Peptide and protein assays using customizable bio-affinity arrays combined with ambient ionization mass spectrometry

High-throughput identification and quantification of protein/peptide biomarkers from biofluids in a label-free manner is achieved by interfacing bio-affinity arrays (BAAs) with nano-electrospray desorption electrospray ionization mass spectrometry (nano-DESI-MS). A wide spectrum of proteins and peptides ranging from phosphopeptides to cis-diol biomolecules as well as thrombin can be rapidly extracted via arbitrarily predefined affinity interactions including coordination chemistry, covalent bonding, and biological recognition. An integrated MS platform allows continuous interrogation. Profiling and quantitation of dysregulated phosphopeptides from small-volume (∼5 μL) serum samples has been successfully demonstrated. As a front-end device adapted to any mass spectrometer, this MS platform might hold much promise in protein/peptide analysis in point-of-care (POC) diagnostics and clinical applications.

Customizable bio-affinity arrays were interfaced with ambient ionization mass spectrometry for high-throughput assays of protein/peptide biomarkers in biofluids.

Gold nanoparticles-based assays for biodetection in urine

Urine is a biofluid easy to collect through a non-invasive technique that allows collecting a large volume of sample. The use of urine for disease diagnosis is not yet well explored. However, it has gained attention over the last three years. It has been applied in the diagnosis of several illnesses such as kidney disease, bladder cancer, prostate cancer and cardiovascular diseases. In the last decade, gold nanoparticles (Au NPs) have attracted attention in biosensors' development for the diagnosis of diseases due to their electrical and optical properties, ability to conjugate with biomolecules, high sensitivity, and selectivity. Therefore, this article aims to present a comprehensive view of state of the art on the advances made in the quantification of analytes in urinary samples using AuNPs based assays, with a focus on protein analysis. The type of diagnosis methods, the Au NPs synthesis approaches and the strategies for surface modification aiming at selectivity towards the different targets are highlighted.

Fully integrated protein absolute quantification platform for analysis of multiple tumor markers in human plasma

In this study, we developed a fully integrated protein absolute quantification platform for simultaneous analysis of multiple tumor markers in human plasma, by which multiple target proteins (alpha-fetoprotein, prostate-specific antigen, carcino-embryonic antigen and mucin-1) were firstly enriched by aptamers immobilized capillary column using graphene oxide modified polymer microsphere as the separation matrix, and then the eluted target proteins were online denatured, reduced, desalted and digested by our developed fully automated sample treatment device (FAST), finally the resulting peptides were analyzed by parallel reaction monitoring (PRM) on LTQ-orbitrap velos mass spectrometry. Compared to traditional ELISA assay, the platform exhibited significant advantages such as short analysis time, low limit of detection, and ease of automation. Furthermore, our developed platform was also applied in the absolute quantification of tumor markers from clinical human plasma samples, and the results were comparable to those obtained by clinical immunoassay. All the results demonstrated that such a platform could provide a promising tool for achieving high sensitivity, high accuracy, and high throughput detection of disease related protein markers in the routine physical examination and clinical disease diagnosis.

Insights into the structure-performance relationships of extraction materials in sample preparation for chromatography

Sample preparation is one of the most crucial steps in analytical processes. Commonly used methods, including solid-phase extraction, dispersive solid-phase extraction, dispersive magnetic solid-phase extraction, and solid-phase microextraction, greatly depend on the extraction materials. In recent decades, a vast number of materials have been studied and used in sample preparation for chromatography. Due to the unique structural properties, extraction materials significantly improve the performance of extraction devices. Endowing extraction materials with suitable structural properties can shorten the pretreatment process and improve the extraction efficiency and selectivity. To understand the structure-performance relationships of extraction materials, this review systematically summarizes the structural properties, including the pore size, pore shape, pore volume, accessibility of active sites, specific surface area, functional groups and physicochemical properties. The mechanisms by which the structural properties influence the extraction performance are also elucidated in detail. Finally, three principles for the design and synthesis of extraction materials are summarized. This review can provide systematic guidelines for synthesizing extraction materials and preparing extraction devices.

Evaluation of Aptamers as Affinity Reagents for an Enhancement of SRM-Based Detection of Low-Abundance Proteins in Blood Plasma

Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the search and verification of novel protein disease markers, is a challenging task due to the immense dynamic range of protein abundance levels. One approach used to overcome this problem is the immunoaffinity enrichment of target proteins for SRM analysis, employing monoclonal antibodies. Aptamers appear as a promising alternative to antibodies for affinity enrichment. Here, using recombinant protein SMAD4 as a model target added at known concentrations to human blood plasma and SRM as a detection method, we investigated a relationship between the initial amount of the target protein and its amount in the fraction enriched with SMAD4 by an anti-SMAD4 DNA-aptamer immobilized on magnetic beads. It was found that the aptamer-based enrichment provided a 30-fold increase in the sensitivity of SRM detection of SMAD4. These results indicate that the aptamer-based affinity enrichment of target proteins can be successfully employed to improve quantitative detection of low-abundance proteins by SRM in undepleted human blood plasma.

Competitive adsorption on gold nanoparticles for human papillomavirus 16 L1 protein detection by LDI-MS

The detection of the HPV L1 protein provides information about the infection status of the virus, reflects the replication status of the HPV virus in cervical cells, and helps understand the regression and progress of cervical lesions. Herein, we report a novel laser desorption ionization mass spectrometry (LDI MS) method for the sensitive detection of the HPV 16 L1 protein, based on non-covalent competitive adsorption between the HPV 16 L1 aptamer and melamine on gold nanoparticles (AuNPs). The intensity of the MS signal corresponding to the mass tag shows a linear relationship with the HPV 16 L1 concentration in the range 2-80 ng mL^-1, with a limit of detection (LOD) of 58.8 pg mL^-1. Using this method, the HPV 16 L1 protein is quantitatively analyzed in both clinical and vaccine samples. The described method is simple and has high sensitivity and good reliability.

Aptamer-functionalized magnetic metal organic framework as nanoprobe for biomarkers in human serum

Human serum is a huge bioinformatics database of human physiological and pathological state, many proteins/peptides among which can serve as biomarkers for monitoring human's health condition, thereby being worth exploring. The simple and fast capture of biomarkers from human serum is the first key step to realize their accurate detection. In this work, we developed the aptamer functionalized magnetic metal organic framework nanoprobe, and furtherly combined with mass spectrometry technology to establish an efficient method of identifying biomarkers. Taking insulin as example of biomarker in human serum, we developed sulfhydryl human insulin aptamer functionalized magnetic metal organic framework (denoted as Mag MOF@Au@HIA) through the post-synthetic modification of MIL-101(Cr)-NH₂ for testing the applicability of the established method. Depending on the strong magnetic responsiveness and high specific area as well as high-loaded human insulin aptamers, the limit of detection of insulin was down to 1 ng/mL and 2 ng/mL in the standard insulin solution and human serum, respectively. Moreover, a good linear relationship (R² = 0.998) was obtained by using standard insulin solution with concentration range from 100 ng/mL to 5 ng/mL, based on which the capture recovery of insulin with Mag MOF@Au@HIA from human serum was demonstrated to be excellent. All of the results indicate that the aptamer-functionalized magnetic metal organic framework is a promising nanoprobe for biomarkers capture in human serum.

[Use of DNA-aptamers for enrichment of low abundant proteins in cellular extracts for quntitative detection by selected reaction monitoring]

The relationship between the amount of a target protein in a complex biological sample and its amount measured by selected reaction monitoring (SRM) mass spectrometry upon the affinity enrichment of target protein with aptamers immobilized on a solid phase was studied. Human thrombin added in known concentrations to cellular extracts derived from bacterial cells was used as model target protein. It has been demonstrated that the affinity enrichment of thrombin in cellular extracts by means of the thrombin-binding aptamer immobilized on the surface of magnetic microbeads results in an approximately 10-fold increase of the concentration of target protein and a 100-fold decrease of the low limit of a target protein concentration range where its quantitative detection by SRM is possible without an interference from other peptides present in a tryptic digest.

Core-shell structured magnetic metal-organic framework composites for highly selective detection of N-glycopeptides based on boronic acid affinity chromatography

Boronic acid affinity chromatography (BAAC) is one of the most significant methods in glycoproteomics research due to its low bias towards glycopeptides and easy enrichment process. In this work, core-shell structured magnetic metal-organic framework (MOF) composites with abundant boronic acid groups were designed and synthesized for selective glycopeptide enrichment based on BAAC. The as-prepared core-shell structured magnetic MOF composites (denoted as Fe₃O₄@PVP/PEI@MOF (B)) inherited strong magnetic responsiveness from the Fe₃O₄ core as well as ultrahigh surface area and abundant boronic acid sites from the MOF shell. The affinity between boronic acid and cis-diols groups endowed the composites with improved sensitivity (0.5 fmol/μL) and selectivity (1:100) towards glycopeptides, achieving remarkable results in glycopeptides detection from standard glycoprotein digests as well as complex bio-samples. As a result, a total of 209 N-glycosylation peptides from 89 different glycoproteins were identified from human serum digests, indicating its broad prospect in glycoproteome study.

Exploring the fungal protein cadre in the biosynthesis of PbSe quantum dots

While a large number of microbial sources have recently emerged as potent sources for biosynthesis of chalcogenide quantum dots (QDs), studies regarding their biomimetic strategies that initiate QD biosynthesis are scarce. The present study describes several mechanistic aspects of PbSe QD biosynthesis using marine Aspergillus terreus. Scanning electron microscopic (SEM) studies indicated distinctive morphological features such as abrasion and agglomeration on the fungal biomass after the biosynthesis reaction. Further, the biomass subsequent to the heavy metal/metalloid precursor was characterized with spectral signatures typical to primary and secondary stress factors such as thiol compounds and oxalic acid using Fourier Transform Infra-Red Spectroscopic (FTIR) analysis. An increase in the total protein content in the reaction mixture after biosynthesis was another noteworthy observation. Further, metal-phytochelatins were identified as the prominent metal-ion trafficking components in the reaction mixture using Liquid Chromatography Mass Spectroscopic analysis (LCMS). Subsequent assays confirmed the involvement of metal binding peptides namely metallothioneins and other anti-oxidant enzymes that might have played a prominent role in the microbial metal detoxification system for the biosynthesis of PbSe QDs. Based on these findings a possible mechanism for the biosynthesis of PbSe QDs by marine A. terreus has been elucidated.

Application of flowerlike MgO for highly sensitive determination of lead via matrix-assisted laser desorption/ionization mass spectrometry

RATIONALE

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is a high-throughput method to achieve fast and accurate identification of lead (Pb) exposure, but is seldom used because of low ionization efficiency and insufficient sensitivity. Nanomaterials applied in MS are a promising technique to overcome the obstacles of MALDI.

METHODS

Flowerlike MgO nanostructures are applied for highly sensitive lead profiling in real samples. They can be used in two ways: (a) MgO is mixed with N-naphthylethylenediamine dihydrochloride (NEDC) as a novel matrix MgO/NEDC; (b) MgO is applied as an absorbent to enrich Pb ions in very dilute solution.

RESULTS

The signal intensities of lead by MgO/NEDC were ten times higher than the NEDC matrix. It also shows superior anti-interference ability when analyzing 10 μmol/L Pb ions in the presence of organic substances or interfering metal ions. By applying MgO as adsorbent, the LOD of lead before enrichment is 1 nmol/L. Blood lead test can be achieved using this enrichment process. Besides, MgO can play the role of internal standard to achieve quantitative analysis.

CONCLUSIONS

Flowerlike MgO nanostructures were applied for highly sensitive lead profiling in real samples. The method is helpful to prevent Pb contamination in a wide range. Further, the combination of MgO with MALDI MS could inspire more nanomaterials being applied in highly sensitive profiling of pollutants. Copyright © 2016 John Wiley & Sons, Ltd.

Organic salt NEDC (N-naphthylethylenediamine dihydrochloride) assisted laser desorption ionization mass spectrometry for identification of metal ions in real samples

The significance of metals in life and their epidemiological effects necessitate the development of a direct, efficient, and rapid method of analysis. The matrix assisted laser desorption/ionization technique is on the horns of a dilemma of metal analysis as the conventional matrixes have high background in the low mass range. An organic salt, NEDC (N-naphthylethylenediamine dihydrochloride), is applied as a matrix for identification of metal ions in the negative ion mode in the present work. Sixteen metal ions, Ba(2+), Ca(2+), Cd(2+), Ce(3+), Co(2+), Cu(2+), Fe(3+), Hg(2+), K(+), Mg(2+), Mn(2+), Na(+), Ni(2+), Pb(2+), Sn(2+) and Zn(2+), in the form of their chloride-adducted clusters were systematically tested. Mass spectra can provide unambiguous identification through accurate mass-to-charge ratios and characteristic isotope patterns. Compared to ruthenium ICP standard solution, tris(2,2'-bipyridyl)dichlororuthenium(ii) (C30H24N6Cl2Ru) can form organometallic chloride adducts to discriminate from the inorganic ruthenium by this method. After evaluating the sensitivity for Ca, Cu, Mg, Mn, Pb and Zn and plotting their quantitation curves of signal intensity versus concentration, we determined magnesium concentration in lake water quantitatively to be 5.42 mg L(-1) using the standard addition method. There is no significant difference from the result obtained with ICP-OES, 5.8 mg L(-1). Human urine and blood were also detected to ascertain the multi-metal analysis ability of this strategy in complex samples. At last, we explored its applicability to tissue slice and visualized sodium and potassium distribution by mass spectrometry imaging in the normal Kunming mouse brain.

Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis

Single-cell proteome analysis has always been an exciting goal because it provides crucial information about cellular heterogeneity and dynamic change. Here we presented an integrated proteome analysis device (iPAD) for 100 living cells (iPAD-100) that might be suitable for single-cell analysis. Once cells were cultured, the iPAD-100 could be applied to inject 100 living cells, to transform the living cells into peptides, and to produce protein identification results with total automation. Due to the major obstacle for detection limit of mass spectrometry, we applied the iPAD-100 to analyze the proteome of 100 cells. In total, 813 proteins were identified in a DLD-cell proteome by three duplicate runs. Gene Ontology analysis revealed that proteins from different cellular compartments were well-represented, including membrane proteins. The iPAD-100 greatly simplified the sampling process, reduced sample loss, and prevented contamination. As a result, proteins whose copy numbers were lower than 1000 were identified from 100-cell samples with the iPAD-100, showing that a detection limit of 200 zmol was achieved. With increased sensitivity of mass spectrometry, the iPAD-100 may be able to reveal bountiful proteome information from a single cell in the near future.

Aptamer/ISET-MS: a new affinity-based MALDI technique for improved detection of biomarkers

With the rapid progress in the development of new clinical biomarkers there is an unmet need of fast and sensitive multiplex analysis methods for disease specific protein monitoring. Immunoaffinity extraction integrated with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis offers a route to rapid and sensitive protein analysis and potentially multiplex biomarker analysis. In this study, the previously reported integrated selective enrichment target (ISET)-MALDI-MS analysis was implemented with ssDNA aptamer functionalized microbeads to address the specific capturing of thrombin in complex samples. The main objective for using an aptamer as the capturing ligand was to avoid the inherently high background components, which are produced during the digestion step following the target extraction when antibodies are used. By applying a thrombin specific aptamer linked to ISET-MALDI-MS detection, a proof of concept of antibody fragment background reduction in the ISET-MALDI-MS readout is presented. Detection sensitivity was significantly increased compared to the corresponding system based on antibody-specific binding as the aptamer ligand does not induce any interfering background residues from the antibodies. The limit of detection for thrombin was 10 fmol in buffer using the aptamer/ISET-MALDI-MS configuration as confirmed by MS/MS fragmentation. The aptamer/ISET-MALDI-MS platform also displayed a limit of detection of 10 fmol for thrombin in five different human serum samples (1/10 diluted), demonstrating the applicability of the aptamer/ISET-MALDI-MS analysis in clinical samples.

DNA Aptamer Technology for Personalized Medicine

This review highlights recent progress in developing DNA aptamers for personalized medicine, with more focus on in vivo studies for potential clinical applications. Examples include design of aptamers in combination with DNA nanostructures, nanomaterials, or microfluidic devices as diagnostic probes or therapeutic agents for cancers and other diseases. The use of aptamers as targeting agents in drug delivery is also covered. The advantages and future directions of such DNA aptamer-based technology for the continued development of personalized medicine are discussed.

Bioresponsive controlled release from mesoporous silica nanocontainers with glucometer readout

A portable and quantitative biosensing platform for monitoring proteins and small molecules without the need for sample separation and washing is developed by using a commercialized personal glucose meter based on bioresponsive controlled release of glucose from aptamer-gated mesoporous silica nanocontainers.