Matthias Rainer

Analysis of protein phosphorylation by monolithic extraction columns based on poly(divinylbenzene) containing embedded titanium dioxide and zirconium dioxide nano‐powders

The potential of an organic monolith with incorporated titanium dioxide (TiO2) and zirconium dioxide (ZrO2) nanoparticles was evaluated for the selective enrichment of phosphorylated peptides from tryptic digests. A pipette tip was fitted with a monolith based on divinylbenzene (DVB) of highly porous structure, which allows sample to pass through the monolithic bed. The enrichment of phosphopeptides was enhanced by increasing the pipetting cycles during the sample preparation and a higher recovery could be achieved with adequate buffer systems. A complete automated process was developed for enrichment of phosphopeptides leading to high reproducibility and resulting in a robust method designed to minimize analytical variance while providing high sensitivity at high sample throughput. The effect of particle size on the selectivity of phosphopeptides was investigated by comparative studies with nano‐ and microscale TiO2 and ZrO2 powders. Eleven phosphopeptides from α‐casein digest could be recovered by an optimized mixture of microscale TiO2/ZrO2 particles, whereas nine additional phosphopeptides could be retained by the same mixture of nano‐structured material. When compared to conventional immobilized metal‐ion affinity chromatography and commercial phosphorylation‐enrichment kits, higher selectivity was observed in case of self fabricated tips. About 20 phosphopeptides could be retained from α‐casein and five from β‐casein digests by using TiO2 and ZrO2 based extraction tips. Further selectivity for phosphopeptides was demonstrated by enriching a digest of in vitro phosphorylated extracellular signal regulated kinase 1 (ERK1). Two phosphorylated peptides of ERK1 could be identified by MALDI‐MS/MS measurements and a following MASCOT database search.

Nanostructured Diamond-Like Carbon on Digital Versatile Disc as a Matrix-Free Target for Laser Desorption/Ionization Mass Spectrometry

A nanostructured diamond-like carbon (DLC) coated digital versatile disk (DVD) target is presented as a matrix-free sample support for application in laser desorption/ionization mass spectrometry (LDI-MS). A large number of vacancies, defects, relative sp(2) carbon content, and nanogrooves of DLC films support the LDI phenomenon. The observed absorptivity of DLC is in the range of 305-330 nm (nitrogen laser, 337 nm). The universal applicability is demonstrated through different analytes like amino acids, carbohydrates, lipids, peptides, and other metabolites. Carbohydrates and amino acids are analyzed as sodium and potassium adducts. Peptides are detectable in their protonated forms, which avoid the extra need of additives for ionization. A bovine serum albumin (BSA) digest is analyzed to demonstrate the performance for peptide mixtures, coupled with the material-enhanced laser desorption/ionization (MELDI) approach. The detection limit of the described matrix-free target is investigated to be 10 fmol/microL for [Glu(1)]-fibrinopeptide B (m/z 1570.6) and 1 fmol/microL for L-sorbose (Na(+) adduct). The device does not require any chemical functionalization in contrast to other matrix-free systems. The inertness of DLC provides longer lifetimes without any deterioration in the detection sensitivity. Broad applicability allows high performance analysis in metabolomics and peptidomics. Furthermore the DLC coated DVD (1.4 GB) sample support is used as a storage device for measured and processed data together with sampling on a single device.

Protein profiling for cancer biomarker discovery using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and infrared imaging: A review

Cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker might be either a molecule secreted by a tumor or it can be a specific response of the body to the presence of cancer. Cancer biomarker-based diagnostics have applications for establishing disease predisposition, early detection, cancer staging, therapy selection, identifying whether or not a cancer is metastatic, therapy monitoring, assessing prognosis, and advances in the adjuvant setting. Full adoption of cancer biomarkers in the clinic has to date been slow, and only a limited number of cancer biomarker products are currently in routine use. Among proteomic technologies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is a technique that has allowed rapid progress in cancer biology. Different further developed methods including e.g. SELDI (surface-enhanced laser desorption/ionization) and MELDI (material-enhanced laser desorption/ionization) are simple and high-throughput techniques that analyze with high sensitivity and specificity intact proteins expressed in complex biological mixtures, such as serum, urine, and tissues. The combination of mass spectrometry (MS) with infrared (IR) spectroscopic imaging is an attempt to combine different technologies in systems analytics. Both MALDI-TOF and infrared tissue imaging enable studying proteins distribution in tissue samples with a resolution down to 50 and 5 μm, respectively. In this review, we summarize recent applications and the synergistic combination of these new technologies to proteomic profiling for cancer biomarker discovery.

Ultrafast microwave-assisted in-tip digestion of proteins.

Trypsin was immobilized on glycidylmethacrylate-co-divinylbenzene (GMA/DVB) polymerized in pipet tips for online enzymatic digestion of proteins. The major advantages of in-tip digestion are easy handling and small sample amount required for analysis. Microwave-assisted digestion was applied for highly efficient and time saving proteolysis. Adaption to an automated robotic system allowed fast and reproducible sample treatment. Investigations with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) and liquid chromatography coupled with electrospray-ionization mass spectrometry (LC-ESI/MS) attested high sequence coverages (SCs) for the three standard proteins, myoglobin (Myo, 89%), bovine serum albumin (BSA, 78%) and alpha-casein (alpha-Cas, 83%). Compared to commercially available trypsin tips, clear predominance concerning the digestion performance was achieved. Storageability was tested over a period of several weeks and results showed only little decrease (<5%) of protein sequence coverages. The application of microwave-assisted in-tip digestion (2 min) with full automation by a robotic system allows high-throughput analysis (96 samples within 80 min) and highly effective proteolysis.

Near Infrared Spectroscopy for Polymer Research, Quality Control and Reaction Monitoring:

This review covers recent applications of near infrared (NIR) spectroscopy in the determination of physico-chemical and morphological parameters of polymeric materials. Near infrared measurements in the diffuse reflection mode are highlighted, which analyse the structural parameters such as porosity, surface area and particle size. Fundamentals and applications of the technique are discussed and examples of quantitative and qualitative analysis are explained. Various approaches like on- and in-line techniques, bulk measurements and kinetic studies for recording spectra are discussed. Furthermore, this review addresses the development of calibrations, which allow for the differentiation and quantification of materials with varying physical and morphological properties. Parameters like constitution, composition and crystallinity have a strong affect on the material characteristics. Therefore, chemical, physical and mechanical properties of synthetic as well as natural substances, such as polymeric composites and cotton or wool, need to be studied in-depth. To sum up, NIR spectroscopy has been developed as a flexible, robust and high-throughput analytical method that can be combined with chemometric and multivariate data analysis for fast and reliable screening in material science.

Laser desorption/ionization mass spectrometric analysis of small molecules using fullerene-derivatized silica as energy-absorbing material

In spite of the growing acceptance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of a wide variety of compounds, including polymers and proteins, its use in analyzing low-molecular-weight molecules (<1000 m/z) is still limited. This is mainly due to the interference of matrix molecules in the low-mass range. Here the derivatized fullerenes covalently bound to silica particles with different pore sizes are applied as thin layer for laser desorption/ionization (LDI) mass spectrometric analysis. Thus, an interference of intrinsic matrix ions can be eliminated or minimized in comparison with the state-of-the-art weak organic acid matrices. The desorption/ionization ability of the developed fullerene-silica materials depends on the applied laser power, sample preparation and pore size of the silica particles. Thus, fullerene-silica serves as an LDI support for mass spectrometric analysis of molecules (<1500 Da). The performance of the fullerene-silica is demonstrated by the mass analysis of variety of small molecules such as carbohydrates, amino acids, peptides, phospholipids and drugs.

Selective enrichment of phosphopeptides by a metal–organic framework

A metal–organic framework, consisting of Er(III) linked together by 1,4-phenylenediacetate, was synthesised by a one-pot reaction and successfully used as an affinity material for the selective capturing of phosphopeptides. An optimised protocol for loading, washing and elution was developed and the eluents were analysed via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A standard protein digest (α-casein, β-casein and ovalbumin) as well as digested egg white proteins were used to test the efficiency and selectivity of the presented approach. 14 phosphopeptides could be recovered from the peptide mixture and in the case of digested egg-white, four phosphorylated peptides which could be assigned to ovalbumin were isolated. Ab initio calculations based on the affinities of various ligands to the material have provided reasonable explanations of the observed experimental properties.

Alternative profiling platform based on MELDI and its applicability in clinical proteomics

The presence of numerous proteomics data and their results in literature reveal the importance and influence of proteins and peptides on human cell cycle. For instance, the proteomic profiling of biological samples, such as serum, plasma or cells, and their organelles, carried out by surface-enhanced laser desorption/ionization mass spectrometry, has led to the discovery of numerous key proteins involved in many biological disease processes. However, questions still remain regarding the reproducibility, bioinformatic artifacts and cross-validations of such experimental set-ups. The authors have developed a material-based approach, termed material-enhanced laser desorption/ionization mass spectrometry (MELDI-MS), to facilitate and improve the robustness of large-scale proteomic experiments. MELDI-MS includes a fully automated protein-profiling platform, from sample preparation and analysis to data processing involving state-of-the-art methods, which can be further improved. Multiplexed protein pattern analysis, based on material morphology, physical characteristics and chemical functionalities provides a multitude of protein patterns and allows prostate cancer samples to be distinguished from non-prostate cancer samples. Furthermore, MELDI-MS enables not only the analysis of protein signatures, but also the identification of potential discriminating peaks via capillary liquid chromatography mass spectrometry. The optimized MELDI approach offers a complete proteomics platform with improved sensitivity, selectivity and short sample preparation times.

Surface-assisted laser desorption/ionization-mass spectrometry using TiO2-coated steel targets for the analysis of small molecules

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI–MS) measurements in the low-molecular-mass region, ranging from 0 to 1000 Daltons are very often difficult to perform because of signal interferences originating from matrix ions. In order to overcome this problem, a stainless steel target was coated with a homogeneous titanium dioxide layer. The layer obtained was further investigated for its ability to desorb small molecules, e.g., amino acids, sugars, poly(ethylene glycol) (PEG) 200, or extracts from Cynara scolymus leaves. The stability of the layer was determined by repeated measurements on the same target location, which was monitored by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) before and after surface-assisted laser desorption/ionization (SALDI) analysis. In addition, this titanium dioxide layer was compared with an already published method with titanium dioxide nanopowder as inorganic matrix. As a result of this work, the titanium dioxide layer produced minimal background interference, enabling simple interpretation of the detected mass spectra. Furthermore, the TiO2 coating provides a target that can be reused many times for SALDI–MS measurements.

Functionalized diamond nanopowder for phosphopeptides enrichment from complex biological fluids.

Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe(3+) and La(3+) ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program (www.matrixscience.com) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification.