共查询到20条相似文献,搜索用时 31 毫秒
1.
Markus Langsdorf Alireza Ghassempour Andreas Römpp Bernhard Spengler 《Analytical and bioanalytical chemistry》2010,398(7-8):2853-2865
Novel peptides were identified in the skin secretion of the tree frog Hyla savignyi. Skin secretions were collected by mild electrical stimulation. Peptides were separated by reversed-phase high-performance liquid chromatography. Mass spectra were acquired by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and fragment ion spectra were obtained after collision-induced dissociation and electron capture dissociation. Peptides were analyzed by manual de novo sequencing and composition-based sequencing (CBS). Sequence analyses of three so far undescribed, structurally unrelated peptides are presented in this paper, having the sequences DDSEEEEVE-OH, P*EEVEEERJK-OH, and GJJDPJTGJVGGJJ-NH2. The glutamate-rich sequences are assumed to be acidic spacer peptides of the prepropeptide. One of these peptides contains the modified amino acid hydroxyproline, as identified and localized by high-accuracy FTICR-MS. Combination of CBS and of experience-based manual sequence analysis as complementary and database-independent sequencing strategies resulted in peptide identification with high reliability. Figure
So-far unknown natural frog skin peptides were identified by high-resolution CID and ECD MS/MS and by composition-based de novo sequencing. Sequences were confirmed by comparison of MS/MS spectra with synthesized analogs 相似文献
2.
Jessica Z. Bereszczak Marlene Havlik Victor U. Weiss Martina Marchetti-Deschmann Esther van Duijn Norman R. Watts Paul T. Wingfield Guenter Allmaier Alasdair C. Steven Albert J. R. Heck 《Analytical and bioanalytical chemistry》2014,406(5):1437-1446
The capsid of hepatitis B virus (HBV) is a major viral antigen and important diagnostic indicator. HBV capsids have prominent protrusions (‘spikes’) on their surface and are unique in having either T?=?3 or T?=?4 icosahedral symmetry. Mouse monoclonal and also human polyclonal antibodies bind either near the spike apices (historically the ‘α-determinant’) or in the ‘floor’ regions between them (the ‘β-determinant’). Native mass spectrometry (MS) and gas-phase electrophoretic mobility molecular analysis (GEMMA) were used to monitor the titration of HBV capsids with the antigen-binding domain (Fab) of mAb 3120, which has long defined the β-determinant. Both methods readily distinguished Fab binding to the two capsid morphologies and could provide accurate masses and dimensions for these large immune complexes, which range up to ~8 MDa. As such, native MS and GEMMA provide valuable alternatives to a more time-consuming cryo-electron microscopy analysis for preliminary characterisation of virus-antibody complexes. Figure
Monitoring the binding of the antigen-binding domain (Fab) of mAb 3120 to hepatitis B capsids by native MS and GEMMA 相似文献
3.
Andrew R. Korte Young Jin Lee 《Journal of the American Society for Mass Spectrometry》2013,24(6):949-955
We have recently developed a multiplex mass spectrometry imaging (MSI) method which incorporates high mass resolution imaging and MS/MS and MS3 imaging of several compounds in a single data acquisition utilizing a hybrid linear ion trap-Orbitrap mass spectrometer (Perdian and Lee, Anal. Chem. 82, 9393–9400, 2010). Here we extend this capability to obtain positive and negative ion MS and MS/MS spectra in a single MS imaging experiment through polarity switching within spiral steps of each raster step. This methodology was demonstrated for the analysis of various lipid class compounds in a section of mouse brain. This allows for simultaneous imaging of compounds that are readily ionized in positive mode (e.g., phosphatidylcholines and sphingomyelins) and those that are readily ionized in negative mode (e.g., sulfatides, phosphatidylinositols and phosphatidylserines). MS/MS imaging was also performed for a few compounds in both positive and negative ion mode within the same experimental set-up. Insufficient stabilization time for the Orbitrap high voltage leads to slight deviations in observed masses, but these deviations are systematic and were easily corrected with a two-point calibration to background ions. Figure
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4.
Daiki Asakawa Nicolas Smargiasso Edwin De Pauw 《Journal of the American Society for Mass Spectrometry》2013,24(2):297-300
MALDI in-source decay (ISD) has been used for top-down sequencing of proteins. The use of the matrix 1,5-diaminonapthalene (1,5-DAN) gave abundant w ions, which are formed from the unimolecular dissociation of z? radical fragments via α cleavage reaction and thus help identify which of the isobaric amino acids, Leu or Ile, is present. The high abundance of w ions in MALDI-ISD with 1,5-DAN results from the low collision rate in the MALDI plume. MALDI-ISD with 1,5-DAN appears to be an useful method for the top-down sequencing of proteins, including discrimination of Leu and Ile near the C-terminal end. 相似文献
5.
Shan M. Randall Helene L. Cardasis David C. Muddiman 《Journal of the American Society for Mass Spectrometry》2013,24(10):1501-1512
Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P?<?0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation. Figure
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6.
Bhavana Shah Xinzhao Grace Jiang Louise Chen Zhongqi Zhang 《Journal of the American Society for Mass Spectrometry》2014,25(6):999-1011
Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. These methods require time-consuming sample preparations and do not provide site-specific glycosylation information. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). Experimental conditions were optimized to achieve accurate profiling of glycoforms. Glycan profiles obtained from LC-MS/MS peptide mapping were compared with those obtained from HPAEC, RPLC, and HILIC analyses of released glycans for several mAb molecules. Accuracy, reproducibility, and linearity of the LC-MS/MS peptide mapping method for glycan profiling were evaluated. The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans. Figure
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7.
Jiong Yang Peter Leopold Roy Helmy Craig Parish Becky Arvary Bing Mao Fanyu Meng 《Journal of the American Society for Mass Spectrometry》2013,24(8):1315-1318
With the development of new synthesis procedures, an ever increasing number of chemical modifications can now be incorporated into synthetic oligonucleotides, representing new challenges for analytical chemists to efficiently identify and characterize such molecules. While conventional mass spectrometry (MS) has proven to be a powerful tool to study nucleic acids, new and improved methods and software are now needed to address this emerging challenge. In this report, we describe a simple yet powerful program that affords great flexibility in the calculation of theoretical masses for conventional as well as modified oligonucleotide molecules. This easy to use program can accept input oligonucleotide sequences and then calculate the theoretical mass values for full length products, process impurities, potential metabolites, and gas phase fragments. We intentionally designed this software so that modified nucleotide residues can be incorporated into oligonucleotide sequences, and corresponding mass values can be rapidly calculated. To test the utility of this program, two oligonucleotides that contain a large number of chemical modifications were synthesized. We have analyzed these samples using a Q-TOF mass spectrometer and compared the calculated masses to the observed ones. We found that all of the data matched very well with less than 30 ppm mass errors, well within the expectation for our instrument operated in its current mode. These data confirmed the validity of calculations performed with this new software. Figure
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8.
Andrea F. Lopez-Clavijo Carlos A. Duque-Daza Isolda Romero Canelon Mark P. Barrow David Kilgour Naila Rabbani Paul J. Thornalley Peter B. O’Connor 《Journal of the American Society for Mass Spectrometry》2014,25(4):673-683
Glycation is a post-translational modification (PTM) that affects the physiological properties of peptides and proteins. In particular, during hyperglycaemia, glycation by α-dicarbonyl compounds generate α-dicarbonyl-derived glycation products also called α-dicarbonyl-derived advanced glycation end products. Glycation by the α-dicarbonyl compound known as glyoxal was studied in model peptides by MS/MS using a Fourier transform ion cyclotron resonance mass spectrometer. An unusual type of glyoxal-derived AGE with a mass addition of 21.98436 Da is reported in peptides containing combinations of two arginine-two lysine, and one arginine-three lysine amino acid residues. Electron capture dissociation and collisionally activated dissociation results supported that the unusual glyoxal-derived AGE is formed at the guanidino group of arginine, and a possible structure is proposed to illustrate the 21.9843 Da mass addition. Figure
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9.
We report on a new type of indium tin oxide (ITO) electrode for sensing ascorbic acid (AA). The ITO film was modified with gold-platinum alloy nanoparticles (Au-Pt NPs) functionalized with a self-assembled film of L-cysteine. The Au-Pt NPs were electrodeposited on the ITO film and characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction. A cyclic voltammetric study revealed that the electrode exhibits excellent electrocatalytic activity towards the oxidation of AA. The calibration plot for AA is linear over the concentration range from 2 to 400???M with a correlation coefficient of 0.9991. The detection limit of AA is 1???M. Figure
Gold-platinum nanoparticles were electrodeposited on the indium tin oxide electrode surface and then self-assembled with cysteine. The resulting sensor exhibited excellent electrocatalytic activity towards the oxidation of ascorbic acid. The modified electrode is high sensitivity, easy fabrication, mediator-free and low cost. 相似文献
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11.
Tatiana Y. Samgina Egor A. Vorontsov Vladimir A. Gorshkov Konstantin A. Artemenko Roman A. Zubarev Jimmy A. Ytterberg Albert T. Lebedev 《Journal of the American Society for Mass Spectrometry》2013,24(7):1037-1044
Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S–S bonds is often used in “bottom up” sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the “hidden” C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S–S bond rupture does not occur in this case. Figure
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12.
Chanjuan Liang Jeroen P. van Dijk Ingrid M. J. Scholtens Martijn Staats Theo W. Prins Marleen M. Voorhuijzen Andrea M. da Silva Ana Carolina Maisonnave Arisi Johan T. den Dunnen Esther J. Kok 《Analytical and bioanalytical chemistry》2014,406(11):2603-2611
The growing number of biotech crops with novel genetic elements increasingly complicates the detection of genetically modified organisms (GMOs) in food and feed samples using conventional screening methods. Unauthorized GMOs (UGMOs) in food and feed are currently identified through combining GMO element screening with sequencing the DNA flanking these elements. In this study, a specific and sensitive qPCR assay was developed for vip3A element detection based on the vip3Aa20 coding sequences of the recently marketed MIR162 maize and COT102 cotton. Furthermore, SiteFinding-PCR in combination with Sanger, Illumina or Pacific BioSciences (PacBio) sequencing was performed targeting the flanking DNA of the vip3Aa20 element in MIR162. De novo assembly and Basic Local Alignment Search Tool searches were used to mimic UGMO identification. PacBio data resulted in relatively long contigs in the upstream (1,326 nucleotides (nt); 95 % identity) and downstream (1,135 nt; 92 % identity) regions, whereas Illumina data resulted in two smaller contigs of 858 and 1,038 nt with higher sequence identity (>99 % identity). Both approaches outperformed Sanger sequencing, underlining the potential for next-generation sequencing in UGMO identification. Figure
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13.
José João Carvalho Michael G. Weller Ulrich Panne Rudolf J. Schneider 《Analytical and bioanalytical chemistry》2010,396(7):2617-2628
A new immunoassay has been developed based on a commercially available anti-caffeine monoclonal antibody and a de novo synthesized tracer, using horseradish peroxidase and UV–visible detection. Caffeine, which is frequently found in surface waters, can be quantified with a relative error lower than 20% for concentrations above 0.025 μg L?1 (limit of quantitation, direct analysis). The limit of detection is 0.001 μg L?1 and can be reduced by solid-phase extraction (SPE). Moreover, with minor adaptations, the assay can be used to quantify caffeine in several beverages, shampoo, and caffeine tablets. The results obtained by ELISA correlate well with those from liquid chromatography–tandem mass spectrometry (LC–MS–MS) for the tested matrices. Several surface waters from Berlin were analysed and all tested positive for caffeine, with concentrations higher than 0.030 μg L?1. In one run 66 samples can be analysed within 2 h. Figure
A caffeine ELISA is described that allows sensitive and selective analysis of surface water concentrations as well as determination of caffeine in beverages. 相似文献
14.
Roland Hellinger Jeannie Horak Wolfgang Lindner 《Analytical and bioanalytical chemistry》2013,405(25):8105-8120
The fluorescent tag 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC; AccQ Fluor reagent kit from Waters) is a commercial N-terminal label for proteinogenic amino acids (AAs), designed for reversed-phase separation and quantification of the AA racemates. The applicability of AQC-tagged AAs and AA-type zwitterionic compounds was tested for enantiomer separation on the tert-butyl carbamate modified quinine and quinidine based chiral stationary phases, QN-AX and QD-AX employing polar-organic elution conditions. The investigated test analytes included the enantiomers of the positional isomers of isoleucine (Ile), threonine, homoserine, and 4-hydroxyproline. Furthermore, β-AAs, cyclic, and heterocyclic AAs including trans-2-amino-cyclohexane carboxylic acid and trans-2-aminocyclohexyl sulfonic acid, phenylalanine derivatives substituted with halides with increasing electronegativity and 3,4-dihydroxyphenylalanine, cysteine-related derivatives including homocysteic acid, methionine sulfone, cysteine-S-acetic acid, and cysteine-S-acetamide as well as a small range of aminophosphonic acids were enantioseparated. A mechanistic interaction study of AQC-AAs in comparison with fluoresceine isothiocyanate-labeled AAs was performed. The chiral and chemoselective recognition processes involved in enantiomer separation and retention was systematically discussed. Special emphasis was set on the influential factors exhibited by the chemistry, branching position, and spatial properties of the investigated zwitterionic analytes. The general interest to separate and distinguish between different types of branched-chained AAs and metabolic side products thereof lies in the toxicity of some of these compounds, which makes for instance allo–Ile an attractive candidate in disease-related biomarker research. Figure
Separation of the four AQC-tagged isomers of 4-hydroxyproline (trans-D, cis-D, trans-L and cis-L) on the chiral stationary phase QD-AX 相似文献
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16.
Scott M. Grayson Brittany K. Myers Jonas Bengtsson Michael Malkoch 《Journal of the American Society for Mass Spectrometry》2014,25(3):303-309
The utilization of dendrimer calibrants as an alternative to peptides and proteins for high mass calibration is explored. These synthetic macromolecules exhibited a number of attractive advantages, including exceptional shelf-lives, broad compatibility with a wide range of matrices and solvents, and evenly spaced calibration masses across the mass range examined, 700–30,000 u. The exceptional purity of these dendrimers and the technical simplicity of this calibration platform validate their broad relevance for high molecular weight mass spectrometry. Figure
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17.
Christopher M. Rath Jane Y. Yang Theodore Alexandrov Pieter C. Dorrestein 《Journal of the American Society for Mass Spectrometry》2013,24(8):1167-1176
Atmospheric ionization methods are ideally suited for prolonged MS/MS analysis. Data-independent MS/MS is a complementary technique for analysis of biological samples as compared to data-dependent analysis. Here, we pair data-independent MS/MS with the ambient ionization method nanospray desorption electrospray ionization (nanoDESI) for untargeted analysis of bacterial metabolites. Proof-of-principle data and analysis are illustrated by sampling Bacillus subtilis and Pseudomonas aeruginosa directly from Petri dishes. We found that this technique enables facile comparisons between strains via MS and MS/MS plots which can be translated to chemically informative molecular maps through MS/MS networking. The development of novel techniques to characterize microbial metabolites allows rapid and efficient analysis of metabolic exchange factors. This is motivated by our desire to develop novel techniques to explore the role of interspecies interactions in the environment, health, and disease. This is a contribution to honor Professor Catherine C. Fenselau in receiving the prestigious ASMS Award for a Distinguished Contribution in Mass Spectrometry for her pioneering work on microbial mass spectrometry. Figure
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18.
Haopeng Wang Ninghang Lin Kaveh Kahen Hamid Badiei Kaveh Jorabchi 《Journal of the American Society for Mass Spectrometry》2014,25(4):692-695
We present plasma-assisted reaction chemical ionization (PARCI) for elemental analysis of halogens in organic compounds. Organohalogens are broken down to simple halogen-containing molecules (e.g., HBr) in a helium microwave-induced plasma followed by negative mode chemical ionization (CI) in the afterglow region. The reagent ions for CI originate from penning ionization of gases (e.g., N2) introduced into the afterglow region. The performance of PARCI-mass spectrometry (MS) is evaluated using flow injection analyses of organobromines, demonstrating 5–8 times better sensitivities compared with inductively coupled plasma MS. We show that compound-dependent sensitivities in PARCI-MS mainly arise from sample introduction biases. Figure
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19.
Huisong Pak Frederic Nikitin Florent Gluck Frederique Lisacek Alexander Scherl Markus Muller 《Journal of the American Society for Mass Spectrometry》2013,24(12):1862-1871
Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window (m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the m/z value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3 m/z units precursor mass window and multiple injections to cover a m/z range of 400–1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community. Figure
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20.
Aaron R. Ledvina Christopher M. Rose Graeme C. McAlister John E. P. Syka Michael S. Westphall Jens Griep-Raming Jae C. Schwartz Joshua J. Coon 《Journal of the American Society for Mass Spectrometry》2013,24(11):1623-1633
We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO2 laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety’s high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides. Figure
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