Self-assembled-monolayer-modified silicon substrate to enhance the sensitivity of peptide detection for AP-MALDI mass spectrometry

Effect of Silane Monolayers and Nanoporous Silicon Surfaces on the Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Detection of Sepsis Metabolites Biomarkers Mixed in Solution

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) is a promising strategy for clinical diagnosis based on metabolite detection. However, several bottlenecks (such as the lack of reproducibility in analysis, the presence of an important background in low-mass range, and the lack of organic matrix for some molecules) prevent its transfer to clinical cases. These limitations can be addressed by using nanoporous silicon surfaces chemically functionalized with silane monolayers. In the present study, sepsis metabolite biomarkers were used to investigate the effects of silane monolayers and porous silicon substrates on MALDI-ToF MS analysis (signal-to-noise value (S/N), relative standard deviation of the S/N of triplicate samples (STDmean), and intra-substrates uniformity). Also, the impact of the physicochemical properties of metabolites, with different isoelectric points and hydrophobic-hydrophilic balances, was assessed. Four different silane molecules, with various alkyl chain lengths and head-group charges, were self-assembled in monolayers on plane and porous silicon surfaces. Their surface coverage and conformity were investigated by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The seven metabolites detected on the stainless-steel target plate (lysophosphatidylcholine, caffeine, phenylalanine, creatinine, valine, arginine, and glycerophosphocholine) are also detected on the silanized and bare, plane and porous silicon surfaces. Moreover, two metabolites, glycine and alanine, which are not detected on the stainless-steel target plate, are detected on all silanized surfaces, except glycine which is not detected on CH3 short-modified porous silicon and on the bare plane silicon substrate. In addition, whatever the metabolites (except phenylalanine and valine), at least one of the silicon surfaces allows to increase the S/N value in comparison with the stainless-steel target plate. Also, the heterogeneity of matrix crystallization features is linked to the STDmean which is poor on the NH3+ monolayer on plane substrate and better on the NH3+ monolayer on porous substrate, for most of the metabolites. Nevertheless, matrix crystallization features are not sufficient to systematically get high STDmean and uniformity in MALDI-ToF MS analysis. Indeed, the physicochemical properties of metabolites and surfaces, limitations in metabolite extraction from the pores, and improvement in metabolite desorption due to the pores are shown to significantly impact MS analysis. In particular, in the case of the most hydrophobic metabolites studied, the highest S/N values and the best STDmean and uniformity (the lowest values) are reached by using porous substrates, while in the case of the most hydrophilic metabolites studied, plane substrates demonstrated the highest S/N and the lowest STDmean. No clear trend of surface chemistry was evidenced.

Effects of the Chemical and Structural Properties of Silane Monolayers on the Organization of Water Molecules and Ions at Interfaces, from Molecular Dynamics Simulations

Understanding the organization of the hydration layer at functionalized silica surfaces is relevant for a large range of biosensing applications or surface phenomena such as biomolecule adsorption. Silane monolayers are widely used to functionalize silica surfaces. Using molecular dynamics simulations, we have investigated the role of silane molecule head-group charge, alkyl chain length, and surface coverage in the structural organization and dynamic properties of Na⁺ ions, Cl^- ions, and water molecules at the interface. The silane molecules studied are 3-aminopropyldimethylethoxysilane, n-propyldimethylmethoxysilane, octadecyldimethylmethoxysilane, and (dimethylamino)dimethylsilylundecanoate. Our results suggest that the distribution of interfacial ions is sensitive to the 2D dispersion of the silane-charged head groups. Also, while charged silane monolayers show a strong orientation of interfacial water molecules, which leads to a rupture in the hydrogen bond network and disturbs their tetrahedral organization, the arrangement of water molecules at the interface with uncharged silane monolayers seems to be related to the surface roughness and to alkyl chain length. In line with these results, the diffusion of ions and water molecules is higher at the CH₃ long monolayer interface than at the CH₃ short monolayer interface and at the charged monolayer interfaces. Also, whatever the silane molecules studied, bulk properties are recovered around 0.7 nm above the interface. The interfacial water organization is known to impact biomolecule adsorption. Therefore, these results could further help in optimizing the functionalization layers to capture analytes.

Single drop microextraction coupled with matrix-assisted laser desorption/ionization mass spectrometry for rapid and direct analysis of hydrophobic peptides from biological samples in high salt solution

Single drop microextraction (SDME) coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been applied for direct analysis of hydrophobic peptides (valinomycin and gramicidin D) from biological samples (urine and plasma) in high salt solution. The optimal conditions such as selection of extraction solvent, stirring rate, extraction time, effect of salt concentration and matrix-to-analyte ratio were investigated. The limits of detection (LODs) were found to be 73 nM to 170 nM for valinomycin and 96 nM to 5.5 µM for gramicidin D in high salt solution (1.7 M of NaCl) in MALDI-MS. The current approach can enhance the LODs by 11-320-fold for gramicidin D analysis in water, urine and plasma in high salt solution. Furthermore, the current approach has been successfully demonstrated for real-world sample analysis (β-carotene from carrots) by MALDI-MS. The current approach is a rapid, simple and efficient clean-up platform for direct analysis of hydrophobic molecules in biological samples from high salt solution.

A radiate microstructure MALDI chip for sample concentration and detection

Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis is an important tool for analyzing and characterizing biomolecules of varying complexity, the sensitivity of MALDI-TOFMS is dependent on proper preparation of the sample, a process that is oftentimes problematic and requires considerable expertise. In this study, we have developed a radiate microstructure chip on which samples can be concentrated for analysis by MALDI-TOFMS. The sample/matrix mixture was deposited onto the central space of the well on the chip and allowed to dry. Microscopic analysis confirmed that the applied samples were confined to the central zone. Sample spots focused on the chip were much smaller than those on an unmodified plate with the same total volume. Optimizing processes of several preparation factors were also performed to ensure matrix homogeneity in our chip. Analysis of the samples with MALDI-TOFMS showed that the signals from samples on our chip were significantly greater than those on the unmodified plate. The feasibility of using this chip to detect peptides and phosphopeptides was also demonstrated.

Inline pneumatically assisted atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry

Atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) is known to suffer from poor ion transfer efficiencies as compared to conventional vacuum MALDI (vMALDI). To mitigate these issues, a new AP-MALDI ion source utilizing a coaxial gas flow was developed. Nitrogen, helium, and sulfur hexafluoride were tested for their abilities as ion carriers for a standard peptide and small drug molecules. Nitrogen showed the best ion transport efficiency, with sensitivity gains of up to 1900% and 20% for a peptide standard when the target plate voltage was either continuous or pulsed, respectively. The addition of carrier gas not only entrained the ions efficiently but also deflected background species and declustered analyte-matrix adducts, resulting in higher absolute analyte signal intensities and greater signal-to-noise (S/N) ratios. With the increased sensitivity of pneumatically assisted (PA) AP-MALDI, the limits of detection of angiotensin I were 20 or 3 fmols for continuous or pulsed target plate voltage, respectively. For analyzing low-mass analytes, it was found that very low gas flow rates (0.3-0.6 l min(-1)) were preferable owing to increased fragmentation at higher gas flows. The analyte lability, type of gas, and nature of the extraction field between the target plate and mass spectrometer inlet were observed to be the most important factors affecting the performance of the in-line PA-AP-MALDI ion source.

Liquid-phase microextraction for rapid AP-MALDI and quantitation of nortriptyline in biological matrices

A liquid-phase microextraction (LPME) method using a micropipette with disposable tips was demonstrated for coupling to atmospheric pressure MALDI-MS (AP-MALDI/MS) as a concentrating probe for rapid analysis and quantitative determination of nortriptyline drug from biological matrices including human urine and human plasma. This technique was named as micropipette extraction (MPE). The best optimized parameters of MPE coupled to AP-MALDI/MS experiments were extraction solvent, toluene; extraction time, 5 min; sample agitation rate, 480 rpm; sample pH, 7; salt concentration, 30%; hole size of micropipette tips, 0.61 mm (id); and matrix concentration, 1000 ppm using alpha-cyano-4-hydroxycinnamic acid (CHCA) as a matrix. Three detection modes of AP-MALDI/MS analysis including full scan, selective ion monitor (SIM), and selective reaction monitor (SRM) of MS/MS were also compared for the MPE performance. The results clearly demonstrated that the MS/MS method provides a wider linear range and lower LODs but poor RSDs than the full scan and SIM methods. The LOD values for the MPE under SIM and MS/MS modes in water, urine, and plasma were 6.26, 47.5, and 94.9 nM, respectively. The enrichment factors (EFs) of this current approach were 36.5-43.0 fold in water. In addition, compared to single drop microextraction (SDME) and LPME using a dual gauge microsyringe with a hollow fiber (LPME-HF) technique, the LODs acquired by the MPE method under MS/MS modes were comparable to those of LPME-HF and SDME but it is more convenient than both methods. The advantages of this novel method are simple, easy to use, low cost, and no contamination between experiments since disposable tips were used for the micropipettes. The MPE has the potential to be widely used in the future because it only requires a simple micropipette to perform all extraction processes. We believe that this technique can be a powerful tool for MALDI/MS analysis of biological samples and clinical applications.

Single drop microextraction using silver nanoparticles as electrostatic probes for peptide analysis in atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry and comparison with gold electrostatic probes and silver hydrophobic probes

Single drop microextraction using tetraalkylammonium bromide coated silver nanoparticles (SDME-AgNPs) prepared in toluene has been successfully applied as electrostatic affinity probes to preconcentrate peptide mixtures in biological samples prior to atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry (AP-MALDI-MS) analysis. This approach is based on the isoelectric point (pI) of peptides and surface charge of AgNPs. Using the SDME-AgNPs technique, from a peptide mixture, Met- and Leu-enkephalins (Met-enk and Leu-enk) were extracted into a droplet of toluene containing AgNPs, but not the neutral peptides (gramicidins). The best peptide extraction efficiency for SDME-AgNPs was observed with the optimized parameters: extraction time 2 min, sample agitation rate 240 rpm, and sample pH 7. The limits of detection (LODs) of the SDME-AgNPs/AP-MALDI-MS technique for Met-enk and Leu-enk peptides were 160 and 210 nM, respectively. Furthermore, the application of the technique has been shown for the analysis of peptides from a sample containing high matrix interferences such as 1% Triton X-100 and 6 M urea. Finally, this approach has been compared with the SDME-AuNPs technique and the results have clearly revealed that the SDME-AgNP affinity probe exhibits higher affinity to extract the sulfur-bearing peptide (Met-enk). We also compared this electrostatic affinity probe of AgNPs with the previously demonstrated hydrophobic affinity probe of AgNPs and found that the electrostatic probe can greatly reduce the extraction time from 1.5 h to 2 min. This is due to the fact that electrostatic attraction forces are much stronger than the hydrophobic attraction forces. Therefore, we concluded that the electrostatic affinity probe based on SDME-AgNPs coupled with AP-MALDI-MS is a high-throughput technique for the analysis of low-abundance peptides from biological samples containing complex matrices.

Reverse micellar microextraction for rapid analysis of thiol-containing peptides and amino acids by atmospheric-pressure matrix-assisted laser desorption/ionization ion trap and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Simple, rapid and inexpensive one-step reverse micellar microextraction (RMME) procedures were combined with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) for the determination of thiol-containing peptides and amino acids. In this investigation, a thiol-containing peptide (HW6) was chosen as model compound to understand the mechanism of RMME. The electrostatic interactions between the thiol-containing peptide and reverse micelles were proposed to be reason for the transfer of analytes from the aqueous phase to the organic phase. Reverse micelles were formed by the cationic surfactant, methyltrioctylammonium chloride (MTOAC). The best extraction efficiency of HW6 was obtained under the following conditions: pH 11.0, ionic strength 5.0 mM of KCl and micelle concentration 7.0 mM of MTOAC. The limits of detection (LODs) obtained for HW6 in water, urine and plasma samples were 0.15, 0.19 and 0.28 microM, respectively, with relative standard deviation (RSD) values in the range +/-8.8-10.5%. The sensitivity obtained in water by the present method was 45-fold higher than that of the conventional use of atmospheric-pressure (AP)-MALDI MS. Furthermore, the applicability of the proposed approach was extended for the determination of thiol-containing amino acids in sample solutions by using MALDI time-of-flight (TOF) MS.

Bare silica nanoparticles as concentrating and affinity probes for rapid analysis of aminothiols, lysozyme and peptide mixtures using atmospheric-pressure matrix-assisted laser desorption/ionization ion trap and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The analysis of peptide mixtures from urine and plasma samples using bare (uncapped) SiO2 nanoparticles (NPs) with atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS) has been reported. The method was based on the adsorption of positively charged peptides on the surface of negatively charged SiO2 NPs through the electrostatic force of attraction. The adsorption on the surface of SiO2 NPs caused enhancement of ionization efficiency of analytes and subsequently increased the signal intensity of peptides. Maximum signal intensity was obtained at optimized concentration of SiO2 NPs and pH of the aqueous solution. The limits of detection (LODs) obtained for different peptides in deionized water with and without using SiO2 NPs were in the range 4.7-360 nM and 0.1-18.0 microM, respectively. The sensitivity of the proposed method was 21-53-fold better than conventional use of AP-MALDI-MS. In addition, linearity in the range 9.5-95 nM was obtained for the peptide angiotensin-II in deionized water with a correlation of estimation of 0.992 using an internal standard. The proposed method provided a simple way to facilitate the ionization of peptides, reduce sample complexity and increase the tolerance to salts and surfactants in the analysis of biological samples. The applicability of the present method was also demonstrated in the real-world sample analysis of aminothiols and lysozyme using MALDI-time-of-flight (TOF)-MS.