Determination of binding sites in carboplatin-bound cytochrome c using electrospray ionization mass spectrometry and tandem mass spectrometry

Interaction of carboplatin with cytochrome c (Cyt. c) has been investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). ESI-MS studies revealed that the ring-opened adducts of carboplatin with Cyt. c were formed in the stoichiometric ratio of 1:1 and 2:1 at pH 5.0 and 37 degrees C and in the stoichiometric ratio of 1:1 only at pH 7.0 and 37 degrees C. It was also found that Cyt. c could be cleaved by carboplatin at pH 2.5 and 50 degrees C. The cleaved fragments of Cyt. c were determined by ESI-MS and MS/MS analysis to be Glu66 approximately Met80, Ac-Gly01 approximately Met65, Glu66 approximately Glu104, Ac-Gly01 approximately Met80 and Ile81 approximately Glu104. The carboplatin prefers to anchor to Met65 first, then to Met80. To further confirm the binding site of Met, AcMet-Gly was used as the model molecule to investigate its interaction with carboplatin and its hydrolysis reaction. On the basis of species detected during the reaction monitored by ESI-MS, a possible pathway of the cleavage reaction was proposed.     

A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution

A new method that utilizes matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and exploits the hydrogen/deuterium (H/D) exchange properties of proteins was developed for measuring the thermodynamic properties of protein-ligand complexes in solution. Dissociation constants (Kd values) determined by the method for five model protein-ligand complexes that included those with small molecules, nucleic acids, peptides, and other proteins were generally in good agreement with Kd values measured by conventional methods. Important experimental advantages of the described method over existing methods include: the ability to make measurements in a high-throughput and automated fashion, the ability to make measurements using only picomole quantitities of protein, and the ability to analyze either purified or unpurified protein-ligand complexes.     

A mass spectrometry-based immunosensor for bacteria using antibody-conjugated gold nanoparticles

We have developed a simple mass spectrometry-based immunosensor using antibody (Ab)-modified gold nanoparticles (Ab-Au NPs) for the rapid quantitation of bacteria via the analysis of Au clusters under pulsed laser irradiation.     

Investigation of multiple binding sites on ribonuclease A using nano-electrospray ionization mass spectrometry

Multiple non-active site interactions between ribonuclease A (RNAse) and selected target molecules were investigated using nano-electrospray ionization mass spectrometry (nano-ESI-MS). Among the building blocks of RNA, phosphate and ribose showed such multiple interactions. Multiple phosphate interactions survived a high cone voltage, while multiple interactions with D-ribose disappeared already at a low cone voltage. Using nano-ESI-MS, only cytosine among the individual bases appeared to interact with RNAse. Interestingly, guanosine binds to the RNAse surface at high cone voltage, probably as a result of cooperative binding of the sugar and the guanine base. Upon binding of deoxycytidine oligonucleotides with six (dC6), nine (dC9) and twelve (dC12) deoxycytidine nucleotide units to RNAse, the dC12 unit showed the strongest interaction. Upon collision-induced dissociation (CID) of the RNAse/dC6 complex, this complex survived dissociation at an energy level where covalently bound cytosine from dC6 was lost. This is in contrast to CID of RNAse complexed with mononucleotide cytidine 2'-monophosphate (CMP), which dissociates from the protein without breaking of covalent bonds.     

Data processing for mass spectrometry-based metabolomics

Modern analytical technologies afford comprehensive and quantitative investigation of a multitude of different metabolites. Typical metabolomic experiments can therefore produce large amounts of data. Handling such complex datasets is an important step that has big impact on extent and quality at which the metabolite identification and quantification can be made, and thus on the ultimate biological interpretation of results. Increasing interest in metabolomics thus led to resurgence of interest in related data processing. A wide variety of methods and software tools have been developed for metabolomics during recent years, and this trend is likely to continue. In this paper we overview the key steps of metabolomic data processing and focus on reviewing recent literature related to this topic, particularly on methods for handling data from liquid chromatography mass spectrometry (LC-MS) experiments.     

Determination of calcium binding sites in gas-phase small peptides by tandem mass spectrometry

Low-energy (LE) and high-energy (HE) collisionally activated decompositions (CAD) of calcium/peptide complexes of the form [M-H+Ca]⁺ and [M+Ca]²⁺ reflect the site of calcium binding in various gas-phase peptides that are models of the calcium binding site III of rabbit skeletal troponin C. The Ca²⁺ binding sites involve an aspartic acid, glutamic acid, and asparagine, which are in the metal-binding loops of calcium-binding proteins. Both fast atom bombardment (FAB) and electrospray ionization (ESI) were used to generate the metal/peptide complexes. When submitted to LE CAD, ESI-produced Ca²⁺/peptide complexes undergo fragmentations that are controlled by Ca²⁺ binding and provide information on the Ca²⁺ binding site. The LE CAD spectra are simple, indicating that Ca²⁺ binding involves specific oxygen ligands including acidic side chains and that only a few low-energy fragmentation channels exist. The HE CAD spectra of FAB-produced Ca²⁺/peptide complexes are more complex, owing to the introduction of high internal energy into the precursor ion. Interactions of the other alkaline-earth metal ions Mg²⁺ and Ba²⁺ with these peptides reveal that the ligand preferences of these metal ions are slightly different than those of Ca²⁺.     

Novel liquid chromatography/mass spectrometry-based approaches for the determination of glyphosate and related compounds: A review

Although glyphosate (Gly) is one of the most widely used agrochemicals, it is also of the most difficult to measure. Gly, its metabolites, and related compounds cannot be sought within the scope of multi-residue methods. Specific so-called single-residue methods are used instead. Liquid chromatography-mass spectrometry (LC-MS) is currently the most widely used technique for determining Gly and its metabolites. This review addresses the different LC-MS-based methods proposed for the determination of Gly and related species in food and environment matrices. Sample preparation (food and environment), as well as their determination based in novel liquid chromatography/mass spectrometry approaches including different specific stationary phases are presented and the specific analytical challenges, strengths and drawbacks are critically discussed.     

Latest developments in sample treatment for O-isotopic labeling for proteomics mass spectrometry-based approaches: A critical review

Nowadays isotopic ¹⁸O-labeling of peptides has recalled the attention of researchers due to its simplicity of application and high versatility for proteomics studies. Protein quantification, differential peptide mass mapping, studies regarding proteins overexpressed or underexpressed, or the searching of biomarkers can be accomplished by using ¹⁸O-labeling. In this critical review we comment on the different ways in which ¹⁸O-labeling can be done, highlighting the key parameters of the different sample treatments to obtain a reliable and reproducible labeling. In addition we describe and compare the latest improvement in terms of sample treatment that allows to reduce the handling and to increase the throughput for this sample treatment. Finally, we hypothesize on the future trends of these methods under the light of the new technological advances to speed protein cleavage.     

Competitive mass spectrometry binding assay for characterization of three binding sites of tubulin

Tubulin is an attractive and established target for anticancer therapy. To date, the only method to determine the binding of inhibitor to tubulin has been competitive radioligand binding assays. We developed a non‐radioactive mass spectrometry (MS) binding assay to study the tubulin binding of colchicine, vinblastine and paclitaxel and to identify which of these three binding sites that a novel inhibitor binds. The method involves a very simple step of separating the unbound ligand from macromolecules using ultrafiltration. The unbound ligand in the filtrate can be accurately determined using highly sensitive and specific liquid chromatography tandem mass spectrometry (LC‐MS/MS) method using multiple reaction monitoring (MRM) mode. The assay was validated using podophyllotoxin, vincristine and docetaxel, drugs that compete to the colchicine‐, vinblastine‐ and paclitaxel‐binding sites in tubulin, respectively. This competitive binding assay allowed the reliable detection of interactions of these drugs with three binding sites on tubulin. This method was subsequently applied to determine the tubulin‐binding site of 4‐substituted methoxylbenzoyl‐aryl‐thiazoles (SMART‐H), a potent antitubulin agent developed in our laboratory. The results indicated that SMART‐H specifically and reversibly bound only to the colchicine‐binding site, but not to vinblastine‐ or paclitaxel sites. This new non‐radioligand binding method to determine the binding site on tubulin will function as a useful tool to study the binding sites of tubulin inhibitors. Copyright © 2010 John Wiley & Sons, Ltd.     

Fast mass spectrometry-based methodologies for pharmaceutical analyses

Historically, most bioanalytical methods for drug analysis in pharmaceutical industry were developed using HPLC coupled with UV or fluorescence detection. However, there is a trend toward interfacing separation technologies with more sensitive tandem mass spectrometry (MS/MS)-based systems. MS/MS detection offers complete resolution of the parent compounds from their first pass metabolites to avoid extra efforts for separation and sample clean-up procedures resulting in shorter run times. With the increasing demand for ever faster screening, there is a continuing demand for bioanalytical methods possessing higher sample throughput for both in vitro and in vivo drug metabolism and pharmacokinetic evaluations to accelerate the discovery process. This review focuses on the current approaches for fast MS-based assays (cycle-time less than 5 min) of pharmaceuticals and their metabolites that have been reported in the peer-reviewed publications.     

An efficient data format for mass spectrometry-based proteomics

The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems.     

Sample preparation by in-gel digestion for mass spectrometry-based proteomics

The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by “in-gel digestion” has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches. Figure Classical in-gel digestion process for a protein band stained with CBB. Protein bands are cut from the polyacrylamide gel (1). CBB molecules (blue circles) bound to the protein are released by iterative incubation in a buffered organic solvent system (2). To increase digestion efficiency and sequence coverage proteins are reduced (3) and alkylated (4). Proteins are subsequently digested with proteolytic enzymes (scissors symbols), typically trypsin (5). Trypsin cleaves at the amino acid residues arginine (R) and lysine (K). The resulting peptides (A, B, and C) are extracted from the polyacrylamide matrix (6). The peptide solution can be further purified for analysis by mass spectrometry (Section “Concentration and desalting of peptides”)     

Determination of drug binding sites to proteins by electrospray ionisation mass spectrometry: the interaction of cisplatin with transferrin

Cisplatin, cis-[PtCl2(NH3)2], is known to bind to human serum transferrin, but the binding site remains a matter of some debate. Electrospray ionisation mass spectrometry has been used to characterise the interaction of cisplatin with transferrin. The studies indicate that cisplatin initially docks with, and subsequently bonds covalently to, the hydroxyl functional group of threonine 457, with the loss of HCl affording a transferrin-O-PtCl(NH3)2 adduct.     

Top-down ESI-ECD-FT-ICR mass spectrometry localizes noncovalent protein-ligand binding sites

Mass spectrometry (MS) with electrospray ionization (ESI) has the capability to measure and detect noncovalent protein-ligand and protein-protein complexes. However, information on the sites of ligand binding is not easily obtained by the ESI-MS methodology. Electron capture dissociation (ECD) favors cleavage of covalent backbone bonds of protein molecules. We show that this characteristic of ECD translates to noncovalent protein-ligand complexes, as covalent backbone bonds of protein complexes are dissociated, but the noncovalent ligand interaction is retained. For the complex formed from 140-residue, 14.5 kDa alpha-synuclein protein, and one molecule of polycationic spermine (202 Da), ECD generates product ions that retain the protein-spermine noncovalent interaction. Spermine binding is localized to residues 106-138; the ECD data are consistent with previous solution NMR studies. Our studies suggest that ECD mass spectrometry can be used to determine directly the sites of ligand binding to protein targets.     

Determination of acidic sites and binding toxic metal ions on cumin surface using nonideal competitive adsorption model

A fundamental study of the application of cumin biomass in the recovery of Cu and Zn metal ion uptake from food and drinks is carried out at different pH's and at fixed ionic strength. The chemical characteristics of protein in cumin seeds were investigated. Results showed that cumin contains 18.25% crude protein, which includes 18 amino acids. The main reactive groups on protein cumin are amino and carboxylic groups of dicarboxylic amino acids, leading to a pH-dependent charge. Therefore, the cumin surface is considered as a heterogeneous system. To describe protonation behavior in a heterogeneous cumin biomass (cumin/0.1 M NaNO(3)) system, acid-base titrations have been performed with conductometric and potentiometric titration. Measurement of the reactivity of cumin surface in the adsorption of Cu and Zn metal ions and determination of metal binding at different pH's were also carried out. To solve broad and ill-defined titration curves, a simplified version of nonideal competitive analysis (NICA) by Plette et al.) was applied. The results show that the sorption of the bivalent metal ions onto the whole surface of cumin could be attributed to a monodentate binding to one site mainly carboxylic-type site.     

Indirect ultrasonication for protein quantification and peptide mass mapping through mass spectrometry-based techniques

We report in this work a fast protocol for protein quantification and for peptide mass mapping that rely on ¹⁸O isotopic labeling through the decoupling procedure. It is demonstrated that the purity and source of trypsin do not compromise the labeling degree and efficiency of the decoupled labeling reaction, and that the pH of the labeling reaction is a critical factor to obtain a significant ¹⁸O double labeling. We also show that the same calibration curve can be used for MALDI protein quantification during several days maintaining a reasonable accuracy, thus simplifying the handling of the quantification process. In addition we demonstrate that ¹⁸O isotopic labeling through the decoupling procedure can be successfully used to elaborate peptide mass maps. BSA was successfully quantified using the same calibration curve in different days and plasma from a freshwater fish, Cyprinus carpio, was used to elaborate the peptide mass maps.     

Synthetic approaches to polypyridyl bridging ligands with proximal multidentate binding sites

[reactions: see text] A series of 12 bridging ligands was prepared. These ligands include a central linker appended to two 1,8-naphthyrid-2-yl or two 1,10-phenanthrolin-2-yl units. The linkers include pyridazin-3,6-diyl, 1,8-naphthyrid-2,7-diyl, 2,2'-bipyrid-6,6'-diyl, 1,10-phenanthrolin-2,9-diyl, 1,2-di(2'-pyrid-6'-yl)ethyne, and 3,6-di(2'-pyrid-6'-yl)pyridazine. The ligands were synthesized from the diacetyl derivative of the central linker by a Friedl?nder condensation with either 2-aminonicotinaldehyde or 8-amino-7-quinolinecarbaldehyde. The precursor diacetyl derivatives were, in turn, prepared by pathways involving Stille and Sonogashira couplings. Examination of the electronic absorption spectra of the bridging ligands shows the strongest correlation to be between pairs of ligands having the same central linker. Complexation studies will follow.     

Identification of binding sites for acetaldehyde adsorption on titania nanorod surfaces using CIMS

The interaction of acetaldehyde with TiO(2) nanorods has been studied under low pressures (acetaldehyde partial pressure range 10(-4)-10(-8) Torr) using chemical ionization mass spectrometry (CIMS). We quantitatively separate irreversible adsorption, reversible adsorption, and an uptake of acetaldehyde assigned to a thermally activated surface reaction. We find that, at room temperature and 1.2 Torr total pressure, 2.1 ± 0.4 molecules/nm(2) adsorb irreversibly, but this value exhibits a sharp decrease as the analyte partial pressure is lowered below 4 × 10(-4) Torr, regardless of exposure time. The number of reversible binding sites at saturation amounts to 0.09 ± 0.02 molecules/nm(2) with a free energy of adsorption of 43.8 ± 0.2 kJ/mol. We complement our measurements with FTIR spectroscopy and identify the thermal dark reaction as a combination of an aldol condensation and an oxidative adsorption that converts acetaldehyde to acetate or formate and CO, at a measured combined initial rate of 7 ± 1 × 10(-4) molecules/nm(2) s. By characterizing binding to different types of sites under dark conditions in the absence of oxygen and gas phase water, we set the stage to analyze site-specific photoefficiencies involved in the light-assisted mineralization of acetaldehyde to CO(2).