Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

A Strategy for Simultaneously Improving Resolution and Sensitivity of Hybrid Quadrupole Ion Trap/Time-of-Flight Mass Spectrometry Using Square Waveform Phase Modulation

The hybrid quadrupole ion trap/time-of-flight mass spectrometry (QIT/TOFMS) device is popular because of its advantages of high sensitivity, high resolution, and MS/MS capability. However, the analytical performance of QIT/TOFMS is severely limited by the parameters of the ion trap, as QIT is typically used as a TOF pulser because the ion initial distributions of space, velocity, and angle change dynamically with the phase angle of rf voltage. In this work, a square waveform phase modulation strategy was proposed to eliminate the influence of the rf phase angle, and the dependence of QIT/TOFMS performance on the phase angle was studied. It was found that the mass resolution and signal intensity showed a "W" trend with the increase of the ion extraction phase angle from 0° to 360°, where the best resolution and sensitivity were obtained at 0°, 180°, and 360° while the worst resolution and sensitivity were obtained at 90° and 270°. Moreover, the optimum phase angle was independent of m/z. As a result, the mass resolution for m/z 106, 164, and 258 was improved by 162%, 160%, and 210% respectively, while the signal intensities for m/z 106, 164, and 258 were enhanced by 25 ± 1, 10 ± 1, and 21 ± 1 fold, respectively, and a limit of detection down to 0.015 ppbv for m/z 164 was obtained. The experiment results indicated that the square waveform phase modulation strategy could be used to simultaneously improve the resolution and sensitivity of QIT/TOFMS.

Omics era in forensic medicine: towards a new age

Background/aim

Forensic medicine and sciences is a multidisciplinary branch of science, which frequently benefit from novel technologies. State of the art omics technologies have begun to be performed in forensic medicine and sciences, particularly in postmortem interval, intoxication, drugs of abuse, diagnosis of diseases and cause of death. This review aims to discuss the role and use of great omics (metabolomics, proteomics, genomics and transcriptomics) in forensic sciences, in detail.

Materials and methods

A detailed review of related literature was performed, and studies were subdivided as per the type of omics.

Results and conclusion

Omics seems as a revolutionary step in forensic science and sure carries it towards a new age. The number of forensic studies utilizing omics steadily increases in last years. Omics strategies should be used together in order to gather more accurate and certain data. Additional studies need to be performed to incorporate omics into routine forensic methodology.

Invited Review: Toxicoproteomics: Proteomics Applied to Toxicology and Pathology

Global measurement of proteins and their many attributes in tissues and biofluids defines the field of proteomics. Toxicoproteomics, as part of the larger field of toxicogenomics, seeks to identify critical proteins and pathways in biological systems that are affected by and respond to adverse chemical and environmental exposures using global protein expression technologies. Toxicoproteomics integrates 3 disciplinary areas: traditional toxicology and pathology, differential protein and gene expression analysis, and systems biology. Key topics to be reviewed are the evolution of proteomics, proteomic technology platforms and their capabilities with exemplary studies from biology and medicine, a review of over 50 recent studies applying proteomic analysis to toxicological research, and the recent development of databases designed to integrate -Omics technologies with toxicology and pathology. Proteomics is examined for its potential in discovery of new biomarkers and toxicity signatures, in mapping serum, plasma, and other biofluid proteomes, and in parallel proteomic and transcriptomic studies. The new field of toxicoproteomics is uniquely positioned toward an expanded understanding of protein expression during toxicity and environmental disease for the advancement of public health.

Polarization induced electrospray ionization mass spectrometry for the analysis of liquid, viscous and solid samples

In this study, a polarization-induced electrospray ionization mass spectrometry (ESI-MS) was developed. A micro-sized sample droplet was deposited on a naturally available dielectric substrate such as a fruit or a stone, and then placed close to (~2 mm) the orifice of a mass spectrometer applied with a high voltage. Taylor cone was observed from the sample droplet, and a spray emitted from the cone apex was generated. The analyte ion signals derived from the droplet were obtained by the mass spectrometer. The ionization process is similar to that in ESI although no direct electric contact was applied on the sample site. The sample droplet polarized by the high electric field provided by the mass spectrometer initiated the ionization process. The dielectric sample loading substrate facilitated further the polarization process, resulting in the formation of Taylor cone. The mass spectral profiles obtained via this approach resembled those obtained using ESI-MS. Multiply charged ions dominated the mass spectra of peptides and proteins, whereas singly charged ions dominated the mass spectra of small molecules such as amino acids and small organic molecules. In addition to liquid samples, this approach can be used for the analysis of solid and viscous samples. A small droplet containing suitable solvent (5-10 µl) was directly deposited on the surface of the solid (or viscous) sample, placed close the orifice of mass spectrometer applied with a high voltage. Taylor cone derived from the droplet was immediately formed followed by electrospray processes to generate gas-phase ions for MS analysis. Analyte ions derived from the main ingredients of pharmaceutical tablets and viscous ointment can be extracted into the solvent droplet in situ and observed using a mass spectrometer.

Dodecyl maltopyranoside enabled purification of active human GABA type A receptors for deep and direct proteomic sequencing

The challenge in high-quality membrane proteomics is all about sample preparation prior to HPLC, and the cell-to-protein step poses a long-standing bottleneck. Traditional protein extraction methods apply ionic or poly-disperse detergents, harsh denaturation, and repeated protein/peptide precipitation/resolubilization afterward, but suffer low yield, low reproducibility, and low sequence coverage. Contrary to attempts to subdue, we resolved this challenge by providing proteins nature-and-activity-promoting conditions throughout preparation. Using 285-kDa hetero-pentameric human GABA type A receptor overexpressed in HEK293 as a model, we describe a n-dodecyl-β-d-maltopyranoside/cholesteryl hemisuccinate (DDM/CHS)-based affinity purification method, that produced active receptors, supported protease activity, and allowed high performance with both in-gel and direct gel-free proteomic analyses-without detergent removal. Unlike conventional belief that detergents must be removed before HPLC MS, the high-purity low-dose nonionic detergent DDM did not interfere with peptides, and obviated removal or desalting. Sonication or dropwise addition of detergent robustly solubilized over 90% of membrane pellets. The purification conditions were comparable to those applied in successful crystallizations of most membrane proteins. These results enabled streamlined proteomics of human synaptic membrane proteins, and more importantly, allowed directly coupling proteomics with crystallography to characterize both static and dynamic structures of membrane proteins in crystallization pipelines.

Mass spectrometry-based proteomics in Chest Medicine, Gerontology, and Nephrology: subgroups omics for personalized medicine

Mass spectrometry (MS) is currently the most promising tool for studying proteomics to investigate largescale proteins in a specific proteome. Emerging MS-based proteomics is widely applied to decipher complex proteome for discovering potential biomarkers. Given its growing usage in clinical medicine for biomarker discovery to predict, diagnose and confer prognosis, MS-based proteomics can benefit study of personalized medicine. In this review we introduce some fundamental MS theory and MS-based quantitative proteomic approaches as well as several representative clinical MS-based proteomics issues in Chest Medicine, Gerontology, and Nephrology.

Bioinformatics in mass spectrometry data analysis for proteomics studies

Mass spectrometry is a technique widely employed for the identification and characterization of proteins. The role of bioinformatics is fundamental for the elaboration of mass spectrometry data due to the amount of data that this technique can produce. To process data efficiently, new software packages and algorithms are continuously being developed to improve protein identification and characterization in terms of high-throughput and statistical accuracy. However, many limitations exist concerning bioinformatics spectral data elaboration. This review aims to critically cover the recent and future developments of new bioinformatics approaches in mass spectrometry data analysis for proteomics studies.

Surface-activated chemical ionization-electrospray ionization source improves biomarker discovery with mass spectrometry

RATIONALE

Mass spectrometry (MS) is increasingly employed for the discovery of clinical biomarkers. However, due to sensitivity limitations related to in-source ionization yield, many potential biomarkers are not detected by standard mass spectrometers. Therefore, more efficient ion-source technologies are needed to improve MS applications in biomarker discovery.

METHODS

Among novel ion-source technologies, Surface-Activated Chemical Ionization (SACI), although endowed with high sensitivity linked to its ability to reduce chemical noise in mass spectra, has seen limited application in biomarker discovery to date, due to its selectivity for highly polar compounds. However, in combination with an Electrospray Ionization (ESI) source, SACI selectivity can be enlarged in the range of less polar compounds. To validate the new SACI-ESI approach in biomarker discovery, we applied it to a translational setting in oncology. We performed MS profiles of 101 human serum samples from a male population, aged 40 or older, coming to the clinic for prostate cancer evaluation based on multiple PSA exams, digital rectal examination and echography. The SACI-ESI MS spectra were analyzed and classified with an innovative bioinformatic approach based on the MS-search freeware developed in house.

RESULTS

Here we demonstrate that the SACI-ESI combination can produce MS spectra with greater sensitivity and lower noise than those obtained with the common ESI alone. We found that the SACI-ESI combination increased the number of detectable compounds and produced better quality of profiles in liquid chromatography (LC) coupled with MS (LC/MS) analysis of human serum samples, improving disease prediction potential.

CONCLUSIONS

SACI-ESI can facilitate MS-based discovery of potential biomarkers in human serum. Combined with the proposed bioinformatic approach (based on XCMS and NIST data elaboration) for the analysis of the MS spectra obtained, the potential for developing biomarkers with diagnostic capabilities are demonstrated in a prostate cancer diagnosis clinical setting.

Detection of protein from detergent solutions by probe electrospray ionization mass spectrometry (PESI-MS)

Detergents are necessarily used for different extraction protocols of proteins from biological cells or tissues. After the extraction, elimination of detergent is necessary for the better performance of electrospray ionization mass spectrometry (ESI-MS). Elimination of detergents is laborious and time-consuming, and also sample loss may be unavoidable. Probe electrospray ionization (PESI) developed in our laboratory has been found to be tolerant to the presence of salts and buffers in sample solutions. In this report, it was examined whether PESI is applicable to the sample solutions that contain high-concentration of detergents. It was found that PESI is highly tolerant to the presence of sodium dodecyl sulphate, cetyl trimethylamminium bromide, Triton X100 and 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate compared with conventional ESI and nanoESI. Therefore, PESI can be a potential analytical tool for direct analysis of protein extracts and digests containing high-concentration detergents.

Dynamics of the beta2-adrenergic G-protein coupled receptor revealed by hydrogen-deuterium exchange

To examine the molecular details of ligand activation of G-protein coupled receptors (GPCRs), emphasis has been placed on structure determination of these receptors with stabilizing ligands. Here we present the methodology for receptor dynamics characterization of the GPCR human beta(2) adrenergic receptor bound to the inverse agonist carazolol using the technique of amide hydrogen/deuterium exchange coupled with mass spectrometry (HDX MS). The HDX MS profile of receptor bound to carazolol is consistent with thermal parameter observations in the crystal structure and provides additional information in highly dynamic regions of the receptor and chemical modifications demonstrating the highly complementary nature of the techniques. After optimization of HDX experimental conditions for this membrane protein, better than 89% sequence coverage was obtained for the receptor. The methodology presented paves the way for future analysis of beta(2)AR bound to pharmacologically distinct ligands as well as analysis of other GPCR family members.

Organization of nucleobase-functionalized beta-peptides investigated by soft electrospray ionization mass spectrometry

The development and validation of analytical methods is a key to succeed in investigating noncovalent interactions between biomolecules or between small molecules and biomolecules. Electrospray ionization mass spectrometry (ESI-MS) was applied with a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) as well as a quadrupole/time-of-flight tandem mass spectrometer (QqToF-MS) for a systematic investigation of noncovalent complexes based on nucleobase pairing in an artificial and noncharged backbone topology. Synthetical beta-peptide helices covalently modified with nucleobases were organized by recognition of a sequence of four nucleobases. Specific duplexes of beta-peptide helices were obtained on the basis of hydrogen bonding base pair complementarity. Oligomer interactions were detected with defined stoichiometry and sensitivity for the respective duplex stability. FTICR-MS and QqToF-MS were used equally well to indicate double strand stabilities in agreement with the dissociation data determined by UV spectroscopy. Furthermore, the dissociation energies of gas phase ions of the noncovalent complexes were analyzed with collision induced dissociation (CID)-MS/MS and infrared multiphoton dissociation (IRMPD)-MS/MS. The CID conditions turned out to be too harsh for a differentiation of the duplex stabilities, whereas IRMPD might be developed as a technique to detect even small interaction energy differences.

Exploring metallodrug-protein interactions by mass spectrometry: comparisons between platinum coordination complexes and an organometallic ruthenium compound

Electrospray ionisation mass spectrometry was used to analyse the reactions of metal compounds with mixtures of selected proteins. Three representative medicinally relevant compounds, cisplatin, transplatin and the organometallic ruthenium compound RAPTA-C, were reacted with a pool of three proteins, ubiquitin, cytochrome c and superoxide dismutase, and the reaction products were analysed using high-resolution mass spectrometry. Highly informative electrospray ionisation mass spectra were acquired following careful optimisation of the experimental conditions. The formation of metal-protein adducts was clearly observed for the three proteins. In addition, valuable information was obtained on the nature of the protein-bound metallofragments, on their distribution among the three different proteins and on the binding kinetics. The platinum compounds were less reactive and considerably less selective in protein binding than RAPTA-C, which showed a high affinity towards ubiquitin and cytochrome c, but not superoxide dismutase. In addition, competition studies between cisplatin and RAPTA-C showed that the two metallodrugs have affinities for the same amino acid residues on protein binding.

Affinity capture using chimeric membrane proteins bound to magnetic beads for rapid ligand screening by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The rapid and specific detection of therapeutically important ligands in complex mixtures, that may bind to membrane proteins, remains challenging for many research laboratories and pharmaceutical industries. Through its use in the development of screening assays, mass spectrometry (MS) is currently experiencing a period of tremendous expansion. In the study presented here, we took advantage of the remarkable stability properties of a bacterial membrane protein, the KcsA K+ channel, produced in E. coli and purified as a tetrameric protein in the presence of a detergent. This membrane protein can subserve as a molecular template to display the pore-forming region of human K+ channels, which are considered as targets in the search for inhibitory ligands. The engineered chimeric proteins were linked to metal-bound magnetic beads, for the screening of complex peptide mixtures, such as that of scorpion venoms. The affinity-captured scorpion toxins were eluted prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), and to nano-electrospray ionization tandem mass QqTOF mass spectrometry (MS/MS) analysis. The de novo sequence of the toxins was deduced by combining the MS/MS fragmentation of the reduced form (up to the 33 first residues) and the trypsin digest peptides of the native toxins. This affinity-capture screening assay led to the isolation and characterization of potent and specific ligands of the human K+ channel, Kv1.3. The affinity-capture procedure is fast and reproducible. When linked to magnetic beads, the chimeric membrane protein can be re-used several times without losing any of its selectivity or specificity. This assay also benefits from the fact that it requires minimal amounts of animal venoms or complex mixtures, which can be expensive or difficult to procure.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2003-2004

This review is the third update of the original review, published in 1999, on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings the topic to the end of 2004. Both fundamental studies and applications are covered. The main topics include methodological developments, matrices, fragmentation of carbohydrates and applications to large polymeric carbohydrates from plants, glycans from glycoproteins and those from various glycolipids. Other topics include the use of MALDI MS to study enzymes related to carbohydrate biosynthesis and degradation, its use in industrial processes, particularly biopharmaceuticals and its use to monitor products of chemical synthesis where glycodendrimers and carbohydrate-protein complexes are highlighted.

Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges

Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H](5-) obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H](5-) ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug.

Biophysical characterisation of adducts formed between anticancer metallodrugs and selected proteins: new insights from X-ray diffraction and mass spectrometry studies

There is considerable interest today for the reactions of anticancer metallodrugs with proteins as these interactions might feature processes that are crucial for the biodistribution, the toxicity and even the mechanism of action of this important group of anticancer agents. We survey here the results of research activities carried out in our "Laboratory of Metals in Medicine" (Department of Chemistry, University of Florence) during the last three years, concerning the molecular characterisation of adducts formed between platinum, ruthenium and gold metallodrugs and a few model proteins. Valuable structural and functional information on these adducts could be derived from several biophysical studies mainly relying on the application of X-ray diffraction and ESI MS techniques. The value and the limitations of both approaches are outlined through a number of examples. Remarkably, the structural and functional information achieved on the respective metallodrug-protein adducts allowed us to identify some general trends in the reactivity of anticancer metallodrugs with protein targets.

Matrix-assisted ultraviolet laser desorption/ionization time-of-flight (UV-MALDI-TOF) mass spectra of N-acylated and N,O-acylated glycosylamines

Matrix-assisted ultraviolet laser desorption/ionization time-of-flight mass spectrometry (UV-MALDI-TOF-MS) has shown to be a very useful technique for the study of the non-volatile and thermally non-stable N-acylated glycopyranosyl- and glycofuranosyl-amines. Of the several matrices tested, 2,5-dihydroxybenzoic acid (DHB) was the most effective giving good spectra in the positive-ion mode. In the linear and reflectron modes, the [M+Na](+) ions appeared with high intensity. Their fragmentation patterns were investigated by post-source decay (PSD) UV-MALDI-TOF-MS showing mainly cross-ring cleavages. In addition, N,O-acylated glycopyranosyl- and glycofuranosyl-amines were also analyzed by this technique. PSD UV-MALDI-TOF-MS gave significant signals for several primary fragment ions, which were proposed but not detected, or observed with very low abundance, in electron ionization mass spectrometry (EI-MS) experiments.

Development and applications of surface-activated chemical ionization

This review regards the recently developed ionization source named surface-activated chemical ionization (SACI) that employs an interaction with a surface placed at low voltage for the activation of the ionization of sample molecules to increase the sensitivity in the analysis of various compounds of biological and clinical interest. These results are due to the strong chemical noise decrease and the increase of ionization efficiency. This ionization source has been employed for the analysis of various compounds of different molecular mass and polarity (addicted and pharmaceutical drugs, amino acids, steroids, peptides, and proteins). The SACI development theoretical mechanism, benefits, disadvantages, applications, and future developments are reported and discussed.

Gentle protein ionization assisted by high-velocity gas flow

Gentle protein electrospray ionization is achieved using the high-velocity gas flow of an air amplifier to improve desolvation in conventional ESI and generate intact folded protein ions in the gas phase. Comparisons are made between the ESI spectra of a number of model proteins, including ubiquitin, cytochrome c, lysozyme, and myoglobin, over a range of pH values under optimized conditions, with and without using an air amplifier to achieve high-velocity gas flow. Previously reported increased ion signals are confirmed. In addition, the peaks recorded using the air amplifier are shown to be narrower, corresponding to more complete desolvation. Significant changes in the charge-state distribution also are observed, with a shift to lower charge state at high-velocity flow. The relationship between the observed charge-state distribution and protein conformation was explored by comparing the charge-state shifts and the distributions of charge states for proteins that are or are not stable in their native conformations in low pH solutions. The data suggest retention of native or nativelike protein conformations using the air amplifier in all cases examined. This is explained by a mechanism in which the air amplifier rapidly creates small droplets from the original large ESI droplets and these microdroplets then desolvate without a significant decrease in pH, resulting in retention of the folded protein conformations. Furthermore, the holoform of ionized myoglobin is visible at pH 3.5, a much lower value than the minimum needed to see this form in conventional ESI. These results provide evidence for the importance of the conditions used in the desolvation process for the preservation of the protein conformation and suggest that the conditions achieved when using high-velocity gas flows to assist droplet evaporation and ion desolvation are much gentler than those in conventional ESI experiments.

An introduction to mass spectrometry based proteomics-detection and characterization of gonadotropins and related molecules

This review introduces fundamental aspects of mass spectrometry (MS) based proteomics and illustrates how MS is an effective tool for the analysis of glycoprotein hormones. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) and electrospray ionization (ESI) MS are complementary approaches that have been applied for the analysis of gonadotropins, e.g. to characterize differences in the oligosaccharide distribution of commercial human chorionic gonadotropin preparations, for isolated nicked beta-subunit, and identification of a metabolite of placental transforming growth factor in pharmaceutical hCG preparations. Immunoaffinity trapping and concentration of digested sample extract prior to MS analysis confers analytical sensitivity akin to immunoassay. A desirable objective would be to develop for clinical purposes a rapid procedure for MS detection and characterization of gonadotropins. Refinement of on-target immobilization and digestion for subsequent ionization by MALDI may eventually help to provide this capability. The advent of hybrid mass spectrometers will further advance the characterization of these complex molecules.

The suitability of different DHB isomers as matrices for the MALDI-TOF MS analysis of phospholipids: which isomer for what purpose?

Although the analysis of large biomolecules is the prime application of matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS), there is also increasing interest in lipid analysis. Since lipids possess relatively small molecular weights, matrix signals should be as small as possible to avoid overlap with lipid peaks. Although 2,5-dihydroxybenzoic acid (DHB) is an established MALDI matrix, the question whether just this isomer is ideal for lipid analysis was not yet addressed. UV absorptions of all six DHB isomers were determined and their laser desorption spectra recorded. In addition, all isomers were used as matrices to record positive and negative ion mass spectra of selected phospholipids (phosphatidylcholine and -serine): In the order 2,5-, 2,6-, 2,3- and 2,4-DHB, the quality of the positive ion lipid spectra decreases. This correlates well with the decreasing acidity of the applied DHB isomers. The 3,4- and 3,5- isomers give only very weak positive ion signals especially of acidic lipids. In contrast, the most suitable matrices in the negative ion mode are 2,5-, 2,4- and 3,5-DHB. 2,6-DHB does not provide any signal in the negative ion mode due to its marked acidity. Finally, differences in the crystallization behavior of the pure matrix and the matrix/lipid co-crystals were also monitored by atomic force microscopy (AFM): 2,5-DHB gave the smallest crystals and the skinniest layer. It is concluded that basically all DHB isomers can be used as MALDI matrices but the 2,5-isomer represents the most versatile compound.

New insights into the glycosylation of the surface layer protein SgsE from Geobacillus stearothermophilus NRS 2004/3a

The surface of Geobacillus stearothermophilus NRS 2004/3a cells is covered by an oblique surface layer (S-layer) composed of glycoprotein subunits. To this S-layer glycoprotein, elongated glycan chains are attached that are composed of [-->2)-alpha-l-Rhap-(1-->3)-beta-l-Rhap-(1-->2)-alpha-L-Rhap-(1-->] repeating units, with a 2-O-methyl modification of the terminal trisaccharide at the nonreducing end of the glycan chain and a core saccharide as linker to the S-layer protein. On sodium dodecyl sulfate-polyacrylamide gels, four bands appear, of which three represent glycosylated S-layer proteins. In the present study, nanoelectrospray ionization time-of-flight mass spectrometry (MS) and infrared matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry were adapted for analysis of this high-molecular-mass and water-insoluble S-layer glycoprotein to refine insights into its glycosylation pattern. This is a prerequisite for artificial fine-tuning of S-layer glycans for nanobiotechnological applications. Optimized MS techniques allowed (i) determination of the average masses of three glycoprotein species to be 101.66 kDa, 108.68 kDa, and 115.73 kDa, (ii) assignment of nanoheterogeneity to the S-layer glycans, with the most prevalent variation between 12 and 18 trisaccharide repeating units, and the possibility of extension of the already-known -->3)-alpha-l-Rhap-(1-->3)-alpha-l-Rhap-(1--> core by one additional rhamnose residue, and (iii) identification of a third glycosylation site on the S-layer protein, at position threonine-590, in addition to the known sites threonine-620 and serine-794. The current interpretation of the S-layer glycoprotein banding pattern is that in the 101.66-kDa glycoprotein species only one glycosylation site is occupied, in the 108.68-kDa glycoprotein species two glycosylation sites are occupied, and in the 115.73-kDa glycoprotein species three glycosylation sites are occupied, while the 94.46-kDa band represents nonglycosylated S-layer protein.

Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface

We report on a new electrodynamic ion funnel that operates at a pressure of 30 torr with no loss of ion transmission. The enhanced performance compared with previous ion funnel designs optimized for pressures of <5 torr was achieved by reducing the ion funnel capacitance and increasing the RF drive frequency (1.7 MHz) and amplitude (100-170 V peak-to-peak). No degradation of ion transmission was observed for pressures from 2 to 30 torr. The ability to operate at higher pressure enabled a new tandem ion funnel mass spectrometer interface design that can accommodate a greater gas load (e.g., from an ESI source). When combined with a multicapillary inlet, the interface provided more efficient introduction of ions, resulting in a significant enhancement in mass spectrometer sensitivity and detection limits.

Assays of Endogenous Caspase Activities: A Comparison of Mass Spectrometry and Fluorescence Formats

This paper describes a label-free assay for measuring endogenous caspase protease activities in cell lysates. The assay format, termed SAMDI-MS (self-assembled monolayers for matrix assisted laser desorption ionization time-of-flight mass spectrometry), is based on the enzymatic modification of peptides immobilized to monolayer substrates, followed by direct detection of the products with mass spectrometry. Monolayers presenting peptide substrates for either caspase-3 or -8 were treated with lysates from Jurkat cells that were stimulated with staurosporine and SKW6.4 cells that were stimulated with LzCD95L. In both cases, the SAMDI assays reported on the activation of endogenous caspase enzymes with levels of detection that are similar to those observed using the commonly employed fluorogenic assays. The use of longer peptide substrates, which are not compatible with the fluorogenic assays, provided for a better resolution of the two caspase activities. This work is significant because it demonstrates that the SAMDI assay can be used to measure endogenous enzyme activities and because it avoids the loss of activity and specificity that often accompany label-dependent assay formats.

Manufacturing of recombinant therapeutic proteins in microbial systems

Recombinant therapeutic proteins have gained enormous importance for clinical applications. The first recombinant products have been produced in E. coli more than 20 years ago. Although with the advent of antibody-based therapeutics mammalian expression systems have experienced a major boost, microbial expression systems continue to be widely used in industry. Their intrinsic advantages, such as rapid growth, high yields and ease of manipulation, make them the premier choice for expression of non-glycosylated peptides and proteins. Innovative product classes such as antibody fragments or alternative binding molecules will further expand the use of microbial systems. Even more, novel, engineered production hosts and integrated technology platforms hold enormous potential for future applications. This review summarizes current applications and trends for development, production and analytical characterization of recombinant therapeutic proteins in microbial systems.

Tandem mass spectrometry of coprogen and deferoxamine hydroxamic siderophores

Mechanisms of fragmentation of hydroxamic siderophores are proposed comparing deuterated and nondeuterated samples. Standard siderophores (e.g. deferoxamine and coprogen) were directly injected into both ion trap and linear quadrupole mass spectrometers with electrospray ionization (ESI). Four and two fragmentation steps were carried out for deferoxamine and coprogen (analyzed by positive and negative ESI, respectively). Deferoxamine cleavages occurred in both peptide and hydroxamic bonds while the coprogen fragmentation pattern is more elaborate, since it contains Fe(III) in its structure.

Surface-activated chemical ionization ion trap mass spectrometry in the analysis of drugs in dilute urine samples. Part II: analysis of morphine and other street drugs

The new ionization method, called surface-activated chemical ionization (SACI), was employed for the analysis of fives drugs (morphine, codeine, 6-monoacetylmorphine (6-MAM), benzoylecgonine and cocaine) by ion trap mass spectrometry. The results so obtained have been compared with those achieved by using atmospheric pressure chemical ionization (APCI), no-discharge-APCI and electrospray ionization (ESI) clearly showing that SACI is the most sensible one mainly due to the high ionization efficiency and the lower chemical noise. The performance of SACI in terms of sensitivity and linearity was compared with the sensitivity and linearity obtained using APCI, no-discharge-APCI and ESI, showing that the new SACI approach gives rise to the best results. Then, SACI was used to analyze morphine, codeine, 6-MAM, benzoylecgonine and cocaine in urine samples. After the optimization of the instrumental parameters for a mixture of the standard compounds, eight urine samples were analyzed. They were strongly diluted (1 : 20 and 1 : 100) in order to prevent the chromatographic column damage due to the matrix composition. Furthermore, the diluted urine samples were directly analyzed, without pretreatment, through LC-MS and LC-MS/MS, and the obtained results are reported.

The role of different phenomena in surface-activated chemical ionization (SACI) performance

In previous studies, the production of ions in an APCI source without any corona discharge was observed, and the intensity of the ion signals showed significant increases on placing a metallic surface at 45 degrees inside an orthogonal ion source. This method was named surface-activated chemical ionization (SACI). The present study was performed to investigate the mechanisms of ion production with or without the presence of the metallic surface, by varying instrumental parameters and the geometrical configuration. Approximate calculations show that, in the absence of corona discharge and of any additional surfaces, ions cannot be produced by collisional phenomena, because of their low kinetic energy, in the 10(-2) to 10(-3) eV range. Two alternative possibilities have been considered: the first takes into account that ions may originate by collision of neutral clusters of polar solvent molecules with the APCI source surfaces through clusterelectric effect. The second takes into account that the water dissociation constant k(w) is temperature dependent, passing from 10(-14.1669) at 20 degrees C to 10(-12.4318) at 90 degrees C. It means that the [H(+)] varies from 8.3 x 10(-8) to 6.1 x 10(-7) M going from 20 to 90 degrees C. Hence, at the high temperatures experimented in the APCI vaporizer, H(+) becomes available in solution in molar quantities analogous to those of analyte, and the protonation of the analyte itself can consequently occur. The activation of further ionization processes in the presence of the metallic surface can be reasonably attributed to interactions between gas-phase analyte molecules and solvent molecules adsorbed on the surface. Experiments performed with a thin layer of deuterated glycerol on the surface led to unequivocal results, i.e. the production of [M + D](+) ions of the analyte.

A review of current applications of mass spectrometry for biomarker/molecular tracer elucidation

Mass spectrometry, especially coupled with gas chromatography or tandem, is the analytical method of choice in elucidation of biomarker compounds present in organic mixtures extracted from geological, environmental, or biological samples. This review describes the biomarker concept; i.e., the precursor natural products to the geological/environmental derivatives, and their application as tracers in the geosphere and ambient environment. The mass spectrometric methods currently utilized for such analyses are reviewed, and typical examples of applications are described with a general key to the literature.

Direct correlation of the crystal structure of proteins with the maximum positive and negative charge states of gaseous protein ions produced by electrospray ionization

Electrospray mass spectrometric studies in native folded forms of several proteins in aqueous solution have been performed in the positive and negative ion modes. The mass spectra of the proteins show peaks corresponding to multiple charge states of the gaseous protein ions. The results have been analyzed using the known crystal structures of these proteins. Crystal structure analysis shows that among the surface exposed residues some are involved in hydrogen-bonding or salt-bridge interactions while some are free. The maximum positive charge state of the gaseous protein ions was directly related to the number of free surface exposed basic groups whereas the maximum negative charge state was related to the number of free surface exposed acidic groups of the proteins. The surface exposed basic groups, which are involved in hydrogen bonding, have lower propensity to contribute to the positive charge of the protein. Similarly, the surface exposed acidic groups involved in salt bridges have lower propensity to contribute to the negative charge of the protein. Analysis of the crystal structure to determine the maximum charge state of protein in the electrospray mass spectrum was also used to interpret the reported mass spectra of several proteins. The results show that both the positive and the negative ion mass spectra of the proteins could be interpreted by simple consideration of the crystal structure of the folded proteins. Moreover, unfolding of the protein was shown to increase the positive charge-state because of the availability of larger number of free basic groups at the surface of the unfolded protein.

Mass spectrometry in metabolome analysis

In the post-genomic era, increasing efforts have been made to describe the relationship between the genome and the phenotype in cells and organisms. It has become clear that even a complete understanding of the state of the genes, messages, and proteins in a living system does not reveal its phenotype. Therefore, researchers have started to study the metabolome (or the metabolic complement of functional genomics). Within this context, mass spectrometry (MS) has increasingly occupied a central position in the methodologies developed for determination of the metabolic state. This review is mainly focused on the status of MS in the metabolome field, trying to direct the reader to the main approaches for analysis of metabolites, reviewing basic methodologies in sample preparation, and the most recent MS techniques introduced. Apart from the description of the different methods, this review will try to state a general comparison between the several different techniques that involve MS and metabolite analysis, and will highlight their limitations and preferred applicability.

On-Probe Sample Preparation without Washes for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using an Anion Exchange Medium

When the mass spectra of biological samples (proteins, peptides, and so on) are obtained routinely by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), a serious problem is the reduction of the ionization efficiency by impurities, such as buffer salts and detergents. We focused our attention on devising a method to maintain the ionization efficiency of protein samples, even in the presence of sodium dodecyl sulfate (SDS), without any extra purification step. Although no protein ion peaks are observed in the presence of 2.5% SDS with the usual methods, the addition of a granular anion exchange silica gel to the matrix solution allowed the protein ion peaks to be obtained with an excellent signal-to-noise ratio. Together with other supporting experiments, we suggest that the positively charged surface (the basic environment derived from the anion exchange groups) and the roughness of the particles were important for good ionization in the presence of a high SDS concentration. For a very uneven surface, the SDS might be absorbed into the particle interiors during the process of cocrystallization with the matrix and analytes, which is known as the molecular sieve effect, and the SDS concentration in the surface crystalline film might be reduced. As a result, we developed an on-probe sample preparation method without washes for MALDI, using a strong anion exchange silica gel. This method is applicable even in the presence of 2.5% SDS, and is not only very simple but also inexpensive, because it can be used with the standard MALDI target plates.

Proteomic approaches in the search for disease biomarkers

Significant technological advances in protein chemistry, physics and computer sciences in the last two decades have greatly improved protein separation methodologies, such as electrophoresis and chromatography, and have established mass spectrometry (MS) as an indispensable tool for protein study. The goal of this review is to provide a brief overview of the recent improvements in these methodologies and present examples from their application in proteome analysis and search for disease biomarkers.

Porous polymer monolith assisted electrospray from a glass microdevice

The coupling of a lab-on-a-chip microfluidic device to a nanoelectrospray ionization mass spectrometer has the potential to automate many routine analytical procedures and produce a powerful analytical tool. However, past coupling strategies have relied on complex manufacturing steps including drilling and etching the device to attach a capillary or building a nanospray emitter directly into the device. This study shows that a nanospray emitter can be easily fabricated using a porous polymer monolith (PPM) at the end of a glass microdevice. These devices are able to obtain a stable electrospray at a variety of flow rates (50-500 nL/min) but optimal results are obtained at lower flow rates (50-100 nL/min) compatible with electroosmotic flow processes. The PPM is photo-patterned so that it can be placed in any position within the channel of the device with no dead volume. The porous character and the hydrophobic nature of the PPM both aid in development of a stable electrospray process. Total ion current traces for the constant infusion of leucine-enkephalin and PPG show relative standard errors as low as 4%, and produce mass spectra with good signal-to-noise (S/N 43) from only 2 fmol of material. In addition, multiple experiments in a given day show good repeatability with variability as low as 13%, and the multiple flow paths inherent in the PPM limit sprayer clogging.

Optical detection methods for mass spectrometry of macroions

Detection of macroions has been a challenge in the field of mass spectrometry. Conventional ionization-based detectors, relying on production and multiplication of secondary electrons, are restricted to detection for charged particles of m/z < 1 x 10(6). While both energy-sensitive and charge-sensitive detectors have been developed recently to overcome the limitation, they are not yet in common use. Photon-sensitive detectors are suggested to be an alternative, with which detection of macroions (or charged particles) by either elastic light scattering (ELS) or laser-induced fluorescence (LIF) has been possible. In this article, we provide a critical review on the developments of novel optical detection methods for mass spectrometry of macroions, including both micron-sized and nano-sized synthetic polymers as well as high-mass biomolecules. Design and development of new spectrometers making possible observations of the mass spectra of macroions with sizes in the range of 10-10(3) nm or masses in the range of 1-10(6) MDa are illustrated. The potential and promise of this optical approach toward macroion detection with high efficiency are discussed in practical aspects.

Carbohydrate–carbohydrate interactions in cell recognition

Obtaining a better understanding of the molecular basis of cell recognition remains an important challenge with regard to the social functioning of cells in multicellular systems. The wide structural diversity of carbohydrates allows many combinatorial possibilities for fine-tuning cell-cell and cell-matrix recognition in multicellular organisms. Direct carbohydrate-carbohydrate interaction would endow both the flexibility and the specificity of reversible contacts at the cell surface during the formation, maintenance and pathogenesis of tissues. The recent development of methods for the characterization of such interactions will help to expand our knowledge of the mechanisms that trigger early events in cell recognition.

Porous Polymer Monolith Assisted Electrospray

Coupling low-flow analytical separation instrumentation such as capillary electrophoresis, capillary electrochromatography, nano-HPLC, and microfluidic-based devices with electrospray ionization mass spectrometry has yielded powerful analytical tools. However, conventional coupling methodologies such as nanospray suffer from limitations including poor conductive coating robustness, constant clogging, complicated fabrication processes, and incompatibility with large flow rate regimes. This study demonstrates that robust nanospray emitters can be fabricated through the formation and utilization of a porous polymer monolith (PPM) at the end of a fused-silica capillary. Stable electrosprays can be produced from capillaries (75-100-microm i.d.) at a variety of flow rates (50-1000 nL/min) without the need to taper the capillaries by etching or pulling. The PPM is photopatterned to be present only near the capillary exit aperture using conditions that generate pore sizes similar to those seen with nanospray tips. The porous nature of the PPM aids in developing a stable electrospray generating a single clearly visible Taylor cone at relatively high flow rates while at low flow rates (<100 nL/min) a mist, presumably from multiple small Taylor cones, develops. The hydrophobic nature of the PPM should limit problems with band broadening associated with droplet spreading at the capillary exit, while the multiple flow paths inherent in the PPM minimize clogging problems associated with conventional nanospray emitters. Total ion current traces for a constant infusion of standard PPG and cytochrome c solutions are very stable with deviations ranging from only 3 to 8%. The PPM-assisted electrospray produces mass spectra with excellent signal-to-noise ratios from only a few femtomoles of material.