Coupling Strong Anion-Exchange Monolithic Capillary with MALDI-TOF MS for Sensitive Detection of Phosphopeptides in Protein Digest

Efficient selection of glycoprotein-binding DNA aptamers via boronate affinity monolithic capillary

Systematic evolution of ligands by exponential enrichment (SELEX) is the workhorse method for selecting aptamers that are capable of binding target molecules from a random oligonucleic acid library. However, conventional SELEX methods are associated with apparent drawbacks including labor-intensive, time-consuming, large reagent consumption and strong nonspecific binding with separation media. Herein, we report a boronate affinity monolithic capillary-based SELEX approach for rapid selection of high-specificity glycoprotein-binding DNA aptamers. Boronate affinity monolithic capillary is an advanced functional material appeared in recent years, which allows for facile capture/release of glycoproteins in a pH-switchable fashion. By using boronate affinity monolithic capillary as a platform for target immobilization and aptamer isolation, the proposed SELEX method allowed for efficient selection of glycoprotein-binding aptamers by 6 rounds and the dissociation constants were at 10(-8) M level. Because of the employment of boronate affinity monolithic capillary, the new SELEX approach overcame the above-mentioned drawbacks and provided several significant advantages, including rapid selection speed (only 2 days were needed), high specificity toward the target molecules, and minute reagent consumption.

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.

Recent advances in preparation and application of hybrid organic-silica monolithic capillary columns

Hybrid organic-silica monolithic columns, regarded as a second generation of silica-based monoliths, have received much interest due to their unique properties over the pure silica-based monoliths. This review mainly focuses on development in the fields of preparation of hybrid monolithic columns in a capillary and their application for CEC and capillary liquid chromatography separation, as well as for sample pretreatment of solid-phase microextraction and immobilized enzyme reactor since July 2010. The preparation approaches are comprehensively summarized with three routes: (i) general sol-gel process using trialkoxysilanes and tetraalkoxysilanes as coprecursors; (ii) "one-pot" process of alkoxysilanes and organic monomers concomitantly proceeding sol-gel chemistry and free radical polymerization; and (iii) other polymerization approaches of organic monomers containing silanes. The modification of hybrid monoliths containing reactive groups to acquire the desired surface functionality is also described.

Fine-tuning the specificity of boronate affinity monoliths toward glycoproteins through pH manipulation

Boronate affinity functionalized materials have recently drawn increasing attention due to their capability to selectively isolate and enrich glycoproteins and glycopeptides. As cheaper and more stable competitors to lectins, boronic acids are generally believed to yield a relatively wider spectrum specificity to glycoproteins. For better understanding and effective utilization of boronate affinity, it is necessary to establish if boronic acids exhibit lectin-like narrow specificity towards individual or a sub-class of glycoproteins. Here we report a pH manipulation strategy for fine-tuning the specificity of boronate affinity monoliths towards two sub-classes of glycoproteins, sialylated and nonsialylated glycoproteins. When the binding pH > the pK(a) of the boronic acid by one pH unit or more, the boronate affinity monolith preferentially binds to glycoproteins containing neutral sugars and excludes sialic acid containing glycoproteins due to electrostatic repulsion. When the binding pH < the pK(a) by one pH unit or more, the boronate affinity monolith binds to sialylated glycoproteins due to the exceptional binding affinity of the boronic acid towards sialic acid residues. The alternative specificity towards sialic acid and neutral sugar was first verified using an off-line combination of boronate affinity extraction with nano-ESI-Orbitrap MS/MS detection. The alternative specificity towards sialylated and nonsialylated glycoproteins was then demonstrated by means of off-line combination of boronate affinity extraction with MALDI-TOF MS. Finally, the developed approach was applied to the alternative extraction of intact sialylated and nonsialylated glycoproteins spiked in human serum.

An optimized matrix-assisted laser desorption/ionization sample preparation using a liquid matrix, 3-aminoquinoline/α-cyano-4-hydroxycinnamic acid, for phosphopeptides

RATIONALE

A liquid matrix, 3-aminoquinoline (3-AQ)/α-cyano-4-hydroxycinnamic acid (CHCA), introduced by Kolli et al. in 1996 for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), has been reported for peptides and proteins, oligonucleotides, oligosaccharides, and glycopeptides. However, it has not been validated for phosphopeptides.

METHODS

We optimized sample preparation using 3-AQ/CHCA for phosphopeptides. The sensitivity of six phosphopeptide species as isolated or in digests was systematically evaluated by using MALDI-quadropole ion trap (QIT)-time of flight (TOF) MS in positive and negative ion modes, and compared with the conventional methods using a solid matrix, 2,5-dihydroxybenzoic acid (2,5-DHB).

RESULTS

The sensitivity of mono- and tetraphosphopeptides was improved 10- to 10 000-fold with the optimized preparation method using 3-AQ/CHCA compared with the conventional methods using 2,5-DHB. Improvement by 3-AQ/CHCA itself was 10-fold. Adding ammonium dihydrogen phosphate or an analyte solvent composition was also effectively improved the sensitivity. Phosphopeptides in isolated form or in digests were detected at femto- or subfemtomole levels.

CONCLUSIONS

Sensitivity of phosphopeptides was improved by the optimized sample preparation method using 3-AQ/CHCA compared with the conventional method using 2,5-DHB. The validation of 3-AQ/CHCA for phosphopeptides was systematically confirmed, expanding the potential of this matrix to phosphoproteomics.

Advances in phosphopeptide enrichment techniques for phosphoproteomics

Phosphoproteomics is increasingly used to address a wide range of biological questions. However, despite some success, techniques for phosphoproteomics are not without challenges. Phosphoproteins are present in cells in low abundance relative to their unphosphorylated counterparts; therefore phosphorylated proteins (or phosphopeptides after protein digestion) are rarely detected in standard shotgun proteomics experiments. Thus, extraction of phosphorylated polypeptides from complex mixtures is a critical step in the success of phosphoproteomics experiments. Intense research over the last decade has resulted in the development of powerful techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Here, we review how the development of IMAC, MOAC, chemical derivatization and antibody affinity purification and chromatography is contributing to the evolution of phosphoproteomics techniques. Although further developments are needed for the technology to reach maturity, current state-of-the-art techniques can already be used as powerful tools for biological research.

Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling

Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.

Preparation and characterization of hybrid-silica monolithic column with mixed-mode of hydrophilic and strong anion-exchange interactions for pressurized capillary electrochromatography

A novel organic-silica hybrid monolithic stationary phase with a mixed-mode of hydrophilic and strong anion-exchange interactions (HI-SAX) was prepared with a modified "one-pot" process of functional monomers and alkoxysilanes. Using a hydrosoluble initiator 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AIBA), the homogeneous prepolymerization system of this hybrid monolith was successfully obtained by a simple operation. The polycondensation of alkoxysilanes (tetramethoxysilane (TMOS) and vinyl-trimethoxysilane (VTMS)) and the in situ copolymerization of a quaternary ammonium group-containing acrylic monomer ([2-(acryloyloxy)ethyl] trimethyl ammonium methyl sulfate (AETA)) on the precondensed siloxanes were achieved. The morphologies of the hybrid-silica monolithic matrixes were observed by SEM, and the performances of the organic-silica hybrid monolithic columns were investigated by pressurized capillary electrochromatography. The mechanical stability and reproducibility of the obtained hybrid monolithic column preformed acceptable. Both hydrophilic interaction chromatography mechanism and strong anion-exchanged interaction were investigated. A mixed mode of HI-SAX was obtained for the analysis of nucleotides with a good resolution, and the separation of polar and basic nucleic acid bases and nucleosides was also achieved without peak tailing.

Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis--an update covering the period 2008-2011

This review article expands on the previous one (Jmeian, Y. and El Rassi, Z. Electrophoresis 2009, 30, 249-261) by reviewing pertinent literature in the period extending from early 2008 to the present. Similar to the previous review article, the present one is concerned with proteomic sample preparation (e.g. depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article differs from the first version published in Electrophoresis 2009, 30, 249-261 by expanding on capturing/enriching subglycoproteomics by lectin affinity chromatography. Ninety-eight articles published in the period extending from early 2008 to the present have been reviewed. By no means is this review article exhaustive: its aim is to give a concise report on the latest developments in the field.

Analysis of synovial fluid in knee joint of osteoarthritis:5 proteome patterns of joint inflammation based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

PURPOSE

The purpose of this study was to use matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in osteoarthritis research. Our aim was to find differentially expressed disease-related and condition-specific peptide in synovial fluid in the knee joint of patients suffering from osteoarthritis (OA), and to develop and validate the peptide classification model for OA diagnosis.

METHODS

Based on the American College of Rheumatology criteria, 30 OA cases and ten healthy donors were enrolled and underwent analysis. Magnetic beads-based weak cation exchange chromatography (MB-WCX) was performed for sample processing, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was conducted for peptide profile. ClinProt software 2.2 was used for data analysis and a genetic algorithm was created for class prediction.

RESULTS

Two peptide peaks were found which may be characterised as the potential diagnostic markers for OA. Two other significantly different peptide peaks were found in OA patients at a medium stage compared to the early and late stages. A genetic algorithm (GA) was used to establish differential diagnosis models of OA. As a result, the algorithm models marked 100% of OA, and of 97.92% of medium-stage OA.

CONCLUSION

This study demonstrated that use of proteomics methods to identify potential biomarkers of OA is possible, and the identified potential biomarkers may be potential markers for diagnosis and monitoring the progression of OA.

Photocatalytically patterned TiO2 arrays for on-plate selective enrichment of phosphopeptides and direct MALDI MS analysis

We report the development of photocatalytically patterned TiO(2) arrays for selective on-plate enrichment and direct matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of phosphopeptides. A thin TiO(2) nanofilm with controlled porosity is prepared on gold-covered glass slides by a layer-by-layer (LbL) deposition/calcination process. The highly porous and rough nanostructure offers high surface area for selective binding of phosphorylated species. The patterned arrays are generated using an octadecyltrichlorosilane (OTS) coating in combination of UV irradiation with a photomask, followed by NaOH etching. The resulting hydrophilic TiO(2) spots are thus surrounded by a hydrophobic OTS layer, which can facilitate the enrichment of low-abundance components by confining a large volume sample into a small area. The TiO(2) arrays exhibit high specificity toward phosphopeptides in complex samples including phosphoprotein digests and human serum, and the detection can be made in the fmole range. Additional advantages of the arrays include excellent stability, reusability/reproducibility, and low cost. This method has been successfully applied to the analysis of phosphopeptides in nonfat milk. The patterned TiO(2) arrays provide an attractive interface for performing on-plate reactions, including selective capture of target species for MALDI-MS analysis, and can serve as a versatile lab-on-a-chip platform for high throughput analysis in phosphoproteome research.

Monolithic phases for ion chromatography

Monolithic media are continuing to increase in popularity in chromatographic applications, and the ongoing use of commercially available materials in ion chromatography (IC) has made monoliths a viable alternative to packed-bed columns for routine use. We discuss different strategies for the synthesis of polymeric and silica monoliths with ion-exchange functionality, such as direct incorporation of ion-exchange functionality during monolith preparation and different postpolymerization alterations such as grafting and coating. The formulations and strategies presented are focused on materials intended for use in IC. We also discuss strategies for materials characterization, with emphasis on nondestructive techniques for the characterization of monolith surface functionality, especially those with applicability to in situ analysis. Finally, we describe selected IC applications of polymeric and silica monoliths published from 2008 to 2010.

Recent advances in micro-scale and nano-scale high-performance liquid-phase chromatography for proteome research

High-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS) is regarded as one of the most powerful techniques for separation and identification of proteins. Recently, much effort has been made to improve the separation capacity, detection sensitivity, and analysis throughput of micro- and nano-HPLC, by increasing column length, reducing column internal diameter, and using integrated techniques. Development of HPLC columns has also been rapid, as a result of the use of submicrometer packing materials and monolithic columns. All these innovations result in clearly improved performance of micro- and nano-HPLC for proteome research.