TOF Mass Spectra Research Articles

Syntheses of high molecular mass polyglycolides via ring‐opening polymerization with simultaneous polycondensation (ROPPOC) by means of tin and zinc catalysts

AbstractGlycolide was polymerized in bulk by means of four different ROPPOC catalysts: tin(II) 2‐ethylhexanoate (SnOct2), dibutyltin bis(pentafluoro‐phenoxide) (BuSnOPF), zinc biscaproate (ZnCap), and zinc bis(pentafluoro‐phenyl sulfide) (ZnSPF). The temperature was varied between 110 and 180°C and the time between 3 h and 7 days. For the few polyglycolides (PGAs) that were soluble extremely high molecular masses were obtained. The MALDI TOF mass spectra had all a low signal‐to‐noise ration and displayed the peaks of cyclic PGAs with a “saw‐tooth pattern” indicating formation of extended‐ring crystallites in the mass range below m/z 2500. The shape of DSC curves varied considerably with catalyst and reaction conditions, whereas the long‐distance values measured by SAXS were small and varied little with the polymerization conditions.

Disentangle a Complex MALDI TOF Mass Spectrum of Polyethylene Glycols into Three Separate Spectra via Selective Formation of Protonated Ions and Sodium or Potassium Adducts.

In MALDI TOF MS analysis, complicated mass spectra can usually be recorded for polymers with high affinities to protons and alkali metal ions. For these polymers, protonated ions and sodium and potassium adducts can often be formed concomitantly. By distributing these ions into three separate spectra of protonated ions, sodium adducts, and potassium adducts, significantly simplified spectra can be acquired. Mass spectra consisting of only sodium or potassium adducts can often be obtained by simply adding sodium salt and potassium salt, respectively. We report here a method to selectively generate protonated ions. A polyethylene glycol (PEG) sample with amino end groups was selected as the model polymer and α-cyano-4-hydroxycinnamic acid (CHCA) as the matrix. Octadecylamine (ODA) or a mixture of a tetrabutylammonium (TBA) salt and an ammonium salt was used as the co-matrix to inhibit the release of sodium and potassium ions and their related adducts into the MALDI gas phase plume. By depositing the polymer sample on top of a preloaded layer of CHCA with a co-matrix, the generation of Na+ and K+ adducts is suppressed, while [ODA + H]+ and NH4+ released from the preloaded matrix layer can serve as protonation reagents to protonate the polymer molecules via proton transfer reactions. It is clearly demonstrated that disentangling a complex mass spectrum filled densely with various series of ions into three separate spectra, with each one consisting of only one type of ions, allows unambiguous identification of mass peaks and greatly helps the interpretation of MS results.

Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica.

Strains P8930T and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus Pedobacter and showed Pedobacter frigidisoli and Pedobacter terrae to be their closest phylogenetic neighbours, with 97.4 and 97.2 % 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA-DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930T and P. frigidisoli RP-3-11T and P. terrae DSM 17933T were 79.7 and 77.6 %, respectively, and the value between P. frigidisoli RP-3-11T and P. terrae DSM 17933T was 77.7 %, clearly demonstrating the phylogenetic distance and the novelty of strain P8930T. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930T and 478 from the other validly named Pedobacter species, and confirmed that they represent a new species for which the name Pedobacter fastidiosus sp. nov. is proposed. The type strain is P8930T (=CCM 8938T=LMG 32098T).

Metabolic determination of decursinol using human liver microsome


 
 
 
 Purpose: To determine new metabolites of the main components of Angelica gigas known to give anti-inflammation and pain relief
 Methods: Decursinol and blank sample were metabolized in human liver microsomes. The metabolized samples were centrifuged and deproteinated by adding 3 mL acetonitrile. The acetonitrile layer was concentrated and reconstituted in methanol. Finally, the prepared sample was injected into the LC-Q- TOF-MS.
 Results: Four new metabolites of decursinol with m/z ranging from 263.0912 ~ 263.0920 were identified as hydroxylated forms of decursinol, and the hydroxylated position of each metabolite was characterized using TOF mass spectrum. Their error values of detected m/z were 0.38 ~ 2.29 ppm, which indicates high accuracy of analysis.
 Conclusion: Previously unreported decursinol metabolites have been identified in this study. The findings provide athe basis for further pharmaceutical studies and functional food development using decursinol.
 
 
 

TOF mass spectra of zircon M257 measured by VUV laser desorption ionization

The time-of-flight mass spectrum of zircon M257 was measured using a VUV laser desorption/ionization method. The VUV laser scanned an area of 10 × 10 μm2 with a step of 0.5 μm, in total 30 layers and 6000 laser pulses, resulting in a depth of ∼20 nm.

Some characteristics of new and innovative COX inhibitor derivatives: Potent hCA‐I and hCA‐II inhibitors supported by molecular docking studies

AbstractIn this study, two novel metallophthalocyanines (ZnPc and CoPc) were synthesized using the corresponding metal salts 4‐(4‐(4‐[4‐chlorophenyl]‐5‐methylisoxazol‐3‐yl)phenoxy)‐phthalonitrile (11), prepared from the reaction of 4‐nitrophthalonitrile and 4‐(4‐[4‐chlorophenyl]‐5‐methylisoxazol‐3‐yl)phenol (9). These metallophthalocyanines (MPcs) showed quite solubility in organic solvents such as dichloromethane (DCM), tetrahydrofuran (THF), dimethyl formamide (DMF), and dimethylsulfoxide (DMSO). The novel compounds 11a and 11b have been characterized using their UV–Vis, FT–IR, 1H NMR, 13C NMR, X‐Ray, and MALDI–TOF mass spectra. Supporting information cocerning with the study has been supplied. Photochemical, photophysical, and cyclic voltagram properties of these novel 4‐(4‐(4‐[4‐chlorophenyl]‐5‐methylisoxazol‐3‐yl)phenoxy substituted metallophthalocyanines (11a and 11b) were determined in DMF. DNA binding, metal chelating effect assay, and DPPH [2,2‐diphenyl‐1‐picrylhydrazyl hydrate] radical scavenging assay and electrochemical studies of MPcs were investigated. Further, the inhibitory effects of the COX‐inhibitor based novel metallophthalocyanines (11a and 11b) and their ligands (10 and 11) were examined on human erythrocyte carbonic anhydrase I (hCA‐I) and II (hCA‐II) isoenzymes, and the synthesized molecules exhibited very strong inhibitory effects on both isoforms. In addition, the hCA‐I and hCA‐II inhibition potential of Zn (II) and Co (II) Phthalocyanine complexes was supported by molecular docking studies. The binding interaction of metallophthalocyanines complexes 11a, 11b enzymes were analyzed in detail.

Sodium salts effect on the time of flight mass spectra of some amino acids in the direct‐laser desorption ionization and matrix‐assisted laser desorption/ionization

AbstractOne of the problems in the matrix‐assisted laser desorption/ionization time of flight mass spectrometry (MALDI‐TOF MS) of small molecules is the overlap between the peaks originated from the matrix and analyte. The MALDI and the direct laser desorption ionization (direct‐LDI) spectrum of the phenylalanine amino acid (FAA) has been recorded and assigned in the absence and presence of the salts, including NaF and NaOH. It was seen that the peaks originated from the matrix were suppressed in the MALDI spectrum of the FFA in the presence of salt. In addition, the salt effect on the TOF mass spectrum of the FAA, recorded by the direct‐LDI, was investigated. The mass spectrum of the FFA, in the presence of NaF, showed a relatively strong and sharp peak assigned to [FAA‐H + 2Na]+ species in both the direct‐LDI and MALDI. The direct‐LDI spectrum was less crowded than the MALDI spectrum. The same results were obtained when NaOH was used instead of NaF. The peak related to [Amino acid‐H + 2Na]+ species was considered a characteristic peak in both the direct‐LDI and MALDI of the selected amino acids in the presence of NaF and NaOH.

Superatomic Signature and Reactivity of Silver Clusters with Oxygen: Double Magic Ag 17 – with Geometric and Electronic Shell Closure

Understanding the stability and reactivity of silver clusters toward oxygen provides insights to design new materials of coinage metals with atomic precision. Herein, we report a systematic study o...

Feasibility of Acetylcholinesterase Reaction Assay Monitoring in DIUTHAME-MS.

DIUTHAME (desorption ionization using through hole alumina membrane) is a novel matrix-free laser desorption/ionization method that enables highly reproducible acquisition of mass spectra. This study aims to evaluate the applicability of DIUTHAME to the acetylcholinesterase reaction assay (AChE assay) commonly used in high-throughput screening (HTS) in the drug discovery process. The commercially available 9-ch DIUTHAME chip was applied to a series of AChE assays prepared with different reaction times. Numerous positive-mode TOF mass spectra were acquired from the raster-scanned sample spots of the AChE assays to analyze the progress of the enzyme reaction and to perform mass spectrometry imaging of the sample spots. The reaction kinetics plots obtained by DIUTHAME were found to reflect the time course of reaction progression as much as those obtained by MALDI and were found to have less error variation than MALDI. DIUTHAME allowed the already irradiated sample spots to be reused to reproduce the reaction kinetics plots by the second measurement conducted a week after, whereas MALDI was not able to properly reproduce the kinetics plots by remeasuring the irradiated sample spots. In DIUTHAME, which does not require a matrix, the experimental procedure for measuring AChE assay becomes extremely simple. DIUTHAME is potentially able to provide more precise AChE reaction kinetics plots than what have been accomplished by MALDI.

Coal Discrimination Analysis Using Tandem Laser-Induced Breakdown Spectroscopy and Laser Ablation Inductively Coupled Plasma Time-of-Flight Mass Spectrometry.

The contribution and impact of combined laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) and laser-induced breakdown spectroscopy (LIBS) were evaluated for the discrimination analysis of different coal samples. This tandem approach allows simultaneous determination of major and minor elements (C, H, Si, Ca, Al, Mg, etc.) and trace elements (V, Ba, Pb, U, etc.) in the coal. The research focused on coal-classification strategies based on principle component analysis (PCA) combined with K-means clustering, partial least-squares discrimination analysis (PLS-DA), and support vector machine (SVM) for analytical performance. Correlation analyses performed from TOF mass and LIBS emission spectra from the coal samples showed that most major, minor, and trace element emissions had negative correlation with the volatile content. Suitable variables for the classification models were determined from these data. The individual TOF data, LIBS data, and combined data of TOF and LIBS as the inputs for different models were analyzed and compared. In all cases, the results obtained with the combined TOF and LIBS data were found to be superior to those obtained with the individual TOF or LIBS data. The nonlinear SVM model combined with TOF and LIBS data provided the best coal-classification performance, with a classification accuracy of up to 98%.

Formation of Al + (C 6 H 6 ) 13 : The Origin of Magic Number in Metal–Benzene Clusters Determined by the Nature of the Core

The identification of highly abundant, “magic” species in the mass spectra of clusters have proven to be valuable in nanoscience, leading to the discovery of new stable species such as fullerenes a...

Electronic data acquisition and operational control system for time‐of‐flight sputtered neutral mass spectrometer

A new electric data acquisition and operational control system was developed for time‐of‐flight sputtered neutral mass spectrometry (TOF‐SNMS). The system is designed for high‐speed data acquisition, data processing, and data streaming. The developed system is constructed on an NI‐PXI platform and provides timing clocks for the TOF‐SNMS operation. The system performs data processing of noise suppression and ion counting while acquiring TOF mass spectrum for 13‐microsecond length at sampling rate of 3 GS/s for every 1 millisecond. In addition, the system acquires and records TOF mass spectrum of 60‐microsecond length at sampling rate of 3 GS/s for every 1 millisecond without data processing. The system detects single ion signals from accumulated TOF mass spectrum of 107 times and counts up to 10 ions accurately from a single event of TOF mass spectrum.

Synthesis of Oligomers by Oxidative Dehydrogenation of Dihydric Phenols and Quinones with 3,3′,5,5′-Tetra-tert-butyl-trans-stilbenequinone

Oxidative dehydrogenation of pyrocatechol and 1,4-benzoquinone with 3,3′,5,5′-tetra-tert-butyl-trans-stilbenequinone as oxidant afforded oligomeric polyhydroquinones and polyquinones. Appropriate reaction conditions have been found, and the resulting oligomers have been characterized by IR and MALDI TOF mass spectra and elemental analyses.

The statistical properties of raw and preprocessed ToF mass spectra

Single-valued summaries, such as signal-to-noise ratio, are insufficient to fully describe the input and output characteristics of time-of-flight mass spectra preprocessing methods. A detailed understanding of uncertainty, biases and correlations is essential for selecting appropriate methods, and for drawing confident scientific conclusions from preprocessed data. We apply a range of diagnostic tests to mass spectra, allowing statistical and systematic sources of uncertainty to be assessed throughout the typical stages of a preprocessing pipeline. Baseline correction, alignment and peak detection are reconsidered, with an emphasis on producing outputs with statistical properties compatible with an independent Poisson ion counting process. Benchmarking is also performed against a range of alternative preprocessing methods. In contrast to other preprocessing methods, new techniques are presented which provide improved statistical stability. The benefits are demonstrated using simulation and also data from the RELAX (refrigerator-enhanced laser analyser for xenon) mass spectrometer. A twofold improvement in accuracy of Xe peak measurement over the original method for the same dataset is observed.

Postharvest Biological Control of Colletotrichum acutatum on Apple by Bacillus subtilis HM1 and the Structural Identification of Antagonists.

Bacillus subtilis HM1 was isolated from the rhizosphere region of halophytes for its antifungal activity against Colletotrichum acutatum, the causative agent of anthracnose. Treatment of postharvest apples with the cell culture or with a cell-free culture supernatant reduced disease severity 80.7% and 69.4%, respectively. Both treatments also exhibited antifungal activity against various phytopathogenic fungi in vitro. The antifungal substances were purified and analyzed by acid precipitation, gel filtration, high-performance liquid chromatography, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Three compounds were identified as fengycin, iturin, and surfactin. The MALDI-TOF/ TOF mass spectrum revealed the presence of cyclized fengycin homologs A and B, which were distinguishable on the basis of the presence of either alanine or valine, respectively, at position 6 of the peptide sequence. In addition, the cyclized structure of fengycin was shown to play a critical role in antifungal activity.

Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry.

Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.

Need for database extension for reliable identification of bacteria from extreme environments using MALDI TOF mass spectrometry

AbstractThe ability of MALDI TOF MS (matrix-assisted laser desorption ionisation time-of-flight mass spectrometry) to identify cultivable microflora from two waste disposal sites from non-ferrous metal industry was analysed. Despite the harsh conditions (extreme pH values and heavy metal content in red mud disposal site from aluminium production or high heavy metal content in nickel sludge), relatively high numbers of bacteria were recovered. In both environments, the bacterial community was dominated by Gram-positive bacteria, especially by actinobacteria. High-quality MALDI TOF mass spectra were obtained but most of the bacteria isolates could be not identified using MALDI Biotyper software. The overall identification rate was lower than 20 %; in two of the environments tested identification rates were lower than 10 %. As a dominant bacterial species, Microbacterium spp. in drainage water from an aluminium red mud disposal site near Žiar nad Hronom, Bacillus spp. in red mud samples from the same site, and Arthrobacter spp. from nickel smelter sludge near Sereï were identified by a combination of the Biolog system and 16S rRNA sequence analysis. As the primary focus of the MALDI TOF MS-based methodology is directed towards medically important bacteria, reference database spectra expansion and refinement are needed to improve the ability of MALDI TOF MS to identify environmental bacteria, especially those from extreme environments.

Synthesis, photophysical and electrochemical characterization of terpyridine-functionalized dendritic oligothiophenes and their Ru(II) complexes

Pd-catalyzed Sonogashira cross-coupling reactions were used to synthesize novel π-conjugated oligothienylene-ethynylene dendrons and their corresponding terpyridine-based ligands. Their complexation with Ru(II) led to interesting novel metallodendrimers with rich spectroscopic properties. All new compounds were fully characterized by 1H and 13C NMR, as well as MALDI–TOF mass spectra. Density functional theory (DFT) calculations performed on these complexes gave more insight into the molecular orbital distributions. Photophysical and electrochemical studies were carried out in order to elucidate structure–property relationships and the effect of the dendritic structure on the metal complexes. Photophysical studies of the complexes revealed broad absorption spectra covering from 250 to 600 nm and high molar extinction coefficients. The MLCT emission of these complexes were significantly red-shifted (up to 115 nm) compared to the parent [Ru(tpy)2]2+ complex.

Erratum to “An integrative analysis of transcriptome and proteome provides new insights into carotenoid biosynthesis and regulation in sweet orange fruits” [J. Proteomics 75 (2012) 2670–2684

The authors sincerely apologize for careless mistake in proof correction as three paragraphs (between the results chapters 3.2 and 3.3) were mistakenly lost during typesetting. The complete content of the results should be as follows: 3.2 Identification of proteins differ in relative abundance in Cara Cara and Newhall In a parallel analysis, and to complement the transcriptomic study, a comparative proteomic survey was performed on Cara Cara and Newhall sweet oranges harvested at 160DAF and 190 DAF using 2DE (Fig.4). Image analysis of 2DE gels presented 595 (Cara Cara) and 560 (Newhall) well separated spots at 160DAF, and 610 (Cara Cara) and 598 spots (Newhall) at 190DAF. Student's t test analysis (P<0.05) identified 56 (160DAF) and 63 (190DAF) protein spots that differed in relative abundance (Fig. 4). These differential protein spots were excised, digested by trypsin and analyzed by MALDITOF–TOF mass spectrum, then the mass spectrum was conducted by searching the NCBI non-redundant green plant database using the Mascot search engine. A total of 48 proteins (as indicated in Fig. 4) were successfully identified with high confidence (Table 3). The completed information about protein identification such as identified peptide sequences were provided in Table S5. According to the metabolic and functional features as described in KEGG pathways, GO annotation and literatures

Poly(ε‐caprolactone) by combined ring‐opening polymerization and azeotropic polycondensation—the role of cyclization and equilibration

AbstractUsing three different catalysts, water‐initiated polymerizations of ε‐caprolactone were conducted in bulk with variation of the monomer/water ratio. The resulting CH2OH and CO2H‐ terminated polylactones were subjected in situ to azeotropic polycondensations. With Bi‐triflate and temperatures, the polycondensations were not much successful and involved side reactions. With ZnCl2, and especially SnCl2, considerably higher molar masses were achieved. The substitution of toluene for chlorobenzene for refluxing gave better results. The polycondensations broadened the molar mass distribution of the ROP‐based prepolymers, and polydispersities between 1.4–1.8 were obtained. The MALDI–TOF mass spectra revealed that the polycondensations significantly enhanced the fraction of rings due to efficient “end‐biting” reactions. By comparison with copolymerization experiments and Sn methoxide‐initiated polymerizations, it was demonstrated that equilibration reactions, such as the formation of rings by “back‐biting,” did not occur. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012