High-speed biomarker identification utilizing porous silicon nanovial arrays and MALDI-TOF mass spectrometry

Novel Ag-modified vanadate nanosheets for determination of small organic molecules with laser desorption ionization mass spectrometry

Laser desorption ionization mass spectrometry (LDI-MS) aroused intensive concerns for the merits of label-free and high-throughput analysis. Here, we designed a silver nanoparticles (AgNP)-modified indium vanadate nanosheets with doping samarium (AgNP@InVO4:Sm) nanosheets. The developed AgNP@InVO4:Sm nanosheets (AIVON) were synthesized based on the microemulsion-mediated solvothermal method and ultraviolet-assisted in situ formation of AgNP, then for the first time applied as a matrix in LDI-MS analysis. With the advantages including enhanced MS signal, little matrix-related background, high reproducibility, and good salt tolerance, AIVON exhibited much better prospect than non-modified indium vanadate nanosheets with doping samarium (IVON) and traditional organic matrix, thus allowing sensitive MS detection for a wide range of low-molecular-weight (LMW) molecules. Moreover, by coupling with headspace sampling thin-film microextraction (TFME), a kind of representative pollutant chlorophenols were identified and quantified via AIVON-assisted LDI-MS in environmental and biological samples. Volatile LMW pollutants could be preconcentrated after TFME, hence a sensitive and rapid assay with negligible sample matrix effect was realized by using AIVON-assisted LDI-MS. It is anticipated that this novel nano-matrix AIVON and the proposed TFME coupling detection strategy were of competitive merits for LDI-MS analysis in the fields of environment, biomedicine, and agriculture.

Temporally and spatially resolved molecular profiling in fingerprint analysis using indium vanadate nanosheets-assisted laser desorption ionization mass spectrometry

This study presents the first-ever synthesis of samarium-doped indium vanadate nanosheets (IVONSs:Sm) via microemulsion-mediated solvothermal method. The nanosheets were subsequently utilized as a nano-matrix in laser desorption/ionization mass spectrometry (LDI-MS). It was discovered that the as-synthesized IVONSs:Sm possessed the following advantages: improved mass spectrometry signal, minimal matrix-related background, and exceptional stability in negative-ion mode. These qualities overcame the limitations of conventional matrices and enabled the sensitive detection of small biomolecules such as fatty acids. The negative-ion LDI mechanism of IVONSs:Sm was examined through the implementation of density functional theory simulation. Using IVONSs:Sm-assisted LDI-MS, fingerprint recognitions based on morphology and chemical profiles of endogenous/exogenous compounds were also achieved. Notably, crucial characteristics such as the age of an individual's fingerprints and their physical state could be assessed through the longitudinal monitoring of particular biomolecules (e.g., ascorbic acid, fatty acid) or the specific biomarker bilirubin glucuronide. Critical information pertinent to the identification of an individual would thus be facilitated by the analysis of the compounds underlying the fingerprint patterns.

A Sol-gel Integrated Dual-readout Microarray Platform for Quantification and Identification of Prostate-specific Antigen

Here, we report a sol-gel integrated affinity microarray for on-chip matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) that enables capture and identification of prostate?specific antigen (PSA) in samples. An anti-PSA antibody (H117) was mixed with a sol?gel, and the mixture was spotted onto a porous silicon (pSi) surface without additional surface modifications. The antibody easily penetrates the sol-gel macropore fluidic network structure, making possible high affinities. To assess the capture affinity of the platform, we performed a direct assay using fluorescein isothiocyanate-labeled PSA. Pure PSA was subjected to on-chip MALDI-TOF-MS analysis, yielding three clear mass peptide peaks (m/z = 1272, 1407, and 1872). The sol-gel microarray platform enables dual readout of PSA both fluorometric and MALDI-TOF MS analysis in biological samples. Here we report a useful method for a means for discovery of biomarkers in complex body fluids.

Methodology and Applications of Disease Biomarker Identification in Human Serum

Biomarkers are biomolecules that serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Because of the high abundance of albumin and heterogeneity of plasma lipoproteins and glycoproteins, biomarkers are difficult to identify in human serum. Due to the clinical significance the identification of disease biomarkers in serum holds great promise for personalized medicine, especially for disease diagnosis and prognosis. This review summarizes some common and emerging proteomics techniques utilized in the separation of serum samples and identification of disease signatures. The practical application of each protein separation or identification technique is analyzed using specific examples. Biomarkers of cancers of prostate, breast, ovary, and lung in human serum have been reviewed, as well as those of heart disease, arthritis, asthma, and cystic fibrosis. Despite the advancement of technology few biomarkers have been approved by the Food and Drug Administration for disease diagnosis and prognosis due to the complexity of structure and function of protein biomarkers and lack of high sensitivity, specificity, and reproducibility for those putative biomarkers. The combination of different types of technologies and statistical analysis may provide more effective methods to identify and validate new disease biomarkers in blood.

Engineering Silicon to Porous Silicon and Silicon Nanowires by Metal-Assisted Chemical Etching: Role of Ag Size and Electron-Scavenging Rate on Morphology Control and Mechanism

We demonstrate controlled fabrication of porous Si (PS) and vertically aligned silicon nanowires array starting from bulk silicon wafer by simple chemical etching method, and the underlying mechanism of nanostructure formation is presented. Silicon-oxidation rate and the electron-scavenging rate from metal catalysis play a vital role in determining the morphology of Si nanostructures. The size of Ag catalyst is found to influence the Si oxidation rate. Tunable morphologies from irregular porous to regular nanowire structure could be tailored by controlling the size of Ag nanoparticles and H₂O₂ concentration. Ag nanoparticles of size around 30 nm resulted in irregular porous structures, whereas discontinuous Ag film yielded nanowire structures. The depth of the porous Si structures and the aspect ratio of Si nanowires depend on H₂O₂ concentration. For a fixed etching time, the depth of the porous structures increases on increasing the H₂O₂ concentration. By varying the H₂O₂ concentration, the surface porosity and aspect ratio of the nanowires were controlled. Controlling the Ag catalyst size critically affects the morphology of the etched Si nanostructures. H₂O₂ concentration decides the degree of porosity of porous silicon, dimensions and surface porosity of silicon nanowires, and etch depth. The mechanisms of the size- and H₂O₂-concentration-dependent dissociation of Ag and the formation of porous silicon and silicon nanowire are described in detail.

A Highly Sensitive Porous Silicon (P-Si)-Based Human Kallikrein 2 (hK2) Immunoassay Platform toward Accurate Diagnosis of Prostate Cancer

Levels of total human kallikrein 2 (hK2), a protein involved the pathology of prostate cancer (PCa), could be used as a biomarker to aid in the diagnosis of this disease. In this study, we report on a porous silicon antibody immunoassay platform for the detection of serum levels of total hK2. The surface of porous silicon has a 3-dimensional macro- and nanoporous structure, which offers a large binding capacity for capturing probe molecules. The tailored pore size of the porous silicon also allows efficient immobilization of antibodies by surface adsorption, and does not require chemical immobilization. Monoclonal hK2 capture antibody (6B7) was dispensed onto P-Si chip using a piezoelectric dispenser. In total 13 × 13 arrays (169 spots) were spotted on the chip with its single spot volume of 300 pL. For an optimization of capture antibody condition, we firstly performed an immunoassay of the P-Si microarray under a titration series of hK2 in pure buffer (PBS) at three different antibody densities (75, 100 and 145 µg/mL). The best performance of the microarray platform was seen at 100 µg/mL of the capture antibody concentration (LOD was 100 fg/mL). The platform then was subsequently evaluated for a titration series of serum-spiked hK2 samples. The developed platform utilizes only 15 µL of serum per test and the total assay time is about 3 h, including immobilization of the capture antibody. The detection limit of the hK2 assay was 100 fg/mL in PBS buffer and 1 pg/mL in serum with a dynamic range of 10⁶ (10⁻⁴ to 10² ng/mL).

Importance of the matrix and the matrix/sample ratio in MALDI-TOF-MS analysis of cathelicidins obtained from porcine neutrophils

Qualitative and quantitative mass spectrometric studies of biomolecules for example proteins, peptides, or lipids contained in biological samples like physiologic fluids are very important for many fields of science such as medicine, veterinary medicine, biology, biochemistry, molecular biology, or environmental sciences. In the last two decades, MALDI TOF MS — matrix-assisted laser desorption mass spectrometry, proved to be an especially convenient tool for these analyses. The main advantages of this method are its rapidity and high sensitivity which is particularly appreciated in the case of studies of complex biological specimen. A major challenge for many researchers is to maximize this sensitivity, among others, by appropriate procedures of sample preparation for the measurement. The objective of this work was to optimize these procedures, selecting the optimal matrix and optimum proportions of the sample and the matrix solution in a mixture of both solutions, aiming at the achievement of the maximum intensity of ion current. In this respect, five low molecular mass cathelicidins were studied: prophenin-2, protegrins 1–3, PR-39. All of them were obtained directly from the porcine blood. As a result of studies, the authors determined such experimental conditions when the intensity of investigated ionic current had the highest value.

Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences

The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.

Diagnostic biomarkers differentiating metastatic melanoma patients from healthy controls identified by an integrated MALDI-TOF mass spectrometry/bioinformatic approach

The prognosis of advanced metastatic melanoma (American Joint Committee on Cancer (AJCC) stage IV) remains dismal with a 5-year survival rate of 6-18%. In the present study, an integrated MALDI mass spectrometric approach combined with artificial neural networks (ANNs) analysis and modeling has been used for the identification of biomarker ions in serum from stage IV melanoma patients allowing the discrimination of metastatic disease from healthy status with high specificities of 92% for protein ions and 100% for peptide biomarkers. Our ANNs model also correctly classified 98% of a blind validation set of AJCC stage I melanoma samples as nonstage IV samples, emphasizing the power of the newly defined biomarkers to identify patients with late-stage metastatic melanoma. Sequence analysis identified peptides derived from metastasis-associated proteins; alpha 1-acid glycoprotein precursor-1/2 (AAG-1/2) and complement C3 component precursor-1 (CCCP-1). Furthermore, quantitation of serum AAG by an immunoassay showed a significant (p<0.001) increase in AAG serum concentration in stage IV patients in comparison with healthy volunteers; moreover; the quantity of AAG plotted against MALDI-MS peak intensity classified the groups into two distinct clusters. Ongoing studies of other disease stages will provide evidence whether our strategy is sufficiently robust to give rise to stage-specific protein/peptide signatures in melanoma.

Porous silicon antibody microarrays for quantitative analysis: measurement of free and total PSA in clinical plasma samples

The antibody microarrays have become widespread, but their use for quantitative analyses in clinical samples has not yet been established. We investigated an immunoassay based on nanoporous silicon antibody microarrays for quantification of total prostate-specific-antigen (PSA) in 80 clinical plasma samples, and provide quantitative data from a duplex microarray assay that simultaneously quantifies free and total PSA in plasma. To further develop the assay the porous silicon chips was placed into a standard 96-well microtiter plate for higher throughput analysis. The samples analyzed by this quantitative microarray were 80 plasma samples obtained from men undergoing clinical PSA testing (dynamic range: 0.14-44 ng/ml, LOD: 0.14 ng/ml). The second dataset, measuring free PSA (dynamic range: 0.40-74.9 ng/ml, LOD: 0.47 ng/ml) and total PSA (dynamic range: 0.87-295 ng/ml, LOD: 0.76 ng/ml), was also obtained from the clinical routine. The reference for the quantification was a commercially available assay, the ProStatus PSA Free/Total DELFIA. In an analysis of 80 plasma samples the microarray platform performs well across the range of total PSA levels. This assay might have the potential to substitute for the large-scale microtiter plate format in diagnostic applications. The duplex assay paves the way for a future quantitative multiplex assay, which analyzes several prostate cancer biomarkers simultaneously.

Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets

We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.

Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels

A perspective overview is given describing the current development of multiplex mass spectrometry assay technology platforms utilized for high throughput clinical sample analysis. The development of targeted therapies with novel personalized medicine drugs will require new tools for monitoring efficacy and outcome that will rely on both the quantification of disease progression related biomarkers as well as the measurement of disease specific pathway/signaling proteins.The bioinformatics developments play a key central role in the area of clinical proteomics where targeted peptide expressions in health and disease are investigated in small-, medium- and large-scaled clinical studies.An outline is presented describing applications of the selected reaction monitoring (SRM) mass spectrometry assay principle. This assay form enables the simultaneous description of multiple protein biomarkers and is an area under a fast and progressive development throughout the community. The Human Proteome Organization, HUPO, recently launched the Human Proteome Project (HPP) that will map the organization of proteins on specific chromosomes, on a chromosome-by-chromosome basis utilizing the SRM technology platform. Specific examples of an SRM-multiplex quantitative assay platform dedicated to the cardiovascular disease area, screening Apo A1, Apo A4, Apo B, Apo CI, Apo CII, Apo CIII, Apo D, Apo E, Apo H, and CRP biomarkers used in daily diagnosis routines in clinical hospitals globally, are presented. We also provide data on prostate cancer studies that have identified a variety of PSA isoforms characterized by high-resolution separation interfaced to mass spectrometry.

Controlling mass transport in microfluidic devices

Microfluidic platforms offer exquisite capabilities in controlling mass transport for biological studies. In this review, we focus on recent developments in manipulating chemical concentrations at the microscale. Some techniques prevent or accelerate mixing, whereas others shape the concentration gradients of chemical and biological molecules. We also highlight several in vitro biological studies in the areas of organ engineering, cancer, and blood coagulation that have benefited from accurate control of mass transfer.

Protein microarrays and biomarkers of infectious disease

Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers.

Laser desorption ionization mass spectrometry on silicon nanowell arrays

This paper describes a new technique for fabrication of nanostructured porous silicon (pSi) for laser desorption ionization mass spectrometry. Porous silicon nanowell arrays were prepared by argon plasma etching through an alumina mask. Porous silicon prepared in this way proved to be an excellent substrate for desorption/ionization on silicon (DIOS) mass spectrometry (MS) using adenosine, Pro-Leu-Gly tripeptide, and [Des-Arg(9)]-bradykinin as the model compounds. It also allows the analyses of complex biological samples such as a tryptic digest of bovine serum albumin and a carnitine standard mixture. Nanowell array surfaces were also used for direct quantification of the illicit drug fentanyl in red blood cell extracts. This method also allows full control of the surface features. MS results suggested that the pore depth has a significant effect on the ion signals. Significant improvement in the ionization was observed by increasing the pore depth from 10 to 50 nm. These substrates are useful for laser desorption ionization in both the atmospheric pressure and vacuum regimes.

Protein microarrays: high-throughput tools for proteomics

Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. This article reviews recent developments in the generation of protein microarrays and their applications in proteomics and diagnostics.

Facile analysis of metabolites by capillary electrophoresis coupled to matrix-assisted laser desorption/ionization mass spectrometry using target plates with polysilazane nanocoating and grooves

We present an inexpensive method and apparatus for the deposition of analytes separated by capillary electrophoresis (CE) onto a custom-designed matrix-assisted laser desorption/ionization (MALDI) target plate. This dedicated CE-MALDI plate is coated with an omniphobic polysilazane nanocoating and has an array of parallel grooves acting as recipients of the separation effluent. The 3-D pattern in the top layer of the coated plate greatly improves loading of the matrix solution prior to separation and facilitates deposition of the separated species. We demonstrate application of this straightforward protocol to the analysis of metabolites from the central metabolic pathway in a complex biological sample spiked with small molecule standards.

Design of high-density antibody microarrays for disease proteomics: key technological issues

Antibody-based microarray is a novel proteomic technology setting a new standard for molecular profiling of non-fractionated complex proteomes. The first generation of antibody microarrays has already demonstrated its potential for generating detailed protein expression profiles, or protein atlases, of human body fluids in health and disease, paving the way for new discoveries within the field of disease proteomics. The process of designing highly miniaturized, high-density and high-performing antibody microarray set-ups have, however, proven to be challenging. In this mini-review we discuss key technological issues that must be addressed in a cross-disciplinary manner before true global proteome analysis can be performed using antibody microarrays.

Antibody-based microarrays

Antibody-based microarrays are a new powerful proteomic technology that can be used to generate rapid and detailed expression profiles of defined sets of protein analytes in complex samples as well as high-resolution portraits of entire proteomes. Miniaturized micro- and nanoarrays can be printed with numerous antibodies carrying the desired specificities. Multiplexed and ultra-sensitive assays, specifically targeting several analytes in a single experiment, can be performed, while consuming only minute amounts of the sample. The array images generated can then be converted into protein expression profiles, or maps, revealing the detailed composition of the sample. This promising proteomic research tool will thus provide unique opportunities for e.g. disease proteomics, biomarker discovery, disease diagnostics, and patient stratification. This review describes the antibody-based microarray technology and applications thereof.

Porous silicon surfaces: a candidate substrate for reverse protein arrays in cancer biomarker detection

This paper introduces a new substrate for reverse-phase protein microarray applications based on macroporous silicon. A key feature of the microarray substrate is the vastly surface enlarging properties of the porous silicon, which simultaneously offers highly confined microarray spots. The proof of principle of the reverse array concept was demonstrated in the detection of different levels of cyclin E, a possible cancer biomarker candidate which regulates G1-S transition and correlates with poor prognosis in different types of human cancers. The substrate properties were studied performing analysis of total cyclin E expression in human colon cancer cell lines Hct116 and SW480. The absence of unspecific binding and good microarray quality was demonstrated. In order to verify the performance of the 3-D textured macroporous surface for complex biological samples, lysates of the human tissue spiked to different levels with cell extract overproducing cyclin E (Hct116) were arrayed on the chip surface. The samples were spotted in a noncontact mode in 100 pL droplets with spots sizes ranged between 50 and 70 mum and spot-to-spot center distances 100 mum, allowing microarray spot densities up to 14 000 spots per cm(2). The different sample types of increasing complexities did not have any impact on the spot intensities recorded and the protein spots showed good homogeneity and reproducibility over the recorded microarrays. The data demonstrate the potential use of macroporous silicon as a substrate for quantitative determination of a cancer biomarker cyclin E in tissue lysates.

Antibody microarray analysis of directly labelled complex proteomes

In recent years, the antibody microarray technology has made significant progress, going from proof-of-concept designs to established high-performing technology platforms capable of targeting non-fractionated complex proteomes. In these cross-disciplinary efforts, a particular focus has lately been placed on two key technological issues: the sample and data handling. To this end, robust protocols have been designed for direct labelling of whole proteomes compatible with a sensitive fluorescent-based sensing. Tagging of the proteins with biotin in a single-colour approach has, in many cases, proven to be the preferred approach. Furthermore, based on modified approaches, adopted from the DNA microarray field, the first bioinformatic standards for performing the antibody microarray data analysis have emerged, though general standard operating procedure(s) remains to be implemented.

Oncoproteomics: current trends and future perspectives

Oncoproteomics is the application of proteomics technologies in oncology. Functional proteomics is a promising technique for the rational identification of biomarkers and novel therapeutic targets for cancers. Recent progress in proteomics has opened new avenues for tumor-associated biomarker discovery. With the advent of new and improved proteomics technologies, such as the development of quantitative proteomic methods, high-resolution, -speed and -sensitivity mass spectrometry and protein arrays, as well as advanced bioinformatics for data handling and interpretation, it is now possible to discover biomarkers that can reliably and accurately predict outcomes during cancer management and treatment. However, there are several difficulties in the study of proteins/peptides that are not inherent in the study of nucleic acids. New challenges arise in large-scale proteomic profiling when dealing with complex biological mixtures. Nevertheless, oncoproteomics offers great promise for unveiling the complex molecular events of tumorigenesis, as well as those that control clinically important tumor behaviors, such as metastasis, invasion and resistance to therapy. In this review, the development and advancement of oncoproteomics technologies for cancer research in recent years are expounded.

Mass spectrometry-based "omics" technologies in cancer diagnostics

Many "omics" techniques have been developed for one goal: biomarker discovery and early diagnosis of human cancers. A comprehensive review of mass spectrometry-based "omics" approaches performed on various biological samples for molecular diagnosis of human cancers is presented in this article. Furthermore, the existing and potential problems/solutions (both de facto experimental and bioinformatic challenges), and future prospects have been extensively discussed. Although the use of present omic methods as diagnostic tools are still in their infant stage and consequently not ready for immediate clinical use, it can be envisaged that the "omics"-based cancer diagnostics will gradually enter into the clinic in next 10 years as an important supplement to current clinical diagnostics.

Porous silicon protein microarray technology and ultra-/superhydrophobic states for improved bioanalytical readout

One attractive method for monitoring biomolecular interactions in a highly parallel fashion is the use of microarrays. Protein microarray technology is an emerging and promising tool for protein analysis, which ultimately may have a large impact in clinical diagnostics, drug discovery studies and basic protein research. This chapter is based upon several original papers presenting our effort in the development of new protein microarray chip technology. The work describes a novel 3D surface/platform for protein characterization based on porous silicon. The simple adjustment of pore morphology and geometry offers a convenient way to control wetting behavior of the microarray substrates. In this chapter, an interesting insight into the surface role in bioassays performance is made. The up-scaled fabrication of the novel porous chips is demonstrated and stability of the developed supports as well as the fluorescent bioassay reproducibility and data quality issues are addressed. We also describe the efforts made by our group to link protein microarrays to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), suggesting porous silicon as a convenient platform for fast on-surface protein digestion protocols linked to MS-readout. The fabrication of ultra- and superhydrophobic states on porous silicon is also described and the utilization of these water-repellent properties for a new microscaled approach to superhydrophobic MALDI-TOF MS target anchor chip is covered.

Current literature in mass spectrometry

In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (6 Weeks journals ‐ Search completed at 4th. Oct. 2006)

Antibody microarrays: current status and key technological advances

Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.

Recent developments in methods and technology for analysis of biological samples by MALDI-TOF-MS

Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is widely used in a variety of fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range for obtaining molecular weights and for structural characterization of macromolecules. In this article we summarize recent developments in matrix additives, new matrices, and sample-pretreatment methods using off-probe or on-probe techniques or nanomaterials for MALDI-TOF-MS analysis of biological samples.

Probing proteins on functionalized silicon surfaces using matrix-assisted laser desorption/ionization mass spectrometry

Flat H-terminated Si(111) substrates modified with alkyl monolayers terminated with hydrophobic and hydrophilic functional groups were prepared using known surface functionalization methods and characterized by FTIR, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The surfaces were then used for the study of non-specific binding of proteins from complex mixtures (using standard mixture of proteins with average molecular weight approximately 6-66 kDa) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protein adsorption on these surfaces (following on-probe fractionation of the mixture) was found to be dependent on the nature of surface functional groups, and nature and pH of rinsing solutions used. The results obtained in this work demonstrate that simple silicon-based surface modifications can be effective for direct analysis of complex mixtures by MALDI-MS. Preliminary results obtained using similarly functionalized porous silicon substrates proved that such substrates are (due to their increased surface areas) better performing than flat silicon.