Decomposition of protein nitrosothiolsin matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry

The S-nitrosylation of proteins is involved in the trafficking of nitric oxide (NO) in intra- and extracellular milieus. To establish a mass spectrometric method for identifying this post-translational modification of proteins, a synthetic peptide and transthyretin were S-nitrosylated in vitro and analyzed by electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The intact molecular ion species of nitrosylated compounds was identified in the ESI mass spectrum without elimination of the NO group. However, the labile nature of the S-NO bond was evident when the in-source fragmentation efficiently generated [M + H - 30](+) ions. The decomposition was prominent for multiply charged transthyretin ions with high charge states under ordinary ESI conditions, indicating that the application of minimum nozzle potentials was essential for delineating the stoichiometry of nitrosylation in proteins. With MALDI, the S-NO bond cleavage occurred during the ionization process, and the subsequent reduction generated [M + H - 29](+) ions.     

Characterization of plant oligosaccharides by matrix-assisted laser desorption/ionization and electrospray mass spectrometry

Structural characterization of arabinoxylans from wheat by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry using a Q-TOF mass analyser (ESI-Q-TOF) or an ion trap (IT) mass analyser is presented. An arabinoxylan sample digested with endoxylanase A was analysed using MALDI-TOF mass spectrometry (MS), resulting in the identification of molecular ions for structures with up to 22 monosaccharide residues. As the two-component monosaccharides xylose and arabinose are isobaric, structures differing in the number of arabinose branching residues were indistinguishable based on molecular mass and also fragmentation pattern upon collision-induced dissociation (CID). Permethylation followed by ESI-CID analyses using ITMS was performed to obtain structural information regarding the number of arabinose branching residues and their spatial arrangement along the xylose backbone. Analysis of the signal corresponding to an oligomer with six monosaccharide residues showed the presence of at least four isomeric structures differing in degree of branching and position of the branched residue relative to the cleavage site of the enzyme. This is the first demonstration of the use of ESI-ITMS for the structural characterization of arabinoxylan mixtures.     

Oxidized carbon nanotubes as matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of biomolecules

Oxidized carbon nanotubes (CNTs), which can form a stable homogeneous suspension in water close to a solution phase, were synthesized and used for matrix-assisted desorption/ionization mass spectrometric (MALDI-MS) analysis of biomolecules. Infrared (IR) spectra, transmission electron microscopy (TEM) and particle size analysis were used for the characterization of the oxidized CNTs. The results indicate that the physical structure of the CNTs was not damaged, but carboxylate groups were introduced onto the surface of the CNTs. In addition, impurities including amorphous carbon, which is one of the main reasons for ion source contamination, were destroyed by the oxidization. The carboxyl groups on the oxidized surface of the CNTs can not only provide an additional proton source, but can also increase the surface polarity and solubility of the CNTs, making it easier to manipulate which is important for MALDI analysis of some biomolecules, especially larger peptides and proteins. The oxidized CNTs were successfully applied to the analysis of neutral oligosaccharides, peptides, and insulin, and thus promise to be an efficient matrix for MALDI-MS analysis of biomolecules.     

Characterization of polyethylenimine by electrospray ionization and matrix-assisted laser desorption/ionization

Branched polyethylenimines (PEIs) with lower average molecular weights (600, 1200 and 1800 Da) have been studied by Electrospray Ionization (ESI) and Matrix‐Assisted Laser Desorption/Ionization (MALDI) mass spectrometry. In both, ESI and MALDI mass spectra, the main distribution arises from protonated PEI oligomers with NH₂ end groups, [PEI + H]⁺, which are observed at m/z 43n + 18. A trace of sodium contamination in the PEI samples results in the presence of a series that appears at m/z 43n + 40 [PEI + Na]⁺. However, only the MALDI mass spectra show a [PEI + K]⁺ series at m/z 43n + 56, because of matrix contamination with potassium, and a series generated by condensation of the matrix with PEI at m/z 43n + 30. Collisionally activated dissociation tandem mass spectrometry (CAD (MS/MS)) of protonated PEI oligomers is shown to yield three fragment ion series b_n, and K_n. The experiments have demonstrated the capabilities of these mass spectrometry techniques, along with CAD MS/MS to detect and characterize such polar synthetic polymers. Copyright © 2011 John Wiley & Sons, Ltd.     

Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification

We describe a new interface for a prototype quadrupole-quadrupole-time-of-flight (TOF) mass spectrometer (Centaur, Sciex) that allows rapid switching between electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) modes of operation. Instrument performance in both modes is comparable (i.e., resolution approximately 10,000 FWHM, mass accuracy <10 ppm, sensitivity approximately 1 fmol) because the ion source is decoupled from the TOF mass analyzer by extensive gas collisions in the quadrupole stages of the instrument. The capacity to obtain side-by-side high quality ESI and MALDI mass spectra from a single proteolytic mixture greatly facilitates the identification of proteins and elucidation of their primary structures. Improved strategies for protein identification result from this ability to measure spectra using both ionization modes in the same instrument and to perform MS/MS on singly charged as well as multiply charged ions. Examples are provided to demonstrate the utility and performance of the modified instrument.     

Direct matrix-assisted laser desorption ionization mass spectrometric analysis of proteins immobilized on nylon-based membranes

Direct analysis of proteins adsorbed onto the surface of nylon membranes has been performed at the picomole level by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Nylon-66 and positive charge-modified nylon (Zetabind) membranes fixed to MALDI probe tips were successfully employed to analyze picomole quantities of sample that were adsorbed onto these inert supports prior to adding a matrix-containing solution. Proteins and peptides are readily solubilized from these types of membrane with conventional matrix solvents and cocrystallize with the matrix on the membrane surface. Because solubilization of membrane-adsorbed protein is necessary for successful sample preparation, nylon membranes are more suitable for use with MALDI-MS than other protein transfer membranes such as polyvinylidene difluoride or nitrocellulose. When compared to samples prepared conventionally, no apparent loss of sensitivity or resolution is observed when analysis by MALDI-MS is performed from nylon-66 or positive charge-modified nylon membranes. Detection limits and resolution are not apparently affected by the membrane immobilization/washing procedure, and no change in the mass accuracy is observed when analysis is performed on the nylon surface. However, there is a time shift (increase) in ion flight time when analysis by MALDI-time-of-flight-MS is performed directly from the membrane fixed to the probe tip (about 200 ns for an ion of mass 379.3). To maintain mass accuracy, the use of internal standards or external calibration performed on a membrane support was necessary. The immobilization of proteins on nylon membranes can be used to facilitate removal of water-soluble contaminants because the sample is retained when the membrane is immersed in water prior to adding the matrix solution. The feasibility of performing both chemical and enzymatic modifications of proteins adsorbed onto inert nylon supports prior to analysis by MALDi-MS is also demonstrated.     

Structural features of polyacylated anthocyanins using matrix-assisted laser desorption/ionization and electrospray ionization time-of-flight mass spectrometry

In our continuing studies to isolate water-soluble vacuolar pigments, we expect to elucidate more structural details using mass spectrometry (MS). Because of its sensitivity, only a small amount of pigment extracted from natural plants is required for MS measurement. Nuclear magnetic resonance is also a useful spectroscopic method for structural determination. In this study, two soft ionization techniques, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI), on time-of-flight (TOF) mass spectrometers, were used to analyze five polyacylated anthocyanins with more than two aromatic acid molecules in the side chains. ESI is advantageous for the detection of individual molecular ions, while MALDI is essential for the detection of characteristic fragment ions originating from the anthocyanidin. Although 2,5-dihydroxybenzoic acid (DHBA) is an effective matrix in MALDI-TOFMS to obtain informative fragment ions of polyacylated anthocyanins, α-cyano-4-hydroxycinnamic acid (CHCA) is the preferred matrix for the identification of aglycones. In particular, in measurements of polyacylated anthocyanins with two acylated glycoside chains, fragment ions originating from anthocyanidin can only be observed in MALDI-TOFMS using CHCA as the matrix.     

Matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometric study of 2,3-dihydro-1,4-benzoxazepines

Fragmentations of the protonated adduct ions [M+H](+) of seven 1,4-benzoxazepine derivatives were studied using 'post-source decay' matrix-assisted laser desorption/ionization (PSD MALDI) and electrospray nozzle-skimmer collisionally induced dissociation (ESI-CID) mass spectrometric methods. It was found that both methods generated mainly product ions arising from the cross-ring cleavages of the benzoxazepine ring. Similar product ions were generated under MALDI and ESI conditions; however, it was observed that the loss of the alkylene unit from the N-substituted benzoxazepine, and the loss of a H(2)X molecule (where X = O or S), are more preferred under ESI conditions. Based on the experimental results a mechanism is also proposed for the fragmentation of the oxazepines studied.     

Investigation of methods suitable for the matrix-assisted laser desorption/ionization mass spectrometric analysis of proteins from ribonucleoprotein complexes

A variety of protein isolation and purification techniques for ribonucleoprotein (RNP) complexes were investigated for their compatibility with downstream analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Ribosomal proteins from Escherichia coli 70S ribosomes were obtained using methods such as phenol extraction and precipitation by organic solvents or acids. Under optimal conditions, more than 90% of the expected ribosomal proteins were detected in a single MALDI-MS experiment. The most effective approach combined ribosome denaturation by buffer exchange with acid precipitation of the ribosomal ribonucleic acids. An improved acid precipitation approach, involving the sequential additions of acetic and trifluoroacetic acid, yielded more complete protein coverage while minimizing loss of ion signal from lower molecular weight proteins. With phenol extraction, substantial gains in ion abundance of higher molecular weight proteins are noted, although some of the lower molecular weight proteins were not efficiently extracted. These results illustrate several effective approaches for protein isolation from protein complexes such as RNPs that are MALDI-MS compatible, and these approaches should extend the use of MALDI-MS for proteomics-based analyses of other protein-nucleic acid complexes.     

基质辅助激光解吸电离质谱和电喷雾电离质谱在辣根过氧化物酶糖肽结构分析中的应用

糖链结构的质谱解析是今后糖蛋白分析中的重要研究内容,其中完整糖肽的分析,由于可以同时获得糖基化位点和对应糖链的结构信息,更具有重要意义和研究前景。本工作对质谱软电离技术在完整糖肽分析中的应用进行了研究,其中包括了基质辅助激光解吸电离(matrix-assisted laser desorption ionization, MALDI)和电喷雾电离(electrospray ionization, ESI)技术。通过平行使用两种串联质谱(tandem mass spectrometry, MS/MS)分析策略: MALDI-MS/MS和ESI-MS/MS对目标糖蛋白——辣根过氧化物酶进行分析,并讨论了其互补性。结果表明,MALDI和ESI技术各有优劣,结合串联质谱分析,可获得糖肽的糖链结构信息;两条路线互补使用,在揭示蛋白质糖基化修饰(位点和结构)的研究中十分必要。     

N-Alkylpyridinium isotope quaternization for matrix-assisted laser desorption/ionization Fourier transform mass spectrometric analysis of cholesterol and fatty alcohols in human hair

Isotope-coded reagents have been developed for labeling of amino acids, phenols and fatty acids, but not for alcohols. In this work, a simple reaction based on direct N-alkylpyridinium isotope quaternization (NAPIQ) was developed for mild derivatization of cholesterol and fatty alcohols. Different from the conventional quaternary reagents with cations on themselves, two simple and charge-neutral reagents: pyridine and d₅-pyridine directly attached N-cationic tag onto the target compounds in the presence of trifluoromethanesulfonic anhydride (Tf₂O) without tedious sample preparation. The derivatization completed in 5 min and achieved charge labeling of the target compounds, which significantly improved the detection limits of analytes by 10³-folds in further analysis by matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI–FTMS). The use of commercially available d₀/d₅-pyridine pairs facilitated isotope-coded chemical derivatization and avoided the use of isotope-labeled internal standards; the excess pyridine did not affect the signals of analytes. Utility of the NAPIQ method was examined in the identification of cholesterol and fatty alcohols in small amount of human hair sample (<0.5 mg). The fluctuation of total cholesterol in human body was profiled during time by quantitatively comparing the different segments of a single strand of hair. This study combines the direct pyridinium quaternization with MALDI–FTMS, which offers a perspective and an alternative tool for the identification and quantification of substances in biological matrix by comparing d₀/d₅ pairs, especially when isotope-labeled internal standards are unavailable.     

Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Serum profiling by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) holds promise as a clinical tool for early diagnosis of cancer and other human diseases. Sample preparation is key to achieving reproducible and well-resolved signals in MALDI-MS; a prerequisite for translation of MALDI-MS based diagnostic methods to clinical applications. We have investigated a number of MALDI matrices and several miniaturized solid-phase extraction (SPE) methods for serum protein concentration and desalting with the aim of generating reproducible, high-quality protein profiles by MALDI-MS. We developed a simple protocol for serum profiling that combines a matrix mixture of 2,5-dihydroxybenzoic acid and alpha-cyano-4-hydroxycinnamic acid with miniaturized SPE and MALDI-MS. Functionalized membrane discs with hydrophobic, ion-exchange or chelating properties allowed reproducible MALDI mass spectra (m/z 1000-12,000) to be obtained from serum. In a proof-of-principle application, SPE with chelating material and MALDI-MS identified protein peaks in serum that had been previously reported for distinguishing a person diagnosed with breast cancer from a control. These preliminary results indicate that this simple SPE/MALDI-MS method for serum profiling provides a versatile and scalable platform for clinical proteomics.     

Development of a dual-spray electrospray deposition system for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A new method of matrix-assisted laser desorption/ionization (MALDI) sample preparation using a dual-spray electrospray deposition system is demonstrated and employed for the investigation of gas-phase cationization reactions in the MALDI plume. The dual-spray electrospray system is found to increase the homogeneity of the sample similarly to that of a conventional single-spray electrospray system. The dual-spray electrospray system allows for intimate mixing of separately prepared sample components and results in improved quantitative results. The development of this device also leads to the possibility of mixing sample components prepared in different solvents without the need to be concerned with solvent miscibility.     

Evaluation of combined matrix-assisted laser desorption/ionization time-of-flight and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry experiments for peptide mass fingerprinting analysis

Peptide Mass Fingerprinting (PMF) is still of significant interest in proteomics because it allows a large number of complex samples to be rapidly screened and characterized. The main part of post-translational modifications is generally preserved. In some specific cases, PMF suffers from ambiguous or unsuccessful identification. In order to improve its reliability, a combined approach using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) was evaluated. The study was carried out on bovine serum albumin (BSA) digest. The influence of several important parameters (the matrix, the sample preparation method, the amount of the analyte) on the MOWSE score and the protein sequence coverage were evaluated to allow the identification of specific effects. A careful investigation of the sequence coverage obtained by each kind of experiment ensured the detection of specific peptides for each experimental condition. Results highlighted that DHB-FTICRMS and DHB- or CHCA-TOFMS are the most suited combinations of experimental conditions to achieve PMF analysis. The association (convolution) of the data obtained by each of these techniques ensured a significant increase in the MOWSE score and the protein sequence coverage.     

Improved matrix-assisted laser desorption/ionization mass spectrometric detection of glycosaminoglycan disaccharides as cesium salts

Ultraviolet matrix-assisted laser desorption/ionization mass spectrometric (UV-MALDI-MS) analysis of highly acidic, thermally labile species such as glycosaminoglycan-derived oligosaccharides is complicated by their poor ionization efficiency and tendency to fragment through the loss of sulfo groups. We have utilized a systematic approach to evaluate the effect of alkali metal counterions on the degree of fragmentation through SO3 loss from a highly sulfated model compound, sucrose octasulfate (SOS). The lithium, sodium, potassium, rubidium, and cesium salts of SOS were analyzed by UV-MALDI-time-of-flight (TOF)MS using an ionic liquid matrix, bis-1,1,3,3-tetramethylguanidinium alpha-cyano-4-hydroxycinnamate. The positive-ion and negative-ion MALDI mass spectra of five alkali metal salts of SOS were compared in terms of the degree of analyte fragmentation through the SO3 loss and the absolute intensity of a molecular ion signal. Experimental results demonstrate that the lithium, sodium, and potassium salts of SOS undergo some degree of fragmentation through the loss of SO3, whereas the fragmentation through the loss of SO3 in the rubidium and cesium salts of SOS is suppressed. A high detection sensitivity associated with the stability of sulfate half-esters was achieved for the cesium salt of SOS using positive-ion detection. Finally, the cesium salt of chondroitin sulfate A disaccharide was successfully analyzed using UV-MALDI-TOFMS.     

Reproducibility of serum protein profiling by systematic assessment using solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Protein profiling of human serum by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is potentially a new diagnostic tool for early detection of human diseases, including cancer. Sample preparation is a key issue in MALDI MS and the analysis of complex samples such as serum requires optimized, reproducible methods for handling and deposition of protein samples. Data acquisition in MALDI MS is also a critical issue, since heterogeneity of sample deposits leads to attenuation of ion signals in MALDI MS. In order to improve the robustness and reproducibility of MALDI MS for serum protein profiling we investigated a range of sample preparation techniques and developed a statistical method based on repeated analyses for evaluation of protein-profiling performance of MALDI MS. Two different solid-phase extraction (SPE) methods were investigated, namely custom-made microcolumns and commercially available magnetic beads. Using these two methods, nineteen different sample preparation methods for serum profiling by MALDI MS were systematically tested with regard to matrix selection, stationary phase, selectivity, and reproducibility. Microcolumns were tested with regard to chromatographic properties; reversed phase (C8, C18, SDB-XC), ion-exchange (anion, weak cation, mixed-phase (SDB-RPS)) and magnetic beads were tested with regard to chromatographic properties; reversed phase (C8) or affinity chromatography (Cu-IMAC). The reproducibility of each sample preparation method was determined by enumeration and analysis of protein signals that were detected in at least six out of nine spectra obtained by three triplicate analyses of one serum sample.A candidate for best overall performance as evaluated by the number of peaks generated and the reproducibility of mass spectra was found among the tested methods. Up to 418 reproducible peaks were detected in one cancer serum sample. These protein peaks can be part of a possible diagnostic profile, suggesting that this sample preparation method and data acquisition approach is suitable for large-scale analysis of serum samples for protein profiling.     

Quantitative aspects in electrospray ionization ion trap and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of malto-oligosaccharides

Mass spectrometry is widely applied in carbohydrate analysis, but still quantitative evaluation of data is critical due to different ionization efficiencies of the constituents in a mixture. Different size and chemical structure of the analytes cause their uneven distribution in droplets (electrospray ionization, ESI) or matrix spots (matrix-assisted laser desorption/ionization, MALDI). In addition, instrumental parameters affect final ion yields. In order to study and optimize the latter, an equimolar mixture of malto-oligosaccharides (DP1-6) was analyzed using varying target masses for ESI as well as different matrices and laser power for MALDI. The sodium adducts and derivatives for positive ion mode (hydrazones with Girard's T Reagent, GT) and negative ion mode (reductively aminated with o-aminobenzoic acid, oABA) were studied. Negatively charged oABA-labeled malto-oligosaccharides turned out to be unsuitable for quantification of the malto-oligomeric composition. Best agreement was achieved when applying target masses in the range of the highest homolog in the mixture in electrospray ionization ion trap (ESI-IT) (1-2% deviation with GT label or as Na(+) adducts). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) gave best results when the laser power was adjusted significantly over the desorption/ionization threshold (1% deviation with GT label). Both parameters show significant influence on the determined oligomeric composition. Consequently, estimation and even quantitative determination of amounts of oligosaccharides in a mixture can be achieved when the analytes are labeled and the proper instrumental parameters are used.     

Liquid secondary ionization,tandem and matrix-assisted laser desorption/ionization time-of-flight mass spectrometric characterization of glycosphingolipid derivatives

Permethylated, peracetylated and perbenzoylated derivatives of glycosphingolipids (GSLs) were prepared to compare their liquid secondary ionization mass spectrometric (LSIMS) and collision-induced dissociation tandem mass spectrometric (CID/MS/MS) fragmentation patterns and also to determine sensitivity improvement in LSIMS and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) relative to the native species. Permethylation was carried out in the liquid phase, whereas peracetylation and perbenzoylation could be effected using either liquid (bulk)-phase or gas-phase procedures. Lower amounts of starting material were required for the gas-phase derivatization (? 100 pmol) compared with the bulk phase (?1 nmol), because the former method permits more efficient sample handling. All three types of derivatives yielded sensitivity improvements of at least two orders of magnitude over the native species in both LSIMS and MALDI-TOFMS. The behavior of the permethylated compounds was used as the benchmark for GSL structural information content in normal and tandem mass spectra. Fragments present in spectra of the three types of derivatives generated complementary information. Permethylated GSLs favored the formation of ions related to the ceramide moieties, whereas peracetylation enhanced the production of carbohydrate-related ions. The LSI mass spectra of perbenzoylated GSLs contained information on both ceramide and sugar portions of the molecules. Each of the LSIMS, MS/MS and MALDI-TOFMS techniques proved to be complementary to the others in this study; the use of all three is recommended for the generation of complete structural information.