membranes with a 22-mm diameter bind 540 nmol of phosphoangiotensin and recover 70% of the phosphopeptides in mixtures with a 15-fold excess of nonphosphorylated proteins. Recovery is 90% for a pure phosphopeptide. Insertion of small membrane disks into HPLC fittings allows rapid enrichment from 5 mL of 1 fmol/μL phosphoprotein digests and concentration into small-volume (tens of microliters) eluates. The combination of membrane enrichment with tandem mass spectrometry reveals seven phosphorylation sites from in vivo phosphorylated tau (p-tau) protein, which is associated with Alzheimer's disease.

Peptide/protein separation with cationic polymer brush nanosponges for MALDI-MS analysis

A cationic polymer nanobrush was synthesized, attached to a MALDI target, and used for the fractionation of peptides and proteins based on their pI, prior to analysis by MALDI-MS. The cationic polymer nanobrush was synthesized on a gold substrate by AIBN photoinitiated polymerization, using a 70:30 ratio of 2-aminoethyl methacrylate hydrochloride (AEMA):N-isopropylacrylamide (NIPAAM). This brush showed selectivity for adsorption of acidic peptides and proteins and allowed fractionation of simple two-component mixtures to be completed in less than 10 min. The brush-adsorbed biomolecules were recovered by treating the nanobrush with ammonium hydroxide, which effectively collapsed the brush, thereby releasing the trapped compounds for MALDI MS analysis. These results demonstrate that nanobrush can serve as a convenient platform for rapid fractionation of biomolecules prior to analysis by MALDI-MS.

High-performance graphene-titania platform for detection of phosphopeptides in cancer cells

Phosphopeptides play a crucial role in many biological processes and constitute some of the most powerful biomarkers in disease detection. However they are often present in very low concentration, which makes their detection highly challenging. Here, we demonstrate the use of a solution-dispersible graphene-titania platform for the selective extraction of phosphopeptides from peptide mixtures. This is followed by direct analysis by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). The efficient charge and energy exchange between graphene and TiO(2) during laser irradiation in SELDI-TOF MS promotes the soft ionization of analytes and affords a detection limit in the attomole range, which is 10(2)-10(5) more sensitive than conventional platforms. The graphene-titania platform can also be used for detecting phosphopeptides in cancer cells (HeLa cells), where it shows high specificity (94%). An expanded library of 967 unique phosphopeptides is detected using significantly reduced loading of extraction matrixes compared to conventional TiO(2) bead-based assays.

Bifunctional polymer brushes for low-bias enrichment of mono- and multi-phosphorylated peptides prior to mass spectrometry analysis

Polymer brushes orthogonally derivatized with oxotitanium and nitrilotriacetate-Fe(III) groups enrich both mono- and multi-phosphorylated peptides for mass spectrometry analysis.

Facile trypsin immobilization in polymeric membranes for rapid, efficient protein digestion

Sequential adsorption of poly(styrene sulfonate) and trypsin in nylon membranes provides a simple, inexpensive method to create stable, microporous reactors for fast protein digestion. The high local trypsin concentration and short radial diffusion distances in membrane pores facilitate proteolysis in residence times of a few seconds, and the minimal pressure drop across the thin membranes allows their use in syringe filters. Membrane digestion and subsequent MS analysis of bovine serum albumin provide 84% sequence coverage, which is higher than the 71% coverage obtained with in-solution digestion for 16 h or the <50% sequence coverages of other methods that employ immobilized trypsin. Moreover, trypsin-modified membranes digest protein in the presence of 0.05 wt % sodium dodecyl sulfate (SDS), whereas in-solution digestion under similar conditions yields no peptide signals in mass spectra even after removal of SDS. These membrane reactors, which can be easily prepared in any laboratory, have a shelf life of several months and continuously digest protein for at least 33 h without significant loss of activity.