Mapping protein-protein interactions by affinity-directed mass spectrometry.

A precise and rapid method for identifying sites of interaction between proteins was demonstrated; the basis of the method is direct mass spectrometric readout from the complex to determine the specific components of the proteins that interact--a method termed affinity-directed mass spectrometry. The strategy was used to define the region of interaction of a protein growth factor with a monoclonal antibody. A combination of proteolytic digestion and affinity-directed mass spectrometry was used to rapidly determine the approximate location of a continuous binding epitope within the growth factor. The precise boundaries of the binding epitope were determined by affinity-directed mass spectrometric analysis of sets of synthetic peptide ladders that span the approximate binding region. In addition to the mapping of such linear epitopes, affinity-directed mass spectrometry can be applied to the mapping of other types of molecule-molecule contacts, including ligand-receptor and protein-oligonucleotide interactions.

Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry.

Amino acid sequencing by recombinant DNA technology, although dramatically useful, is subject to base reading errors, is indirect, and is insensitive to posttranslational processing. Mass spectrometry techniques can provide molecular weight data from even relatively large proteins for such cDNA sequences and can serve as a check of an enzyme's purity and sequence integrity. Multiply-charged ions from electrospray ionization can be dissociated to yield structural information by tandem mass spectrometry, providing a second method for gaining additional confidence in primary sequence confirmation. Here, accurate (+/- 1 Da) molecular weight and molecular ion dissociation information for human muscle and brain creatine kinases has been obtained by electrospray ionization coupled with Fourier-transform mass spectrometry to help distinguish which of several published amino acid sequences for both enzymes are correct. The results herein are consistent with one published sequence for each isozyme, and the heterogeneity indicated by isoelectric focusing due to 1-Da deamidation changes. This approach appears generally useful for detailed sequence verification of recombinant proteins.

Innovative analytical strategies for the development of sensor devices and mass spectrometry methods

Il lavoro presentato in questa tesi di Dottorato è incentrato sullo sviluppo di strategie analitiche innovative basate sulla sensoristica e su tecniche di spettrometria di massa in ambito biologico e della sicurezza alimentare. Il primo capitolo tratta lo studio di aspetti metodologici ed applicativi di procedure sensoristiche per l’identificazione e la determinazione di biomarkers associati alla malattia celiaca. In tale ambito, sono stati sviluppati due immunosensori, uno a trasduzione piezoelettrica e uno a trasduzione amperometrica, per la rivelazione di anticorpi anti-transglutaminasi tissutale associati a questa malattia. L’innovazione di questi dispositivi riguarda l’immobilizzazione dell’enzima tTG nella conformazione aperta (Open-tTG), che è stato dimostrato essere quella principalmente coinvolta nella patogenesi. Sulla base dei risultati ottenuti, entrambi i sistemi sviluppati si sono dimostrati una valida alternativa ai test di screening attualmente in uso per la diagnosi della celiachia. Rimanendo sempre nel contesto della malattia celiaca, ulteriore ricerca oggetto di questa tesi di Dottorato, ha riguardato lo sviluppo di metodi affidabili per il controllo di prodotti “gluten-free”. Il secondo capitolo tratta lo sviluppo di un metodo di spettrometria di massa e di un immunosensore competitivo per la rivelazione di prolammine in alimenti “gluten-free”. E’ stato sviluppato un metodo LC-ESI-MS/MS basato su un’analisi target con modalità di acquisizione del segnale selected reaction monitoring per l’identificazione di glutine in diversi cereali potenzialmente tossici per i celiaci. Inoltre ci si è focalizzati su un immunosensore competitivo per la rivelazione di gliadina, come metodo di screening rapido di farine. Entrambi i sistemi sono stati ottimizzati impiegando miscele di farina di riso addizionata di gliadina, avenine, ordeine e secaline nel caso del sistema LC-MS/MS e con sola gliadina nel caso del sensore. Infine i sistemi analitici sono stati validati analizzando sia materie prime (farine) che alimenti (biscotti, pasta, pane, etc.). L’approccio sviluppato in spettrometria di massa apre la strada alla possibilità di sviluppare un test di screening multiplo per la valutazione della sicurezza di prodotti dichiarati “gluten-free”, mentre ulteriori studi dovranno essere svolti per ricercare condizioni di estrazione compatibili con l’immunosaggio competitivo, per ora applicabile solo all’analisi di farine estratte con etanolo. Terzo capitolo di questa tesi riguarda lo sviluppo di nuovi metodi per la rivelazione di HPV, Chlamydia e Gonorrhoeae in fluidi biologici. Si è scelto un substrato costituito da strips di carta in quanto possono costituire una valida piattaforma di rivelazione, offrendo vantaggi grazie al basso costo, alla possibilità di generare dispositivi portatili e di poter visualizzare il risultato visivamente senza la necessità di strumentazioni. La metodologia sviluppata è molto semplice, non prevede l’uso di strumentazione complessa e si basa sull’uso della isothermal rolling-circle amplification per l’amplificazione del target. Inoltre, di fondamentale importanza, è l’utilizzo di nanoparticelle colorate che, essendo state funzionalizzate con una sequenza di DNA complementare al target amplificato derivante dalla RCA, ne permettono la rivelazione a occhio nudo mediante l’uso di filtri di carta. Queste strips sono state testate su campioni reali permettendo una discriminazione tra campioni positivi e negativi in tempi rapidi (10-15 minuti), aprendo una nuova via verso nuovi test altamente competitivi con quelli attualmente sul mercato.

Kinetic study of the decompositions involved in the thermal degradation of commercial azodicarbonamide

The transitions and reactions involved in the thermal treatment of several commercial azodicarbonamides (ADC) in an inert atmosphere have been studied by dynamic thermogravimetry analysis (TGA), mass spectrometry and Fourier transform infrared (FTIR) spectroscopy. A pseudo-mechanistic model, involving several competitive and non-competitive reactions, has been suggested and applied to the correlation of the weight loss data. The model applied is capable of accurately representing the different processes involved, and can be of great interest in the understanding and quantification of such phenomena, including the simulation of the instantaneous amount of gases evolved in a foaming process. In addition, a brief discussion on the methodology related to the mathematical modeling of TGA data is presented, taking into account the complex thermal behaviour of the ADC.

Determination of cyclic and linear siloxanes in wastewater samples by ultrasound-assisted dispersive liquid-liquid microextraction followed by gas chromatography-mass spectrometry

A fast, simple and environmentally friendly ultrasound-assisted dispersive liquid-liquid microextraction (USA-DLLME) procedure has been developed to preconcentrate eight cyclic and linear siloxanes from wastewater samples prior to quantification by gas chromatography-mass spectrometry (GC-MS). A two-stage multivariate optimization approach has been developed employing a Plackett-Burman design for screening and selecting the significant factors involved in the USA-DLLME procedure, which was later optimized by means of a circumscribed central composite design. The optimum conditions were: extractant solvent volume, 13 µL; solvent type, chlorobenzene; sample volume, 13 mL; centrifugation speed, 2300 rpm; centrifugation time, 5 min; and sonication time, 2 min. Under the optimized experimental conditions the method gave levels of repeatability with coefficients of variation between 10 and 24% (n=7). Limits of detection were between 0.002 and 1.4 µg L−1. Calculated calibration curves gave high levels of linearity with correlation coefficient values between 0.991 and 0.9997. Finally, the proposed method was applied for the analysis of wastewater samples. Relative recovery values ranged between 71–116% showing that the matrix had a negligible effect upon extraction. To our knowledge, this is the first time that combines LLME and GC-MS for the analysis of methylsiloxanes in wastewater samples.

TGA/FTIR study of the MCM-41-catalytic pyrolysis of tobacco and tobacco–glycerol mixtures

In this work, the catalytic effect of MCM-41 on the qualitative composition of the gases evolved in the pyrolysis of glycerol, tobacco and tobacco–glycerol mixtures has been studied by TGA/FTIR. The results obtained reflect that the amount of volatile products obtained from tobacco or from tobacco containing mixtures is noticeably decreased if the catalyst is used as a tobacco additive. The addition of the catalyst also produces noticeable changes in the composition of the gases obtained at each temperature. Such changes are more significant in the case of the pyrolysis of the tobacco–glycerol–mixture than in the pyrolysis of tobacco. The evolution patterns for different types of compounds reveal that the catalyst contributes to a noticeable decrease of the yields of methane, CO, CO2 and carbonylic compounds, which could be interesting from the point of view of the use of MCM-41 as a tobacco additive in order to reduce tobacco smoke toxicity.

Evaluation of the multi-element capabilities of collision/reaction cell inductively coupled plasma - mass spectrometry in wine analysis

This work explores the multi-element capabilities of inductively coupled plasma - mass spectrometry with collision/reaction cell technology (CCT-ICP-MS) for the simultaneous determination of both spectrally interfered and non-interfered nuclides in wine samples using a single set of experimental conditions. The influence of the cell gas type (i.e. He, He+H2 and He+NH3), cell gas flow rate and sample pre-treatment (i.e. water dilution or acid digestion) on the background-equivalent concentration (BEC) of several nuclides covering the mass range from 7 to 238 u has been studied. Results obtained in this work show that, operating the collision/reaction cell with a compromise cell gas flow rate (i.e. 4 mL min−1) improves BEC values for interfered nuclides without a significant effect on the BECs for non-interfered nuclides, with the exception of the light elements Li and Be. Among the different cell gas mixtures tested, the use of He or He+H2 is preferred over He+NH3 because NH3 generates new spectral interferences. No significant influence of the sample pre-treatment methodology (i.e. dilution or digestion) on the multi-element capabilities of CCT-ICP-MS in the context of simultaneous analysis of interfered and non-interfered nuclides was observed. Nonetheless, sample dilution should be kept at minimum to ensure that light nuclides (e.g. Li and Be) could be quantified in wine. Finally, a direct 5-fold aqueous dilution is recommended for the simultaneous trace and ultra-trace determination of spectrally interfered and non-interfered elements in wine by means of CCT-ICP-MS. The use of the CCT is mandatory for interference-free ultra-trace determination of Ti and Cr. Only Be could not be determined when using the CCT due to a deteriorated limit of detection when compared to conventional ICP-MS.

Electrochemical and In Situ FTIR Study of o-Cresol on Platinum Electrode in Acid Medium

The electrochemical behaviour of o-cresol in acidic medium on platinum electrode has been studied by cyclic voltammetry and in situ Fourier transform infrared spectroscopy. The o-cresol suffers hydrolysis during oxidation giving rise to the formation of methyl-p-benzoquinone. In situ FTIR spectroscopic studies also reveal the presence of CO2, formed as a consequence of the rupture of the aromatic ring. Moreover, the oxidation of o-cresol in acidic medium produces a polymeric film on the platinum surface that precludes further oxidation of o-cresol. The reduction of o-cresol at potentials below 0 V produces in the first step the partial reduction of the aromatic ring and when the potential goes to values below 0 V, methyl-cyclohexanone.

Development of a novel pyrolysis-gas chromatography/mass spectrometry method for the analysis of poly(lactic acid) thermal degradation products

Thermal degradation of PLA is a complex process since it comprises many simultaneous reactions. The use of analytical techniques, such as differential scanning calorimetry (DSC) and thermogravimetry (TGA), yields useful information but a more sensitive analytical technique would be necessary to identify and quantify the PLA degradation products. In this work the thermal degradation of PLA at high temperatures was studied by using a pyrolyzer coupled to a gas chromatograph with mass spectrometry detection (Py-GC/MS). Pyrolysis conditions (temperature and time) were optimized in order to obtain an adequate chromatographic separation of the compounds formed during heating. The best resolution of chromatographic peaks was obtained by pyrolyzing the material from room temperature to 600 °C during 0.5 s. These conditions allowed identifying and quantifying the major compounds produced during the PLA thermal degradation in inert atmosphere. The strategy followed to select these operation parameters was by using sequential pyrolysis based on the adaptation of mathematical models. By application of this strategy it was demonstrated that PLA is degraded at high temperatures by following a non-linear behaviour. The application of logistic and Boltzmann models leads to good fittings to the experimental results, despite the Boltzmann model provided the best approach to calculate the time at which 50% of PLA was degraded. In conclusion, the Boltzmann method can be applied as a tool for simulating the PLA thermal degradation.

A systematic study on the influence of carbon on the behavior of hard-to-ionize elements in inductively coupled plasma–mass spectrometry

A systematic study on the influence of carbon on the signal of a large number of hard-to-ionize elements (i.e. B, Be, P, S, Zn, As, Se, Pd, Cd, Sb, I, Te, Os, Ir, Pt, Au, and Hg) in inductively coupled plasma–mass spectrometry has been carried out. To this end, carbon matrix effects have been evaluated considering different plasma parameters (i.e. nebulizer gas flow rate, r.f. power and sample uptake rate), sample introduction systems, concentration and type of carbon matrix (i.e. glycerol, citric acid, potassium citrate and ammonium carbonate) and type of mass spectrometer (i.e. quadrupole filter vs. double-focusing sector field mass spectrometer). Experimental results show that P, As, Se, Sb, Te, I, Au and Hg sensitivities are always higher for carbon-containing solutions than those obtained without carbon. The other hard-to-ionize elements (Be, B, S, Zn, Pd, Cd, Os, Ir and Pt) show no matrix effect, signal enhancement or signal suppression depending on the experimental conditions selected. The matrix effects caused by the presence of carbon are explained by changes in the plasma characteristics and the corresponding changes in ion distribution in the plasma (as reflected in the signal behavior plot, i.e. the signal intensity as a function of the nebulizer gas flow rate). However, the matrix effects for P, As, Se, Sb, Te, I, Au and Hg are also related to an increase in analyte ion population caused as a result of charge transfer reactions involving carbon-containing charged species in the plasma. The predominant specie is C+, but other species such as CO+, CO2+, C2+ and ArC+ could also play a role. Theoretical data suggest that B, Be, S, Pd, Cd, Os, Ir and Pt could also be involved in carbon based charge transfer reactions, but no experimental evidence substantiating this view has been found.

On-line microwave-based preconcentration device for inductively coupled plasma atomic emission spectrometry: Application to the elemental analysis of spirit samples

A microwave-based thermal nebulizer (MWTN) has been employed for the first time as on-line preconcentration device in inductively coupled plasma atomic emission spectrometry (ICP-AES). By the appropriate selection of the experimental conditions, the MWTN could be either operated as a conventional thermal nebulizer or as on-line analyte preconcentration and nebulization device. Thus, when operating at microwave power values above 100 W and highly concentrated alcohol solutions, the amount of energy per solvent mass liquid unit (EMR) is high enough to completely evaporate the solvent inside the system and, as a consequence, the analyte is deposited (and then preconcentrated) on the inner walls of the MWTN capillary. When reducing the EMR to the appropriate value (e.g., by reducing the microwave power at a constant sample uptake rate) the retained analyte is swept along by the liquid-gas stream and an analyte-enriched aerosol is generated and next introduced into the plasma cell. Emission signals obtained with the MWTN operating in preconcentration-nebulization mode improved when increasing preconcentration time and sample uptake rate as well as when decreasing the nozzle inner diameter. When running with pure ethanol solution at its optimum experimental conditions, the MWTN in preconcentration-nebulization mode afforded limits of detection up to one order of magnitude lowers than those obtained operating the MWTN exclusively as a nebulizer. To validate the method, the multi-element analysis (i.e. Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Pb and Zn) of different commercial spirit samples in ICP-AES has been performed. Analyte recoveries for all the elements studied ranged between 93% and 107% and the dynamic linear range covered up to 4 orders of magnitude (i.e. from 0.1 to 1000 μg L−1). In these analysis, both MWTN operating modes afforded similar results. Nevertheless, the preconcentration-nebulization mode permits to determine a higher number of analytes due to its higher detection capabilities.

TGA/FTIR study of tobacco and glycerol–tobacco mixtures

In this work, the evolution with temperature of the qualitative composition of the gases evolved in the pyrolysis of glycerol, tobacco and tobacco–glycerol mixtures has been studied. The pathways for different types of compounds (i.e., water, CO, CO2, carbonylic compounds, alkenyl or alkyl groups containing compounds, alcohols and phenols and aromatic compounds) have been established, and their relationship with the different reaction steps involved in the pyrolysis process have been suggested. The comparison among the behavior observed in the pyrolysis of tobacco, glycerol and a mixture glycerol–tobacco has permitted us to suggest possible interactions between tobacco and glycerol affecting the composition of the gases evolved.

Disintegrability under composting conditions of plasticized PLA–PHB blends

The disintegration under composting conditions of films based on poly(lactic acid)–poly(hydroxybutyrate) (PLA–PHB) blends and intended for food packaging was studied. Two different plasticizers, poly(ethylene glycol) (PEG) and acetyl-tri-n-butyl citrate (ATBC), were used to limit the inherent brittleness of both biopolymers. Neat PLA, plasticized PLA and PLA–PHB films were processed by melt-blending and compression molding and they were further treated under composting conditions in a laboratory-scale test at 58 ± 2 °C. Disintegration levels were evaluated by monitoring their weight loss at different times: 0, 7, 14, 21 and 28 days. Morphological changes in all formulations were followed by optical and scanning electron microscopy (SEM). The influence of plasticizers on the disintegration of PLA and PLA–PHB blends was studied by evaluating their thermal and nanomechanical properties by thermogravimetric analysis (TGA) and the nanoindentation technique, respectively. Meanwhile, structural changes were followed by Fourier transformed infrared spectroscopy (FTIR). The ability of PHB to act as nucleating agent in PLA–PHB blends slowed down the PLA disintegration, while plasticizers speeded it up. The relationship between the mesolactide to lactide forms of PLA was calculated with a Pyrolysis–Gas Chromatography–Mass Spectrometry device (Py–GC/MS), revealing that the mesolactide form increased during composting.

Ion balance in waters through inductively coupled plasma optical emission spectrometry

Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) has been employed to carry out the determination of both major anions and cations in water samples. The anion quantification has been performed by means of a new automatic accessory. In this device chloride has been determined by continuously adding a silver nitrate solution. As a result solid silver chloride particles are formed and retained on a nylon filter inserted in the line. The emission intensity is read at a silver characteristic wavelength. By plotting the drop in silver signal versus the chloride concentration, a straight line is obtained. As regards bicarbonate, this anion has been on-line transformed into carbon dioxide with the help of a 2.0 mol L−1 nitric acid stream. Carbon signal is linearly related with bicarbonate concentration. Finally, information about sulfate concentration has been achieved by means of the measurement of sulfur emission intensity. All the steps have been simultaneously and automatically performed. With this setup detection limits have been 1.0, 0.4 and 0.09 mg L−1 for chloride, bicarbonate and sulfate, respectively. Furthermore, it affords good precision with RSD below 6 %. Cation (Ca, Mg, Na and K) concentration, in turn, has been obtained by simultaneously reading the emission intensity at characteristic wavelengths. The obtained limits of detection have been 8 × 10−3, 2 × 10−3, 8 × 10−4 and 10−2 mg L−1 for sodium, potassium, magnesium and calcium, respectively. As regards sample throughput, about 30 samples h−1 can be analysed. Validation results have revealed that the obtained concentrations for these anions are not significantly different as compared to the data provided by conventional methods. Finally, by considering the data for anions and cations, precise ion balances have been obtained for well and mineral water samples.

Carbon-, sulfur-, and phosphorus-based charge transfer reactions in inductively coupled plasma–atomic emission spectrometry

In this work, the influence of carbon-, sulfur-, and phosphorus-based charge transfer reactions on the emission signal of 34 elements (Ag, Al, As, Au, B, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, Ga, Hg, I, In, Ir, K, Li, Mg, Mn, Na, Ni, P, Pb, Pd, Pt, S, Sb, Se, Sr, Te, and Zn) in axially viewed inductively coupled plasma–atomic emission spectrometry has been investigated. To this end, atomic and ionic emission signals for diluted glycerol, sulfuric acid, and phosphoric acid solutions were registered and results were compared to those obtained for a 1% w w− 1 nitric acid solution. Experimental results show that the emission intensities of As, Se, and Te atomic lines are enhanced by charge transfer from carbon, sulfur, and phosphorus ions. Iodine and P atomic emission is enhanced by carbon- and sulfur-based charge transfer whereas the Hg atomic emission signal is enhanced only by carbon. Though signal enhancement due to charge transfer reactions is also expected for ionic emission lines of the above-mentioned elements, no experimental evidence has been found with the exception of Hg ionic lines operating carbon solutions. The effect of carbon, sulfur, and phosphorus charge transfer reactions on atomic emission depends on (i) wavelength characteristics. In general, signal enhancement is more pronounced for electronic transitions involving the highest upper energy levels; (ii) plasma experimental conditions. The use of robust conditions (i.e. high r.f. power and lower nebulizer gas flow rates) improves carbon, sulfur, and phosphorus ionization in the plasma and, hence, signal enhancement; and (iii) the presence of other concomitants (e.g. K or Ca). Easily ionizable elements reduce ionization in the plasma and consequently reduce signal enhancement due to charge transfer reactions.