Screening of sugar converting enzymes using quantitative MALDI-ToF mass spectrometry

Quantitative matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) was applied for the screening of ten pyranose oxidase variants. Quantitative MALDI-ToF MS using isotopic labeled internal standards and ionic liquid matrices was performed using aliquots of enzyme reaction mixtures without prepurification steps. The results obtained were in good agreement with HPLC measurements. Analysis time was approx. 3.5 min for a five-fold determination. Thus, quantitative MALDI-ToF MS can be used as a tool for screening of sugar converting enzymes.     

Combination of a SAW-biosensor with MALDI mass spectrometric analysis

A S-sens K5 surface acoustic wave biosensor was coupled with mass spectrometry (SAW-MS) for the analysis of a protein complex consisting of human blood clotting cascade factor alpha-thrombin and human antithrombin III, a specific blood plasma inhibitor of thrombin. Specific binding of antithrombin III to thrombin was recorded as a function of time with a S-sens K5 biosensor. Two out of five elements of the sensor chip were used as references. To the remaining three elements coated with RNA anti-thrombin aptamers, thrombin and antithrombin III were bound consecutively. The biosensor measures mass changes on the chip surface showing that 20% of about 400fmol/cm2 thrombin formed a complex with the 1.7-times larger antithrombin III. Mass spectrometry (MS) was applied to identify the bound proteins. Sensor chips with aptamer-captured (1) thrombin and (2) thrombin-antithrombin III complex (TAT-complex) were digested with proteases on the sensor element and subsequently identified by peptide mass fingerprint (PMF) with matrix assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry. A significant identification of thrombin was achieved by measuring the entire digest with MALDI-ToF MS directly from the sensor chip surface. For the significant identification of both proteins in the TAT-complex, the proteolytic peptides had to be separated by nano-capillary-HPLC prior to MALDI-ToF MS. SAW-MS is applicable to protein interaction analysis as in functional proteomics and to miniaturized diagnostics.     

Outcome prediction in pneumonia induced ALI/ARDS by clinical features and peptide patterns of BALF determined by mass spectrometry

Background

Peptide patterns of bronchoalveolar lavage fluid (BALF) were assumed to reflect the complex pathology of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) better than clinical and inflammatory parameters and may be superior for outcome prediction.

Methodology/Principal Findings

A training group of patients suffering from ALI/ARDS was compiled from equal numbers of survivors and nonsurvivors. Clinical history, ventilation parameters, Murray''s lung injury severity score (Murray''s LISS) and interleukins in BALF were gathered. In addition, samples of bronchoalveolar lavage fluid were analyzed by means of hydrophobic chromatography and MALDI-ToF mass spectrometry (MALDI-ToF MS).Receiver operating characteristic (ROC) analysis for each clinical and cytokine parameter revealed interleukin-6>interleukin-8>diabetes mellitus>Murray''s LISS as the best outcome predictors. Outcome predicted on the basis of BALF levels of interleukin-6 resulted in 79.4% accuracy, 82.7% sensitivity and 76.1% specificity (area under the ROC curve, AUC, 0.853). Both clinical parameters and cytokines as well as peptide patterns determined by MALDI-ToF MS were analyzed by classification and regression tree (CART) analysis and support vector machine (SVM) algorithms. CART analysis including Murray''s LISS, interleukin-6 and interleukin-8 in combination was correct in 78.0%. MALDI-ToF MS of BALF peptides did not reveal a single identifiable biomarker for ARDS. However, classification of patients was successfully achieved based on the entire peptide pattern analyzed using SVM. This method resulted in 90% accuracy, 93.3% sensitivity and 86.7% specificity following a 10-fold cross validation (AUC = 0.953). Subsequent validation of the optimized SVM algorithm with a test group of patients with unknown prognosis yielded 87.5% accuracy, 83.3% sensitivity and 90.0% specificity.

Conclusions/Significance

MALDI-ToF MS peptide patterns of BALF, evaluated by appropriate mathematical methods can be of value in predicting outcome in pneumonia induced ALI/ARDS.     

A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids

Microbial cell factories have been extensively engineered to produce free fatty acids (FFAs) as key components of crucial nutrients, soaps, industrial chemicals, and fuels. However, our ability to control the composition of microbially synthesized FFAs is still limited, particularly, for producing medium-chain fatty acids (MCFAs). This is mainly due to the lack of high-throughput approaches for FFA analysis to engineer enzymes with desirable product specificity. Here we report a mass spectrometry (MS)-based method for rapid profiling of MCFAs in Saccharomyces cerevisiae by using membrane lipids as a proxy. In particular, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) MS was used to detect shorter acyl chain phosphatidylcholines from membrane lipids and a higher m/z peak ratio at 730 and 758 was used as an indication for improved MCFA production. This colony-based method can be performed at a rate of ~2 s per sample, representing a substantial improvement over gas chromatography-MS (typically >30 min per sample) as the gold standard method for FFA detection. To demonstrate the power of this method, we performed site-saturation mutagenesis of the yeast fatty acid synthase and identified nine missense mutations that resulted in improved MCFA production relative to the wild-type strain. Colony-based MALDI-ToF MS screening provides an effective approach for engineering microbial fatty acid compositions in a high-throughput manner.     

Phyloproteomics: species identification of Enterobacteriaceae using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

To evaluate matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) as a tool for rapid identification of common clinical bacterial isolates, we analyzed 25 carefully selected isolates of pathogenic Escherichia coli (E. coli) and additional Enterobacteriaceae members. Organisms were prepared according to clinical microbiological protocols and analyzed with minimal additional processing. Spectra were reproducible from preparation to preparation and comprised 40-100 peaks primarily representing intracellular proteins with masses up to 25 kDa. Spectra of 14 genetically diverse bacteremic isolates of E. coli were compared with isolates representing other genera within the Enterobacteriaceae family. Using a new spectrum comparison algorithm, E. coli isolates were closely related to each other and were readily distinguishable from other Enterobacteriaceae, including Salmonella and Shigella. Presently, the methodology permits the analysis of 40 unknown isolates per hour per instrument. These results suggest that MALDI-ToF MS offers a rapid and reliable approach for performing phyloproteomics i.e., identification of unknown bacterial isolates based on similarities within protein biomarker databases.     

Techniques for boron determination and their application to the analysis of plant and soil samples

This paper reviews techniques for determining B concentration and isotopic ratio and their application to soil and plant samples. Boron concentration has been determined utilising spectrophotometry, potentiometry, chromatography, flame atomic emission and absorption spectrometry, inductively coupled plasma (ICP) optical emission (OES) and mass spectrometry (MS), and neutron activation analysis using neutron radiography and prompt- activation analysis. Isotopic ratios of B have been measured by ICP–MS, thermal ionisation mass spectrometry (TIMS) and secondary ion mass spectrometry (SIMS). For isotopic measurements, TIMS and SIMS are more sensitive and provide higher degrees of accuracy and resolution than ICP–MS, however, extensive sample preparation and purification, and time-consuming measurements limit their usefulness for routine analyses.While the spectrophotometric technique using a colorimetric reaction of B with azomethine-H has been the most extensively applied B determination method for soil and plant samples, colorimetric methods, in general, suffer from numerous interferences and have poor sensitivity and precision. The prompt- method can determine B concentration in intact samples which enables this method to be especially useful for some applications in agriculture. Research involving B behaviour in plant and soil environments would benefit from this technology. In recent years, the use of ICP–OES and ICP–MS for B determination in plant and soil samples has grown tremendously. The application of ICP–OES brought a significant improvement in B analysis because of its simplicity, sensitivity and multielement detection capability. However, besides matrix interferences, the two most sensitive emission lines for B suffer strong spectral interference from Fe. The ICP–OES is not adequately sensitive for some nutritional work involving low B concentrations and B translocation studies using the isotope tracer technique.Plasma is one of the most effective analyte ionisers and MS is the most sensitive ion detector. Coupling of plasma with MS resulted in the development of plasma source MS technology (ICP–MS) which has outperformed all previous analytical methods for trace element determination. Boron determination by ICP–MS suffers no spectroscopic interferences, and is considered the most practical and convenient technique for B isotope determination. The ability of ICP–MS to measure isotopic ratios as well as B concentration enables: (1) B concentration determination by the isotope dilution method, (2) verification of B concentration by isotope fingerprinting in routine analysis and (3) determination of total B concentration as well as B isotope ratio in the same run for biological tracer studies. Therefore, ICP–MS is the method of choice among the present-day technologies for determining B concentration and a convenient method for B isotope determination. In recent years, new generations of plasma-source MS instruments have been developed using alternative plasma generation methods and high-resolution mass spectrometers. These instruments are expected to bring further improvements in accuracy, sensitivity and precision of B determination.     

New insights from MALDI-ToF MS, NMR, and GC-MS: mass spectrometry techniques applied to palynology

Summary. The present study for the first time describes the application of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-ToF MS) to palynology. With an accessible mass range of up to about 350,000 Da at subpicomolar range, this technique is ideal for the characterisation of bio-macromolecules, such as sporopollenin, found in fossil and extant pollen and spore walls, which often can only be isolated in very small quantities. At this stage, the limited solubility of sporopollenin allows for the identification of sections of this biopolymer, but with the optimisation of MALDI-ToF matrices, further structure elucidation will become possible. Furthermore, gas chromatography–mass spectrometry (GC-MS) and ¹H nuclear magnetic resonance (¹H NMR) spectroscopy data obtained from a number of experiments revealed that some previously reported data were misinterpreted. These results add support to the hypothesis that common plasticizers were wrongly described as sporopollenin compounds. Correspondence and reprints: School of Earth, Ocean and Planetary Sciences, Cardiff University, Park Place, Cardiff CF10 3YE, United Kingdom. Permanent address: Albion College, Albion, Michigan, U.S.A.     

Mass-Spectrometry Based Characterisation of Infant Whole Saliva Peptidome

The objective of the study was to determine optimal conditions for sampling, sample processing and mass-spectrometry based analysis of infants’ salivary peptidome. Saliva was sampled in 3- and 6-month-old infants and peptide extracts were prepared. Various sample pretreatments before profiling by MALDI-ToF were evaluated and peptide identification was undertaken by MALDI-ToF/ToF or nanoLC-ESI-IT tandem MS. A fast and simple protocol (cut-off filtration at 5 kDa) was satisfactory to produce extracts where no proteolysis was detected even when no protease inhibitor was added. Optimal MALDI spectra were generated after purification on C18 tips. Variability of spectra between two samples exceeded that of the technical replicates, validating that the method is suitable to conduct differential studies. Salivary peptides, identified by means of the two complementary mass spectrometry techniques, were fragments of proline-rich proteins and histatins. The fragments originated mainly from the C-terminal protein extremities. Indications on the proteolytic systems involved and the anatomic location where they intervene are proposed.     

Physiological proteomics: cells, organs, biological fluids, and biomarkers

Proteomic research is accelerating rapidly because of marked advances in protein labeling techniques, mass spectrometry (MS), and bioinformatics. Two-dimensional difference gel electrophoresis (2D-DIGE) is being used effectively in conjunction with liquid chromatography tandem MS (LC-MS/MS) and/or matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-ToF MS) and database search software to quantify relative changes in the levels of proteins in two samples. It is now possible in a single study to identify and quantify large numbers of proteins and their posttranslational modifications in different biological samples. Comparisons can be made between groups of animals in different physiological states or in response to experimental treatment. Differences between normal individuals and those in disease states can form the foundation for elucidation of causative factors of disease and the identification of biomarkers for the diseased state. This symposium includes original research that compares the erythrocyte plasma membrane proteome in the normal and the sickle cell state, evaluates the anterior pituitary gland proteome in the ovariectomized rat in response to estrogen, and assesses proteomic methodology employed to identify potentially useful biomarkers in human cells and fluids for clinical medicine. It is directed not only to investigators working in these fields but also to a diverse group of scientists working in the biological and biomedical fields to stimulate cross-disciplinary awareness, interest, and collaboration.     

Mapping phosphoproteins in Neisseria meningitidis serogroup A

To investigate the phosphorylation capability of serogroup A Neisseria meningitidis (MenA) and to implement our knowledge in meningococcal biology and in bacterial post-translational modifications, cell extracts were separated by 2-DE and 51 novel phosphoproteins were revealed by the use of the highly specific Ser/Thr/Tyr-phosphorylated proteins staining by Pro-Q Diamond and identified by MALDI-ToF/MS. Our results indicate that phosphorylation in MenA is comparable to that of other bacterial species. A first functional characterization of the identified modified proteins was also given, in order to understand their role in meningococcal physiopathology.     

A sorghum 85 kDa heat stress-modulated protein shows calmodulin-binding properties and cross-reactivity to anti-Neurospora crassa Hsp 80 antibodies

The present study, carried out to identify stress-modulated calmodulin (CaM)-binding proteins in sorghum, resulted in the isolation of several proteins, which showed binding to CaM-Sepharose matrix. Calmodulin gel overlay assay and MALDI-ToF MS analysis revealed that an 85 kDa protein (Hsp85), which interacted with calmodulin, cross-reacted with anti-N. crassa Hsp80 antibodies. Since these antibodies bind to plant Hsp90, sorghum Hsp85 is likely to be a member of the Hsp90 family. This study provides the first evidence that a member of Hsp90 (Hsp85) in plants exhibits CaM-binding properties.     

Proteomic analysis of the etioplast inner membranes of wheat (Triticum aestivum) by two-dimensional electrophoresis and mass spectrometry

The proteome of the etioplast inner membranes (EPIM) of dark-grown wheat leaves ( Triticum aestivum L.) was mapped as an essential part of studies on plastid differentiation. Proteins were separated by two-dimensional gel electrophoresis and analysed with mass spectrometry (MS). Over 200 protein spots were resolved and visualized by Coomassie blue staining. More than 100 spots were submitted for subsequent mass spectrometry analyses by matrix-assisted laser desorption ionization–time of flight (MALDI-ToF) MS, electrospray tandem MS (ESI-MS/MS) or liquid chromatography–mass spectrometry (LC-MS/MS). There were 46 identified spots, from which at least 21 different proteins were identified. Among these were FtsH proteases and the peptidyl-prolyl cis – trans isomerase TLP40, as well as chloroplast coupling factor subunits and extrinsic subunits of photosystem II (PSII). Of special interest is the NADPH:protochlorophyllide oxidoreductase (POR), which is the predominant protein of prolamellar bodies, where it accumulates in a highly stable ternary complex with protochlorophyllide and NADPH. This complex is known to play an important role in the formation and dispersal of prolamellar bodies. Five different isoforms of POR, with different pI values, were identified. We discuss the possibility of these isoforms being differently phosphorylated as part of the regulation of POR–pigment complexes. The proteome mapping of EPIM is a crucial step in the understanding of the light-dependent transition of etioplasts to chloroplasts, and provides a basis for functional studies on factors influencing the greening process.     

Ammonia cleaves polypeptides at asparagine proline bonds.

Polypeptides that contain the sequence Asn-Pro undergo complete cleavage at this amide bond with ammonia. One cleavage product possesses Pro as the new amino terminus and the other Asn or isoAsn as the new C-terminus, the formation of the latter probably arising by way of a cyclic succinimide intermediate. Other Asn-X bonds where X = Tyr, Gln, Ile, Glu, Ala, Gly, Asn or Phe did not exhibit any peptide bond cleavage, whereas when X = Leu, Thr and Ser partial cleavage was observed. Asn residues not involved in chain-cleavage underwent deamidation to Asp as shown by MALDI-ToF mass spectrometry (MS) analysis. The partial conversion of in-chain Asp residues to isoAsp under the reaction conditions was inferred from RP-HPLC and MS analysis of reaction mixtures.     

Determination of tetrabromobisphenol A in human serum by liquid chromatography-electrospray ionization tandem mass spectrometry

A method for the determination of tetrabromobisphenol A (TBBPA) in human serum utilizing solid-phase extractions (SPEs) and liquid chromatography (LC) with electrospray ionization tandem MS (MS/MS) has been developed. After purification and concentration of TBBPA using consecutive SPEs on reversed-phase and normal-phase cartridges, the serum sample was subjected to LC. TBBPA was separated on a C18 reversed-phase column by gradient elution with a mixture of water, methanol, and acetonitrile as the mobile phase, and then detected with electrospray ionization MS/MS in negative ion mode. 13C12-TBBPA was suitable as an internal standard for the reproducible determination of TBBPA in human serum samples (5 g). The method has been validated in TBBPA concentration range of 5-100 pg per g serum, and the recoveries in the concentration range were higher than 83.3%. The repeatabilities of the proposed method of non-spiked control serum (6.3 pg per g serum) and spiked serum (added 5-100 pg per g serum) were within 10.0% as relative standard deviations. The limit of quantification (LOQ) for TBBPA was 4.1 pg per g serum, which was corresponded to 0.63 fmol on column.     

Clostridium difficile sortase recognizes a (S/P)PXTG sequence motif and can accommodate diaminopimelic acid as a substrate for transpeptidation

Covalent attachment of surface proteins to the cell wall of Gram-positive bacteria requires a sortase-mediated transpeptidation reaction. In almost all Gram-positive bacteria, the housekeeping sortase, sortase A, recognizes the canonical recognition sequence LPXTG (X = any amino acid). The human pathogen Clostridium difficile carries a single putative sortase gene (cd2718) but neither transpeptidation activity nor specificity of CD2718 has been investigated. We produced recombinant CD2718 and examined its transpeptidation activity in vitro using synthetic peptides and MALDI-ToF(-ToF) MS analysis. We demonstrate that CD2718 has sortase activity with specificity for a (S/P)PXTG motif and can accommodate diaminopimelic acid as a substrate for transpeptidation.     

Microsatellite genotyping by primer extension and MALDI-ToF mass spectrometry

A novel method for genotyping microsatellite alleles using primer extensions and mass spectrometry analysis has been developed. Following PCR amplification of the target region, a genotyping primer, with its 3′ end directly flanking the microsatellite repeats, was extended by a mixture of dNTPs complementary to the nucleotides composing the microsatellite. The length and molecular weight of extended primers vary with the number of repeats present in the allele(s) under examination. The weights of extension products were determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF MS) and used to identify genotypes on the basis of differential primer extension. This is a platform that is not gel based and is amenable to multiplexing and automation. The technique enables identification of heterozygous progeny in which alleles differ by a single trinucleotide repeat. The method is illustrated by genotyping a polymorphic microsatellite identified in an intron of the barleyMlo gene.     

LC-MS/MS分析人支气管上皮细胞与烟曲霉共培养模型中胶霉毒素的含量

目的：采用液相色谱-串联质谱法（LC-MS/MS）分析人支气管上皮细胞与烟曲霉共培养模型中胶霉毒素的含量。方法建立人支气管上皮细胞与烟曲霉共培养模型并于不同时间段检测共培养模型中胶霉毒素的含量。以支气管上皮细胞单独培养为对照组,分别于12h、24h、36h收集对照组、AF293（烟曲霉标准株）共培养组、AFB5233WT（烟曲霉野生株）及AFB5233ΔGlip（烟曲霉胶霉毒素基因敲除株）共培养组细胞培养上清液,采用LC-MS/MS检测胶霉毒素的含量。结果共培养模型中胶霉毒素水平随培养时间增加而逐渐升高（P〈005）,胶霉毒素回收率为687%~726%。结论该方法快速、灵敏、结果准确,适用于测定人支气管上皮细胞与烟曲霉共培养模型中胶霉毒素的含量。     

An estimation of the exposure to organophosphorus pesticides through the simultaneous determination of their main metabolites in urine by liquid chromatography-tandem mass spectrometry

A rapid method has been developed for the determination of 4-nitrophenol (PNP) (parathion and methyl-parathion metabolite) and 3-methyl-4-nitrophenol (3-Me-PNP) (fenitrothion metabolite) in human urine by coupled-column liquid chromatography combined with tandem mass spectrometry (LC-LC-MS/MS). The LC-LC-MS/MS approach allows the determination at sub-ppb level of free metabolites by injecting the urine directly into the system and the total metabolites after a simple enzymatic hydrolysis. The method has been validated, obtaining limits of detection of 0.1 and 0.2 microg/L for 4-nitrophenol and 3-methyl-4-nitrophenol, respectively. Additionally, a multi-residue LC-MS/MS method is proposed in order to evaluate the levels of other parathion and methyl parathion metabolites. This approach allows the simultaneous determination of dimethyl phosphate (DMP), dimethyl thiophosphate (DMTP), 4-nitrophenolsulphate and 4-nitrophenolglucuronide without tedious sample treatments. The applicability of both methods is demonstrated by applying them to various urine samples from an unexposed population and a grower who applied methyl parathion. The combination of both methods allows a general overview on the presence of different metabolites (free and conjugated) and the concentration ratios between them, giving useful information on organophosphorus pesticides metabolism and excretion.     

Determination of imidapril and imidaprilat in human plasma by high-performance liquid chromatography–electrospray ionization tandem mass spectrometry

A sensitive and specific assay of imidapril and its active metabolite, imidaprilat, in human plasma has been developed. This method is based on rapid isolation and high-performance liquid chromatography (HPLC)–electrospray ionization (ESI)-tandem mass spectrometry (MS–MS). Imidapril and imidaprilat were isolated from human plasma using OASIS HLB (solid-phase extraction cartridge), after deproteinization. The eluent from the cartridge was evaporated to dryness, and the residue was reconstituted in mobile phase and injected into the HPLC–ESI-MS–MS system. Each compound was separated on a semi-micro ODS column in acetonitrile–0.05% (v/v) formic acid (1:3, v/v). The selected ion monitoring using precursor→product ion combinations of m/z 406→234 and 378→206, was used for determination of imidapril and imidaprilat, respectively. The linearity was confirmed in the concentration range of 0.2 to 50 ng/ml in human plasma, and the precision of this assay, expressed as a relative standard deviation, was less than 13.2% over the entire concentration range with adequate assay accuracy. The HPLC–ESI-MS–MS method correlates well with the radioimmunoassay method, therefore, it is useful for the determination of imidapril and imidaprilat with sufficient sensitivity and specificity in clinical studies.     

Assign-MALDI – A free software for assignment of MALDI-TOF MS spectra of glycans derivatized using common and novel labeling strategies

Matrix Assisted Laser Desorption/Ionization Time-of-flight (MALDI-ToF) MS is a popular method to analyze glycans released from proteins, cell lines, and tissue samples. Chemical modification of glycans (derivatization) can enhance ionization, enable semi-quantitation, and assist in linkage identification. However, the mass changes incurred by novel and more recently developed derivatizations are not accommodated by most spectral assignment programs, necessitating manual assignment which increases both the difficultly and the likelihood of error. AssignMALDI is a software tool designed to create glycan databases with customized derivatizations (labels) and automatically assign glycan masses in MALDI-TOF spectra using the new database. It can also average peak intensities across multiple spectra and prepare publication-ready assignment tables. To make it easy to use with different platforms, all input files and most output files are in text format. An interactive display enables users to inspect and edit peak assignments prior to producing charts and tables for publication. The program is freely available through GitHUB and Python-savvy users can add or adjust features as needed.