MALDI mass spectrometry in prostate cancer biomarker discovery

Matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry (MS) is a highly versatile and sensitive analytical technique, which is known for its soft ionisation of biomolecules such as peptides and proteins. Generally, MALDI MS analysis requires little sample preparation, and in some cases like MS profiling it can be automated through the use of robotic liquid-handling systems. For more than a decade now, MALDI MS has been extensively utilised in the search for biomarkers that could aid clinicians in diagnosis, prognosis, and treatment decision making. This review examines the various MALDI-based MS techniques like MS imaging, MS profiling and proteomics in-depth analysis where MALDI MS follows fractionation and separation methods such as gel electrophoresis, and how these have contributed to prostate cancer biomarker research. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.     

Synthesis and biological studies of 4', 7, 8-trihydroxy-isoflavone metal complexes

A new series of complexes of a ligand 4′, 7, 8-trihydroxy-isoflavone with transition metal (zinc, copper, manganese, nickel, cobalt) and selenium have been synthesized and characterized with the aid of elemental analysis, IR, electron ionization mass spectrum (EI-MS) and ¹H NMR spectrometric techniques. The compounds were evaluated for their in vitro antibacterial activities and antitumor properties. The metal complexes were found to be more active than the free ligand. Investigation on the interaction between the complexes and calf-thymus DNA (CT DNA) showed that the absorbance of CT DNA increased and the maximum peak (λ_max = 260 nm) red-shifted, while the intensity of fluorescence spectra of Epstein-Bart DNA (EB-DNA) gradually weakened, which indicated that all of these metal complexes tightly combined with CT DNA.     

Elucidation of the interactions of an anticancer ruthenium complex in clinical trials with biomolecules utilizing capillary electrophoresis hyphenated to inductively coupled plasma-mass spectrometry. Short communication

The application of capillary electrophoresis (CE) combined with highly sensitive inductively-coupled-plasma mass spectrometric (ICP-MS) detection allows the interactions of metal complexes with biomolecules to be characterized. This technique has been used to provide new insights into the mode of action of the ruthenium-based anticancer drug candidate indazolium [trans-tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019). While the compound binds rapidly and efficiently to serum proteins, especially albumin, its reactivity towards the model DNA compound 2'-deoxyguanosine 5'-monophosphate (5'-dGMP) is moderate.     

Surface trapped electrons on metal vapour modified magnesium oxide. Nature of the surface centres and reactivity with adsorbed molecules

The first part of the present paper reports a wide investigation on the interaction between metals of low ionisation energy (magnesium and alkali metals) and the surface of the ionic oxide MgO. The interaction basically consists in the ionisation of the metal and in the stabilisation of both the released electrons and the corresponding cations at the surface. Various types of paramagnetic electron centers have been identified including surface F centers, monoalkali cationic centers and ionic clusters. In the second part the reactivity of the electron rich MgO surface with simple inorganic molecules is described.     

Mass spectrometric techniques for characterisation of platinum–humic substance complexes in soil and street dust samples

Abstract

Increased platinum concentrations have been detected in environmental samples since the introduction of catalytic converters in Europe. It was previously believed that PGE are relatively inert and that the soluble fraction of automobile catalyst emitted PGE is only a few percent. However, new studies suggested that metallic Pt is oxidised in the soil and that the majority of the Pt species could be humic substance complexes.

The aim of the present paper is the characterisation of platinum-humic acid complexes in spiked soil and street dust samples. A number of different soft ionisation mass spectrometric techniques, such as ESI-Q-MS, ESI-ION TRAP-MS and MALDI-TOF-MS have been tested. The ESI mass spectra of the soil humic acids were characterised by high complexity and irreproducibility.

MALDI-TOF-MS was used for humic acid complexes characterisation in positive and negative modes. Positive ionisation was less effective and produced more simple and less informative spectra than negative ionisation. Two different MALDI matrices (CHCA, DHBA) were tested for use with humic substances. DHBA yielded better results, exhibiting superior ionisation efficiency, low spectral background and the matrix peaks were almost completely suppressed causing no interferences with identified analyte peaks. The application of MALDI-TOF-MS shows its suitability for humic substance characterisation. The comparison of the MALDI-spectra of humic acids, extracted from spiked and native soil proved that Pt undergoes transformation in the environment to humic acid complexes.     

Highlighting the roles of transition metals and speciation in chemical biology

Transition metal ions play key structural and functional roles, affecting structures of biomolecules and enzyme function. The importance of transition metal ions in chemical biology is, thus, undisputed. However, the aqueous chemistry of metal ions is complicated because they form species in several protonation and redox states. In the presence of metabolites, metal ions can also form coordination complexes. The existence of several species is relevant because enzymes and membrane receptors can distinguish between species even when they are rapidly equilibrating. Thus, metal ions, enzyme cofactors, and therapeutic agents are sensitive to the metal ion speciation chemistry because it affects their interaction with enzymes and other biomolecules. Speciation is also crucial for metal-containing bioorthogonal reactions, since water and metabolites stabilize active catalysts, affect chemoselectivity and reaction yields.     

A generic approach for the purification of signaling complexes that specifically interact with the carboxyl-terminal domain of G protein-coupled receptors

G protein-coupled receptors (GPCRs) constitute the largest family of membrane receptors and are major drug targets. Recent progress has shown that GPCRs are part of large protein complexes that regulate their activity. We present here a generic approach for identification of these complexes that is based on the use of receptor subdomains and that overcomes the limitations of currently used genetics and proteomics approaches. Our approach consists of a carefully balanced combination of chemically synthesized His6-tagged baits, immobilized metal affinity chromatography, one- and two-dimensional gel electrophoresis separation and mass spectrometric identification. The carboxyl-terminal tails (C-tails) of the human MT1 and MT2 melatonin receptors, two class A GPCRs, were used as models to purify protein complexes from mouse brain lysates. We identified 32 proteins that interacted with the C-tail of MT1, 14 proteins that interacted with the C-tail of MT2, and eight proteins that interacted with both C-tails. Several randomly selected proteins were validated by Western blotting, and the functional relevance of our data was further confirmed by showing the interaction between the full-length MT1 and the regulator of G protein signaling Z1 in transfected HEK 293 cells and native tissue. Taken together, we have established an integrated and generic purification strategy for the identification of high quality and functionally relevant GPCR-associated protein complexes that significantly widens the repertoire of available techniques.     

Interaction of bacterial endotoxins with chitosan. Effect of endotoxin structure, chitosan molecular mass, and ionic strength of the solution on the formation of the complex

The interaction of endotoxins of different structure (lipopolysaccharides (LPS) and lipopolysaccharide-protein complexes (LPPC)) with chitosan has been studied. It was shown that the mechanism of interaction is rather complicated and depends on the macromolecular organization of endotoxin as well as on the degree of polymerization of the chitosan. Chitosan with molecular mass of 20 kD reveals higher affinity to LPS than chitosan with molecular mass of 140 kD. Endotoxins with long O-specific chains can bind completely with chitosan with the formation of LPS-chitosan and LPPC-chitosan complexes with weight ratios between the original components of 1:1 and 1:5. When endotoxins with higher degree of hydrophobicity and short O-specific chains were mixed with chitosan, a part of the LPS remained unbound. The stability of the complexes formed depends on ionic strength. It was shown that, in addition to electrostatic forces, other types of forces take part in the formation of the complexes. A decrease in acute toxicity of various LPSs is observed on their binding with chitosans.     

MALDI-TOF质谱技术对克罗诺杆菌的鉴定与分型

以基质辅助激光解析电离飞行时间质谱(MALDI-TOFMS)技术用于克罗诺杆菌的鉴定与分型。通过对获得的克罗诺杆菌属典型菌株、阴沟肠杆菌和产气肠杆菌近似菌株以及克罗诺杆菌分离株的蛋白质质量图谱进行对比分析,找出克罗诺杆菌特征性离子峰,将其作为鉴定克罗诺杆菌的生物标识物;对全细菌蛋白质质量图谱进行聚类分析,将克罗诺杆菌属进一步划分为不同类型,结果显示,4株克罗诺杆菌参考菌株质量图谱约在5740(m/z)离子质荷比处出现1个相近离子峰,28株克罗诺杆菌分离株中27株(占96.4%)表现出相同结果;32株克罗诺杆菌被分为6种类型(以50%距离水平为分类界限)。MALDI-TOFMS作为一种新的技术,不仅能够用于克罗诺杆菌的鉴定,而且根据获得的细菌蛋白质质量图谱可将克罗诺杆菌划分为不同类型。     

Capillary liquid chromatography combined with tandem mass spectrometry for the study of neurosteroids and oxysterols in brain

Neurosteroids and neurosterols are found in brain at low levels (ng/g-microg/g) against a high background of cholesterol (mg/g). As such their analysis can be challenging. Traditionally, these molecules have been analysed by gas chromatography (GC)-mass spectrometry (MS), however, the absence of molecular ions in GC-MS spectra, even from derivatised molecules, can make the discovery and identification of novel neurosteroids/sterols difficult. To avoid this scenario, liquid chromatography (LC) combined with desorption ionisation methods are employed. In this review we discuss the application of LC-MS and LC-tandem mass spectrometry (MS/MS) for the identification of neurosteroids/sterols, paying particular attention to the use of low-flow-rate LC to maximise chromatographic and mass spectrometric performance.     

Synthesis and characterisation of sulfated amphiphilic alpha-, beta- and gamma-cyclodextrins: application to the complexation of acyclovir

The synthesis of sulfated amphiphilic alpha-, beta- and gamma-cyclodextrins was achieved according to the standard protection-deprotection procedure. The formation of inclusion complexes between the amphiphilic alpha-, beta- and gamma-cyclodextrins and an antiviral molecule, acyclovir (ACV) was investigated by UV-visible spectroscopy (UV-Vis) and electrospray ionisation mass spectrometry (ESIMS). UV-Vis spectroscopy allowed determination of the stoichiometry and stability constants of complexes, whereas ESIMS, a soft ionisation technique, allowed the detection of the inclusion complexes. The results showed that the non-sulfated amphiphilic cyclodextrins exhibit a 1:2 stoichiometry with acyclovir, while sulfated amphiphilic cyclodextrins, except gamma-cyclodextrin, exhibit a 1:1 stoichiometry indicating the loss of one interaction site. Non-covalent interactions between acyclovir and non-sulfated amphiphilic cyclodextrins appear to take place both in the cavity of the cyclodextrin and inside the hydrophobic zone generated by alkanoyl chains. In contrast, in the case of sulfated amphiphilic cyclodextrins, the interactions appear to involve only the hydrophobic region of the alkanoyl chains.     

Fast atom bombardment mass spectrometry of bleomycin A2 and B2 and their metal complexes

The new mass spectrometric technique of fast atom bombardment is applied to the analysis of bleomycins either separately or in mixtures. The spectra are reproducible and afford valuable analytical data and structurally significant fragmentation patterns on these important antibiotics. The procedures outlined have also enabled the characterisation of various metal complexes.     

Succinylhydroxamic derivatives of alpha-amino acids as MMP inhibitors. Study of complex-formation equilibria with Cu2+, Ni2+ and Zn2+

A series of Pro- and Phe-succinyl hydroxamate derivatives, whose nanomolar inhibitory activity towards a series of matrix metalloproteinases (MMPs) was previously reported, have been studied and described herein in their interaction with Cu(2+), Zn(2+), Ni(2+) in aqueous solution, by using potentiometric, spectroscopic and ESI-MS (electrospray ionization mass) spectrometric techniques. A systematic study at various ligand-to-metal molar ratios allowed the determination of the stability constants of the complexes as well as the estimation of the coordination modes. The similarity in the biological activity of these compounds seems to be paralleled by the identical metal-complexation behaviour at neutral pH, namely in terms of chelating effectiveness and coordination modes, irrespective of the presence of one carboxylic or hydroxamate as extra groups, or also of the type of amino-acid residue at the other flank of the succinyl chain, which seems to be enough away from the succinyl hydroxamate metal-binding group. The stability order of the metal complexes with these ligands follows the Irving-Williams trend for this type of complex systems. Noteworthy is the identification of an interesting pentanuclear copper(II) species with the monohydroxamic ligands which structure was ascribed to a 12-metallacrown-4.     

Biomolecule–nanoparticle interactions: Elucidation of the thermodynamics by isothermal titration calorimetry

BackgroundNanomaterials (NMs) are often exposed to a broad range of biomolecules of different abundances. Biomolecule sorption driven by various interfacial forces determines the surface structure and composition of NMs, subsequently governs their functionality and the reactivity of the adsorbed biomolecules. Isothermal titration calorimetry (ITC) is a nondestructive technique that quantifies thermodynamic parameters through in-situ measurement of the heat absorption or release associated with an interaction.Scope of reviewThis review highlights the recent applications of ITC in understanding the thermodynamics of interactions between various nanoparticles (NPs) and biomolecules. Different aspects of a typical ITC experiment that are crucial for obtaining accurate and meaningful data, as well as the strengths, weaknesses, and challenges of ITC applications to NP research were discussed.Major conclusionsITC reveals the driving forces behind biomolecule–NP interactions and the effects of the physicochemical properties of both NPs and biomolecules by quantifying the crucial thermodynamics parameters (e.g., binding stoichiometry, ΔH, ΔS, and ΔG). Complimentary techniques would strengthen the interpretation of ITC results for a more holistic understanding of biomolecule–NP interactions.General significanceThe thermodynamic information revealed by ITC and its complimentary characterizations is important for understanding biomolecule–NP interactions that are fundamental to the biomedical and environmental applications of NMs and their toxicological effects. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

Challenges in mass spectrometry-based proteomics

During the last decade, protein analysis and proteomics have been established as new tools for understanding various biological problems. As the identification of proteins after classical separation techniques, such as two-dimensional gel electrophoresis, have become standard methods, new challenges arise in the field of proteomics. The development of "functional proteomics" combines functional characterization, like regulation, localization and modification, with the identification of proteins for deeper insight into cellular functions. Therefore, different mass spectrometric techniques for the analysis of post-translational modifications, such as phosphorylation and glycosylation, have been established as well as isolation and separation methods for the analysis of highly complex samples, e.g. protein complexes or cell organelles. Furthermore, quantification of protein levels within cells is becoming a focus of interest as mass spectrometric methods for relative or even absolute quantification have currently not been available. Protein or genome databases have been an essential part of protein identification up to now. Thus, de novo sequencing offers new possibilities in protein analytical studies of organisms not yet completely sequenced. The intention of this review is to provide a short overview about the current capabilities of protein analysis when addressing various biological problems.     

Transition metal derivatives of peptide nucleic acid (PNA) oligomers-synthesis, characterization, and DNA binding

This work describes the first automated solid-phase synthesis of metal derivatives of peptide nucleic acid (PNA) oligomers and their interaction with DNA and PNA. PNA constitutes a relatively young and very promising class of DNA analogues with excellent DNA and RNA binding properties. However, PNA lacks a suitable handle that would permit its sensitive detection on its own as well as when hybridized with complementary oligonucleotides. Metal complexes, on the other hand, offer high potential as markers for biomolecules. In this paper, we describe the synthesis of PNA heptamers (tggatcg-gly, where gly is a C-terminal glycine carboxylic acid amide) with two covalently attached metal complexes at the PNA N-terminus, namely a ferrocene carboxylic acid derivative and a tris(bipyridine)ruthenium(II) derivative. We show how all synthesis steps may be carried out with high yield on a DNA synthesizer, including attachment of the metal complexes. The conjugates were characterized by HPLC (>90% purity) and ESI-MS. Binding studies of the purified Ru-PNA heptamer to complementary DNA and PNA and comparison to the isosequential metal-free acetyl PNA heptamer proves that the attached metal complex has an influence on the stability (UV-T(m)) and structure (CD spectroscopy) of the conjugates, possibly by disruption of the nearby A:T base pair.     

Iron binding β-hairpin peptides

Posttranslational modification of tyrosine to 3,4-dihydroxyphenylalanine (dopa) yields a unique functional group in biomolecular systems. Oxidation produces a quinone, which can undergo cross linking while deprotonation is well suited to metal binding. Mussels, tunicates and bacteria chelate iron and other metals with multiple dopa subunits. Solution equilibria between catechols and iron indicate favorable assembly though this interaction has not been studied with highly structured biomolecules, such as peptides, despite their widespread biological applications. Here, a series of β-hairpin peptides are generated. Dopa is involved in an aromatic interaction as the edge position. Despite the presence of the surrounding secondary structure dopa readily undergoes oxidation and cross linking. Formation of bispeptide:iron complexes also occur in the presence of mild to significant aromatic interactions.     

Determination of beta-carboline alkaloids in fruiting bodies of Hygrophorus spp. by liquid chromatography/electrospray ionisation tandem mass spectrometry

The beta-carboline alkaloids harmane (1) and norharmane (2) were isolated from fruiting bodies of Hygrophorus eburneus (Bull.) Fr. as well as brunnein A (3) from Hygrophorus hyacinthinus Quél. (Tricholomataceae, Agaricales) for the first time. Their occurrence within the genus was investigated using liquid chromatography/electrospray ionisation tandem mass spectrometric methods, especially by selected reaction monitoring. Based on these results their chemotaxonomical relevance is discussed.     

生物大分子质谱电离技术的突破及核磁共振三维结构测定方法的建立——2002年诺贝尔化学奖简介

2002年诺贝尔化学奖授予了质谱和核磁共振领域的三位科学家以表彰他们对生物大分子鉴定及结构分析方法做出的贡献．其中两位科学家J．B．Fenn和K．Tanaka分别发展了生物大分子质谱分析的软解吸电离方法;另一科学家K．Wüthrich则将核磁共振技术成功地应用于生物大分子如蛋白质的溶液三维结构测定．他们的研究成果已使质谱和核磁共振技术成为生物大分子强有力的研究手段,极大地促进了生物大分子的研究进程,必将对整个生命科学研究产生深远的影响．