Control of Selectivity via Nanochemistry: Monolithic Capillary Column Containing Hydroxyapatite Nanoparticles for Separation of Proteins and Enrichment of Phosphopeptides

A novel halloysite nanotubes-based hybrid monolith for in-tube solid-phase microextraction of polar cationic pesticides

The accurate determination of polar cationic pesticides in food poses a challenge due to their high polarity and trace levels in complex matrices. This study hypothesized that the use of halloysite nanotubes (HNTs) can significantly enhance the extraction efficiency and sensitivity of these analytes because of their rich hydroxyl groups and cation exchange sites. Therefore, we chemically incorporated HNTs with organic polymer monoliths for in-tube solid-phase microextraction (SPME). This novel hybrid monolith extended service life, improved adsorption capacity, and exhibited excellent extraction performance for polar cationic pesticides. Based on these advancements, a robust and sensitive in-tube SPME-HILIC-MS/MS method was constructed to determine trace levels of polar cationic pesticides in complex food matrices. The method achieved limits of detection of 1.9, 2.1, and 0.1 μg/kg for maleic hydrazide, amitrole, and cyromazine, respectively. The spiked recoveries in five food samples ranged from 80.2 to 100.8%, with relative standard deviations below 10.7%.

Profiling of phosphorylated metabolites from lung cancer by zeolite loaded Mg-Al-Ce ternary hydroxide (Zeolite@MAC) composite

Phosphorylated metabolites are linked to metabolism, and the dysregulation of metabolic reactions brings cancer. Dysregulated levels lead to hyperactivation of glycolytic and mitochondrial oxidative phosphorylation pathways. Abnormal concentrations are the indicators of energy-related disorders. In this work, Zeolite-loaded Mg-Al-Ce hydroxides (Zeolite@MAC) are prepared by co-precipitation and characterized through FTIR, XRD, SEM, BET, AFM, TEM, and DLS. Magnesium-Aluminum-Cerium-Zeolite particles enrich phosphate-containing small molecules. These ternary hydroxides carried out the main adsorption mechanism, which swapped the surface hydroxyl group ligands for phosphate and the inner-sphere complex of CePO₄. XH₂O. Cerium plays a significant role in the complexation of phosphate, and adding Mg and Al further helps disperse Ce and increase the surface charge on the adsorbent. ΑTP and AMP are the standard molecules for parameter optimization. Zeolite@MAC enriches phosphorylated metabolites followed by their desorption via UV-vis spectrophotometry. MS profiles for healthy and lung cancer serum samples are obtained for phosphorylated metabolites. Characteristic phosphorylated metabolites have been detected in lung cancer samples with high expression. The role of phosphorylated metabolites is explored for abnormal metabolic pathways in lung cancer. The fabricated material is sensitive, selective, and highly enriched for identifying phosphate-specific biomarkers.

Two-dimensional magnetic bimetallic organic framework nanosheets for highly efficient enrichment of phosphopeptides

Highly selective enrichment and sensitive detection of phosphopeptides is pivotal for comprehensive phosphoproteomics analysis; however, it also poses a long-standing challenge. Here, a novel two-dimensional (2D) magnetic bimetallic organic framework (MOF) nanosheet with Zr-O clusters and Ti-O clusters (denoted as the Fe₃O₄@Zr-Ti BPDC nanosheet) is prepared via a solvothermal method and in situ deposition of Fe₃O₄ nanoparticles for the first time. Taking advantage of the abundant dual affinities of Zr-O and Ti-O clusters for phosphopeptides, large surface area and high chemical stability, the Fe₃O₄@Zr-Ti BPDC nanosheets exhibit excellent enrichment performance for phosphopeptides. Within the framework of density functional theory, the interaction between Zr-O clusters, Ti-O clusters and phosphorylated molecules was studied to find the possible reason behind the superior adsorption performance of the bimetallic MOF nanosheets. We found that electrons would migrate from Ti to Zr spontaneously after doping Ti element and enhance the electrostatic traction between Zr species and phosphorylated molecules, demonstrating that the synergistic effect of Zr-Ti was helpful to improve the enrichment efficiency for phosphopeptides. Furthermore, the Fe₃O₄@Zr-Ti BPDC nanosheets showed good enrichment performance in complex bio-samples, including nonfat milk, human saliva, and a breast cancer cell lysate, indicating their tremendous potential in the analysis of trace phosphorylated biomolecules in complex bio-samples.

Styrene-based polymerised high internal phase emulsions using monomers in the internal phase as co-surfactants for improved liquid chromatography

Poly(styrene-co-divinylbenzene)-based monoliths were prepared from the polymerisation of water-in-monomer high internal phase emulsions, where the water-soluble monomers acrylamide (AAm) or poly(ethylene glycol) diacrylate (PEGDA) (M w 258) were also included in the 90 vol% internal phase. Both AAm and PEGDA were found to act as co-surfactants, resulting in the obtainment of monoliths with greater homogeneity in some cases. As a result these materials demonstrated significantly improved chromatographic performance for the separation of a standard mixture of proteins using reversed-phase liquid chromatography, in comparison to monoliths prepared with no internal phase monomer. In particular, the columns grafted with PEGDA were capable of separating a more complex mixture consisting of seven components. The inclusion of monomers in the internal phase also allowed for the functionalisation of the monolith's surface where the degree of polymerisation that occurred in the internal phase, which was governed by the monomer content in the internal phase and initiation location, determined whether polymeric chains or a hydrogel were grafted to the surface. A monolith grafted with AAm was also found to be capable of retaining polar analytes as a result of the increase in surface hydrophilicity.

Hydroxyapatite surface-functionalized monolithic column for selective in-tube solid phase microextraction of zoleronic acid and risedronic acid

To date, hydroxyapatite (HAP) based monoliths were mainly fabricated by directly doping of HAP, which suffered from less effective coverage of HAP. Herein, a HAP surface-functionalized monolithic column (HAP@PDA@UF) has been prepared by in-situ biomineralization and applied as sorbent for selective in-tube solid phase microextraction of zoleronic acid and risedronic acid. A polydopamine coating was first generated on the surface of the parent urea-formaldehyde resin monolith; and then HAP microcrystals were further grew on the polydopamine coating to achieve this preparation. SEM, EDAX, FTIR, XPS and mercury intrusion method were utilized for the characterization of the HAP@PDA@UF monolith, and provided evidences of this successful preparation. The selective extraction mechanism of the HAP@PDA@UF monolith was investigated by the optimization of methanol percentage in the sampling solution, phosphate concentration in the eluent. Other crucial factors, including sampling and elution flow rate, and collection time span, were also optimized for the desired SPME performance. Under the optimal conditions, the proposed method showed low LODs of 0.1 μg/mL, satisfactory recoveries of 79.6%-92.5% with RSDs less than 2.7%, and good reproducibility with RSD less than 6.9%, which demonstrated the excellent application of the HAP@PDA@UF monolith, and its potential as a promising selective sorbent for bisphosphonates.

WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT

Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.

[Fabrication of nanomaterials incorporated polymeric monoliths and application in sample pretreatment]

Polymeric monolithic columns are fabricated by in situ polymerization of the corresponding monomer, crosslinkers, porogenic solvents and radical initiators within a mold. Compared with the conventional packed solid phase extraction adsorbents, polymeric monolithic columns with a continuous porous structure process distinctive advantages of rapid mass transfer and excellent permeability, which facilitates the extraction of trace amounts of the target from the matrix even at high flow velocities. Besides, these materials can be easily fabricated in situ within various cartridges, avoiding a further packing step associated with packed particulate adsorbents. Additionally, the abundant monomer availability, flexible porous structure, and wide applicable pH range make monoliths versatile for use in separation science. Thus, polymeric monolithic columns have been increasingly applied as efficient and promising extraction media for sample pretreatment food, pharmaceutical, biological and environmental analyses. However, these materials usually have the difficulty in morphology control and their interconnected porous micro-globular structure, which may result in low porosity, limited specific surface area and poor efficiency. In addition, polymeric monoliths suffer from the swelling in organic solvents, thus decreasing the service life and precision while increasing the cost consumption. Recently, the development of nanomaterial-incorporated polymeric monoliths with an improved ordered structure, enhanced adsorption efficiency and outstanding selectivity has attracted considerable attention. Nanoparticles are considered as particulates within the size range of 1-100 nm in at least one dimension, which endows them with unique optical, electrical and magnetic properties. These materials have a large surface area, excellent thermal and chemical stabilities, remarkable versatility, as well as a wide variety of active functional groups on their surface. With the aim of exploiting these advantages, researchers have shown great interest in applying nanomaterial-incorporated polymeric monoliths to separation science. Accordingly, significant progress has been achieved in this field. Nanomaterials can be entrapped via the direct synthesis of a polymerization solution that contains well dispersed nanomaterials in porogens. In addition, nanoparticles can be incorporated into the monolithic matrix by copolymerization and post-polymerization modification via specific interactions. Therefore, nanomaterial-incorporated polymeric monoliths combined the different shapes, chemical properties, and physical properties of the polymers with those of the nanoparticles. The presence of nanoparticles can improve the structural rigidity as well as the thermal and chemical stabilities of monolithic adsorbents. Besides, nanoparticles are capable of increasing the specific surface area and providing multiple active sites, which leads to enhanced extraction performance and selectivity of polymeric monolithic materials. In recent years, diverse types of nanomaterials, such as carbonaceous nanoparticles, metallic materials and metal oxides, metal-organic frameworks, covalent organic frameworks and inorganic nanoparticles have been extensively explored as hybrid adsorbents in the modes of solid phase extraction, solid phase microextraction, stir bar sorption extraction and on-line solid phase extraction. This review specifically summarizes the fabrication methods for nanomaterial incorporated polymeric monoliths and their application to the field of sample pretreatment. The existing challenges and future possible perspectives in the field are also discussed.

Engineering Magnetic Guanidyl-Functionalized Supramolecular Organic Framework for Efficient Enrichment of Global Phosphopeptides

Comprehensive mass spectrometry-based proteomics analysis is currently available but remains challenging, especially for post-translational modifications of phosphorylated proteins. Herein, multifunctional magnetic pillar[5]arene supramolecular organic frameworks were fabricated and immobilized with arginine (mP5SOF-Arg) for highly effective enrichment of global phosphopeptides. The specific phosphate-P5/phosphate-guanidine affinities and large surface area with regular porosity contribute to the high enrichment capacity. By coupling with mass spectrometry, high detection sensitivity (0.1 fmol), excellent selectivity (1:5000 molar ratios of β-casein/cytochrome c), and high recyclability (seven cycles) were achieved for phosphopeptide analysis. mP5SOF-Arg can efficiently enrich phosphopeptides from practical samples, including defatted milk, egg yolk, and human saliva. Notably, a total of 450 phosphopeptides were explored for highly selective identification from A594 cells and 1445 phosphopeptides were identified from mouse liver tissue samples. mP5SOF-Arg exhibited great potential to serve as the basis for peptidomic research to identify phosphopeptides and provided insight for biomarker discovery.

Determination of bisphosphonates anti-resorptive properties based on three forms of ceramic materials: Sorption and release process evaluation

There is a strong need to search for more effective compounds with bone anti-resorptive properties, which will cause fewer complications than commonly used bisphosphonates. To achieve this goal, it is necessary to search for new techniques to characterize the interactions between bone and drug. By studying their interaction with hydroxyapatite (HA), this study used three forms of ceramic materials, two of which are bone-stimulating materials, to assess the suitability of new active substances with anti-resorptive properties. In this study, three methods based on HA in loose form, polycaprolactone/HA (a polymer-ceramic materials containing HA), and polymer-ceramic monolithic in-needle extraction (MINE) device (a polymer inert skeleton), respectively, were used. The affinity of risedronate (a standard compound) and sixteen aminomethylenebisphosphonates (new compounds with potential antiresorptive properties) to HA was defined according to the above-mentioned methods. Ten monolithic materials based on 2-hydroxyethyl methacrylate/ethylene dimethacrylate are prepared and studied, of which one was selected for more-detailed further research. Simulated body fluids containing bisphosphonates were passed through the MINE device. In this way, sorption-desorption of bisphosphonates was evaluated using this MINE device. The paper presents the advantages and disadvantages of each technique and its suitability for assessing new active substances. All three methods allow for the selection of several compounds with potentially higher anti-resorptive properties than risedronate, in hope that it reflects their higher bone affinity and release ability.

Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics Research

High-performance liquid chromatography integrated with tandem mass spectrometry (HPLC-MS/MS) has become a powerful technique for proteomics research. Its performance heavily depends on the separation efficiency of HPLC, which in turn depends on the chromatographic material. As the "heart" of the HPLC system, the chromatographic material is required to achieve excellent column efficiency and fast analysis. Monolithic materials, fabricated as continuous supports with interconnected skeletal structure and flow-through pores, are regarded as an alternative to particle-packed columns. Such materials are featured with easy preparation, fast mass transfer, high porosity, low back pressure, and miniaturization, and are next-generation separation materials for high-throughput proteins and peptides analysis. Herein, the recent progress regarding the fabrication of various monolithic materials is reviewed. Special emphasis is placed on studies of the fabrication of monolithic capillary columns and their applications in separation of biomolecules by capillary liquid chromatography (cLC). The applications of monolithic materials in the digestion, enrichment, and separation of phosphopeptides and glycopeptides from biological samples are also considered. Finally, advances in comprehensive 2D HPLC separations using monolithic columns are also shown.

Hydroxyapatite-embedded monolithic column for selective on-line solid-phase extraction of adenosine triphosphate and its phosphorylated metabolites

A novel hydroxyapatite-embedded monolithic column has been facilely prepared in a stainless-steel column with inner diameter of 2.1 mm by the strong adhesion of urea-formaldehyde (UF) resin and exploited as a sorbent for selective on-line solid-phase extraction (on-line SPE) of adenosine triphosphate and its phosphorylated metabolites. The composition for this preparation, including the amount of hydroxyapatite nanopowders and the porogen were investigated to obtain a suitable monolith with large surface area and satisfactory permeability. Owing to anion exchange interaction of hydroxyapatite and hydrophilic interaction of UF monolithic matrix, the prepared monolith showed good extraction efficiency and selectivity towards these phosphorylated analytes. Several parameters for on-line SPE, including ACN percentage in the sampling solution, collection time span, salt concentration of the eluent, sampling and elution flow rate, were optimized with respect to the extraction efficiencies of the target compounds. Under the optimized conditions, the LODs of the analytes were in the range of 0.01-0.04 μg/g, the recoveries in the spiked samples ranged from 78.3%-92.5% with RSDs <4.7%. Due to the excellent extraction ability towards phosphorylated compounds in practical samples, a simple on-line SPE-HPLC method using hydroxyapatite-embedded monolith as sorbent has been proposed for monitoring freshness of grass carp.

Determination of protein kinase A activity and inhibition by using hydroxyapatite nanoparticles as a fluorescent probe

The authors describe a fluorometric method for the determination of the activity and inhibition of protein kinase A (PKA). In the presence of ATP, PKA catalyzes the transfer of phosphate groups from ATP to a peptide, and the generated phosphorylated peptide quenches the fluorescence (measured at excitation/emission peaks of 340/440 nm) of the hydroxyapatite nanoparticles (HAP-NPs). A linear logarithmic relationship of PKA concentrations with fluorescence intensity in the range from 1 to 50 U·L^-1 was obtained, and the lower limit of detection (LOD) is 0.5 U·L^-1. This is much lower than LODs reported in the literature. The PKA inhibitor H-89 was studied, and the inhibition plot has a sigmoidal shape with a half-maximal inhibitory concentration of around 750 nM of H-89. At a 4.5 nM level of H-89, fluorescence of HAP-NPs fell to levels of no PKA controls, demonstrating that the assay is a viable tool to screen for kinase inhibitors. An assay with Hela cell lysates in combination with forskolin (an activator of adenylyl cyclase) and IBMX (a phosphodiesterase inhibitor used to activate the cellular activity of PKA) resulted in decreased fluorescence of HAP-NPs. This suggests that the assay can be applied for testing in vitro cell kinase activity. In our perception, this method will enable high-throughput screening for kinase-related drugs and fluorometric enzymatic detection in various areas. Graphical abstract Fluorescence assay based on hydroxyapatite nanoparticles (HAP) fluorescence quenching was developed for analysis of the activity and inhibition of protein kinase A (PKA).

Organic polymer-based monolithic stationary phases with incorporated nanostructured materials for HPLC and CEC

This review article is concerned with the recent advances made in the field of organic polymer-based monoliths with incorporated nanostructured materials (NSMs) for use in liquid chromatography and capillary electrochromatography. It covers the pertinent literature published over the last 7-8 years with a total of 56 references. The present article has two distinct parts: one major part encompassing "traditional" organic polymer-based monoliths modified with NSMs and a minor part on cryogels modified with NSMs.

Facile Preparation of Titanium(IV)-Immobilized Hierarchically Porous Hybrid Monoliths

Hierarchically porous materials have become a key feature of biological materials and have been widely applied for adsorption or catalysis. Herein, we presented a new approach to directly prepare a phosphate-functionalized hierarchically porous hybrid monolith (HPHM), which simultaneously contained mesopores and macropores. The design was based on the copolymerization of polyhedral oligomeric vinylsilsesquioxanes (vinylPOSS) and vinylphosphonic acid (VPA) by adding degradable polycaprolactone (PCL) additive. The phosphate groups could be directly introduced into the hybrid monoliths. This approach was simple and time-saving, and overcame the defect of a rigorous, complex process for preparing traditional Ti⁴⁺-immobilized metal ion affinity chromatography (IMAC) materials. The specific surface area of an optimal hybrid monolith could reach 502 m²/g obtained by nitrogen adsorption/desorption measurements, which originated from the degradation of PCL. Meanwhile, the characterization of scanning electron microscopy (SEM) and mercury intrusion porosimetry (MIP) also suggested that the macropores existed in the hybrid monoliths. The size of macropores could be controlled by the content of PCL in the polymerization mixture. The prepared Ti⁴⁺-IMAC HPHMs exhibited high adsorption capacity (63.6 mg/g for pyridocal 5'-phosphatemonohydrate), and excellent enrichment specificity (tryptic digest of β-casein/BSA at a molar ratio of 1:1000) and sensitivity (tryptic digest of 5 fmol of β-casein). Moreover, the Ti⁴⁺-IMAC HPHMs provided effective enrichment ability of low-abundance phosphopeptides from human serum and HeLa cell digests.

Methacrylate Polymer Monoliths for Separation Applications

This review summarizes the development of methacrylate-based polymer monoliths for separation science applications. An introduction to monoliths is presented, followed by the preparation methods and characteristics specific to methacrylate monoliths. Both traditional chemical based syntheses and emerging additive manufacturing methods are presented along with an analysis of the different types of functional groups, which have been utilized with methacrylate monoliths. The role of methacrylate based porous materials in separation science in industrially important chemical and biological separations are discussed, with particular attention given to the most recent developments and challenges associated with these materials. While these monoliths have been shown to be useful for a wide variety of applications, there is still scope for exerting better control over the porous architectures and chemistries obtained from the different fabrication routes. Conclusions regarding this previous work are drawn and an outlook towards future challenges and potential developments in this vibrant research area are presented. Discussed in particular are the potential of additive manufacturing for the preparation of monolithic structures with pre-defined multi-scale porous morphologies and for the optimization of surface reactive chemistries.

TiO₂ nanoparticles functionalized monolithic capillary microextraction online coupled with inductively coupled plasma mass spectrometry for the analysis of Gd ion and Gd-based contrast agents in human urine

In this work, a novel method of TiO2 nanoparticles (NPs) functionalized monolithic capillary microextraction (CME) online coupling with inductively coupled plasma mass spectrometry (ICPMS) was developed for the sequential determination of Gd(3+) and Gd-based contrast agents in human urine samples. The monolithic capillary was prepared by embedding anatase TiO2 NPS in the poly(methacrylic acid-ethylene glycol dimethacrylate) (MAA-EDMA) framework. The Gd(3+) and Gd-based contrast agents (such as gadolinium-diethylene triamine pentaacetic acid (Gd-DTPA) and Gd-DTPA-bismethylamide (Gd-DTPA-BMA)) display different adsorption behaviors on the prepared monolithic capillary which possesses the adsorption properties of both anatase TiO2 NPS and poly(MAA-EDMA) monolith. Under the optimized conditions, the limits of detection (LODs) were found to be 3.6, 3.2, and 4.5 ng L(-1) for Gd(3+), Gd-DTPA, and Gd-DTPA-BMA, respectively, which are the lowest up to date. The enrichment factor was 25-fold with the sample throughput of 5 h(-1). The proposed method was validated by the analysis of Gd(3+) and Gd-DTPA in the healthy human urine samples as well as Gd(3+) and Gd-DTPA-BMA in patient urine samples. It was found that only a small amount of the free Gd(3+) was released from Gd-DTPA-BMA, and accurate results could be obtained since no oxidation/reduction or subtraction is involved in this method. This method is simple, sensitive, and rapid and provides a very attractive nonchromatography strategy for the speciation of Gd(3+) and Gd-based contrast agents in urine samples.

High-performance liquid chromatography separation of unsaturated organic compounds by a monolithic silica column embedded with silver nanoparticles

The optimization of a porous structure to ensure good separation performances is always a significant issue in high-performance liquid chromatography column design. Recently we reported the homogeneous embedment of Ag nanoparticles in periodic mesoporous silica monolith and the application of such Ag nanoparticles embedded silica monolith for the high-performance liquid chromatography separation of polyaromatic hydrocarbons. However, the separation performance remains to be improved and the retention mechanism as compared with the Ag ion high-performance liquid chromatography technique still needs to be clarified. In this research, Ag nanoparticles were introduced into a macro/mesoporous silica monolith with optimized pore parameters for high-performance liquid chromatography separations. Baseline separation of benzene, naphthalene, anthracene, and pyrene was achieved with the theoretical plate number for analyte naphthalene as 36,000 m(-1). Its separation function was further extended to cis/trans isomers of aromatic compounds where cis/trans stilbenes were chosen as a benchmark. Good separation of cis/trans-stilbene with separation factor as 7 and theoretical plate number as 76,000 m(-1) for cis-stilbene was obtained. The trans isomer, however, is retained more strongly, which contradicts the long- established retention rule of Ag ion chromatography. Such behavior of Ag nanoparticles embedded in a silica column can be attributed to the differences in the molecular geometric configuration of cis/trans stilbenes.

Preparation of Highly Porous Coordination Polymer Coatings on Macroporous Polymer Monoliths for Enhanced Enrichment of Phosphopeptides

We describe a protocol for the preparation of hybrid materials based on highly porous coordination polymer coatings on the internal surface of macroporous polymer monoliths. The developed approach is based on the preparation of a macroporous polymer containing carboxylic acid functional groups and the subsequent step-by-step solution-based controlled growth of a layer of a porous coordination polymer on the surface of the pores of the polymer monolith. The prepared metal-organic polymer hybrid has a high specific micropore surface area. The amount of iron(III) sites is enhanced through metal-organic coordination on the surface of the pores of the functional polymer support. The increase of metal sites is related to the number of iterations of the coating process. The developed preparation scheme is easily adapted to a capillary column format. The functional porous polymer is prepared as a self-contained single-block porous monolith within the capillary, yielding a flow-through separation device with excellent flow permeability and modest back-pressure. The metal-organic polymer hybrid column showed excellent performance for the enrichment of phosphopeptides from digested proteins and their subsequent detection using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The presented experimental protocol is highly versatile, and can be easily implemented to different organic polymer supports and coatings with a plethora of porous coordination polymers and metal-organic frameworks for multiple purification and/or separation applications.

A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA

The production of structurally significant product ions during the dissociation of phosphopeptides is a key to the successful determination of phosphorylation sites. These diagnostic ions can be generated using the widely adopted MS/MS approach, MS3 (Data Dependent Neutral Loss - DDNL), or by multistage activation (MSA). The main purpose of this work is to introduce a false-localization rate (FLR) probabilistic model to enable unbiased phosphoproteomics studies. Briefly, our algorithm infers a probabilistic function from the distribution of the identified phosphopeptides' XCorr Delta scores (XD-Scores) in the current experiment. Our module infers p-values by relying on Gaussian mixture models and a logistic function. We demonstrate the usefulness of our probabilistic model by revisiting the "to MSA, or not to MSA" dilemma. For this, we use human leukemia-derived cells (K562) as a study model and enriched for phosphopeptides using the hydroxyapatite (HAP) chromatography. The aliquots were analyzed with and without MSA on an Orbitrap-XL. Our XD-Scoring analysis revealed that the MS/MS approach provides more identifications because of its faster scan rate, but that for the same given scan rate higher-confidence spectra can be achieved with MSA. Our software is integrated into the PatternLab for proteomics freely available for academic community at http://www.patternlabforproteomics.org. Biological significance Assigning statistical confidence to phosphorylation sites is necessary for proper phosphoproteomic assessment. Here we present a rigorous statistical model, based on Gaussian mixture models and a logistic function, which overcomes shortcomings of previous tools. The algorithm described herein is made readily available to the scientific community by integrating it into the widely adopted PatternLab for proteomics. This article is part of a Special Issue entitled: Computational Proteomics.

Development of a silica monolith modified with Fe3O4 nano-particles in centrifugal spin column format for the extraction of phosphorylated compounds

In this study, citrate-stabilised iron oxide nano-particles (∼16 nm) have been immobilised on commercial silica monolithic centrifugal spin columns (MonoSpin) for the extraction of phosphorylated compounds. Two alternative strategies were adopted involving either direct electrostatic attachment to an aminated MonoSpin (single-layer method) in the first instance, or the use of a layer-by-layer method with poly(diallyldimethylammonium) chloride. Field-emission scanning electron spectroscopy and energy-dispersive X-ray spectroscopy was used for confirming notably higher coverage of nano-particles using the layer-by-layer method (2.49 ± 0.53 wt%) compared with the single-layer method (0.43 ± 0.30 wt%). The modified monolith was used for the selective separation/extraction of adenosine monophosphate, adenosine diphosphate and adenosine triphosphate with elution using a phosphate buffer. A reversed-phase liquid chromatographic assay was used for confirming that adenosine, as a non-phosphorylated control was not retained on the modified MonoSpin devices, whereas recovery of 80% for adenosine monophosphate, 86% for adenosine diphosphate and 82% for adenosine triphosphate was achieved.