Mass spectral characterization of a protein-nucleic acid photocrosslink

A photocrosslink between basic fibroblast growth factor (bFGF155) and a high affinity ssDNA oligonucleotide was characterized by positive ion electrospray ionization mass spectrometry (ESIMS). The DNA was a 61-mer oligonucleotide photoaptamer bearing seven bromodeoxyuridines, identified by in vitro selection. Specific photocrosslinking of the protein to the oligonucleotide was achieved by 308 nm XeCl excimer laser excitation. The cross-linked protein nucleic acid complex was proteolyzed with trypsin. The resulting peptide crosslink was purified by PAGE, eluted, and digested by snake venom phosphodiesterase/alkaline phosphatase. Comparison of the oligonucleotide vs. the degraded peptide crosslink by high performance liquid chromatography coupled to an electrospray ionization triple quadrupole mass spectrometer showed a single ion unique to the crosslinked material. Sequencing by collision induced dissociation (MS/MS) on a triple quadrupole mass spectrometer revealed that this ion was the nonapeptide TGQYKLGSK (residues 130-138) crosslinked to a dinucleotide at Tyr133. The MS/MS spectrum indicated sequential fragmentation of the oligonucleotide to uracil covalently attached to the nonapeptide followed by fragmentation of the peptide bonds. Tyr133 is located within the heparin binding pocket, suggesting that the in vitro selection targeted this negative ion binding region of bFGF155.     

质谱技术解析磷酸化蛋白质组

蛋白质磷酸化是生物体内存在的一种普遍的调节方式,在细胞信号传递中占有极重要的地位.质谱已逐渐被人们认为是挑战这一领域的有利工具.综述了目前利用质谱技术分析磷酸化蛋白质的方法,包括利用固定化的金属亲和层析柱、抗体和化学标签技术富集目的分子,肽片段质量图和前体离子扫描（precusor ion scans）等技术检测磷酸化肽段,串联质谱对磷酸化肽段测序鉴定磷酸化位点,以及引入质量标签对蛋白质的磷酸化水平进行定量等.虽然现在已经有很多可行的方法用于分析磷酸化蛋白质,但要达到从少量生物样品中解析其全部磷酸化蛋白质仍需要有很多技术上的突破.     

重组人源性抗HBsAg Fab抗体的肽质量图谱分析

重组人源性抗HBsAg Fab抗体具有较好的特异性和抗原结合活性,为了更好的阐明毕赤 酵母表达的重组人源性抗HBsAg Fab抗体的性质,用基质辅助激光解析飞行时间质谱(MALDI- TOF-MS)对重组Fab抗体的分子质量和肽质量图谱进行了分析。结果显示,毕赤酵母表达的重组 人源性抗HBsAg Fab抗体的分子质量为50678．49Da,与根据其一级结构计算的理论分子质量相 比多2763．84 Da,显示酵母表达的重组Fab抗体为糖蛋白。用胰蛋白酶酶解重组Fab抗体后进行 MALDI-TOF-MS分析显示,大部分的酶解肽段均能检测出来。结果表明毕赤酵母表达的重组Fab 抗体与预期的结构一致。     

The Heat and Mass Transfer Analysis of a Leaf

Understanding the heat and mass transfer processes of plant leaves is essential for plant bionic engineering. A general thermophysical model was established for a plant leaf with particular emphasis on the transpiration process. The model was verified by the field measured stomatal resistance and temperature of a camphor leaf. A dynamical simulation revealed that diurnal transpiration water consumption is dominated by the solar irradiance and the day-average temperature of the leaf is dominated by the ambient air temperature; transpiration plays an important role in the cooling of the leaf, in average it could dissipate around 32.9% of the total solar energy absorbed by the leaf in summer. To imitate the thermal infared characteristic of the real leaf, the up surface of the bionic leaf must have emissivity and solar absorptivity close to those of a real leaf and its shape and surface roughness must be similar to those of the real leaf. The key point is that the bionic leaf must be able to evaporate water to simulate the transpiration of a plant leaf, appropriate adsorbent can be used to realize this function.     

Mass spectrometry-based proteomics for translational research: a technical overview

Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionation coupled with tandem mass spectrometry is well suited to handle mixtures of hundreds or thousands of proteins. Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease.     

Mass spectrometry of nucleotides and oligonucleotides

Recent advances in the use of mass spectrometry for the determination of the molecular weight and sequencing of oligonucleotides are disscussed. Matrix-assisted laser desorption (MALDI) and electrospray ionization (ESI) mass spectrometry have been shown to be especially important techniques for both molecular weight assignment and sequencing of oligonucleotides, and are the focus of this article which covers the literature through early 1996.     

Mass distributions of a macromolecular assembly based on electrospray ionization mass spectrometric masses of the constituent subunits

Macromolecular assemblies containing multiple protein subunits and having masses in the megadalton (MDa) range are involved in most of the functions of a living cell. Because of variation in the number and masses of subunits, macromolecular assemblies do not have a unique mass, but rather a mass distribution. The giant extracelular erythrocruorins (Ers), ∼ 3.5 MDa, comprized of at least 180 polypeptide chains, are one of the best characterized assemblies. Three-dimensional reconstructions from cryoelectron microscopic images show them to be hexagonal bilayer complexes of 12 subassemblies, each comprised of 12 globin chains, anchored to a subassembly of 36 nonglobin linker chains. We have calculated the most probable mass distributions forLumbricus andRiftia assemblies and their globin and linker subassemblies, based on theLumbricus Er stoichiometry and using accurate subunit masses obtained by electrospray ionization mass spectrometry. The expected masses ofLumbricus andRiftia Ers are 3.517 MDa and 3.284 MDa, respectively, with a possible variation of ∼ 9% due to the breadth of the mass distributions. TheLumbricus Er mass is in astonishingly good agreement with the mean of 23 known masses, 3.524 ± 0.481 MDa.     

Mass Cytometry: Protocol for Daily Tuning and Running Cell Samples on a CyTOF Mass Cytometer

In recent years, the rapid analysis of single cells has commonly been performed using flow cytometry and fluorescently-labeled antibodies. However, the issue of spectral overlap of fluorophore emissions has limited the number of simultaneous probes. In contrast, the new CyTOF mass cytometer by DVS Sciences couples a liquid single-cell introduction system to an ICP-MS.¹ Rather than fluorophores, chelating polymers containing highly-enriched metal isotopes are coupled to antibodies or other specific probes.^2-5 Because of the metal purity and mass resolution of the mass cytometer, there is no "spectral overlap" from neighboring isotopes, and therefore no need for compensation matrices. Additionally, due to the use of lanthanide metals, there is no biological background and therefore no equivalent of autofluorescence. With a mass window spanning atomic mass 103-203, theoretically up to 100 labels could be distinguished simultaneously. Currently, more than 35 channels are available using the chelating reagents available from DVS Sciences, allowing unprecedented dissection of the immunological profile of samples.^6-7Disadvantages to mass cytometry include the strict requirement for a separate metal isotope per probe (no equivalent of forward or side scatter), and the fact that it is a destructive technique (no possibility of sorting recovery). The current configuration of the mass cytometer also has a cell transmission rate of only ~25%, thus requiring a higher input number of cells.Optimal daily performance of the mass cytometer requires several steps. The basic goal of the optimization is to maximize the measured signal intensity of the desired metal isotopes (M) while minimizing the formation of oxides (M+16) that will decrease the M signal intensity and interfere with any desired signal at M+16. The first step is to warm up the machine so a hot, stable ICP plasma has been established. Second, the settings for current and make-up gas flow rate must be optimized on a daily basis. During sample collection, the maximum cell event rate is limited by detector efficiency and processing speed to 1000 cells/sec. However, depending on the sample quality, a slower cell event rate (300-500 cells/sec) is usually desirable to allow better resolution between cells events and thus maximize intact singlets over doublets and debris. Finally, adequate cleaning of the machine at the end of the day helps minimize background signal due to free metal.     

质谱流式技术用于单细胞检测

质谱流式技术(mass cytometry)是利用质谱原理对单细胞进行多参数检测的流式技术,能够在单细胞水平实现超过50种标志物的同时测量,显著增强了对细胞生长进程和复杂细胞系统的评估能力。该文简要介绍了质谱流式技术的基本工作原理,并从金属元素标记、质量分析器、高维单细胞数据处理等方面展开论述,阐明设计新型金属元素标签和选择飞行时间质谱的必要性,归纳分析高维单细胞数据的算法并总结各种算法的优点和局限性。     

Mass spectrometric identification of a kaempferol tetraglycoside from Solanum seed

The trisaccharide present in the kaempferol 3-triglucoside-7-rhamnoside of potato seed has been identified by hydrolytic experiments and by MS measurements on the perdeuteriomethylated glycoside as sophorotriose (glucosyl-β1 → 2-glucosyl-β1 → 2-glucose).     

生物质谱技术在蛋白质组学研究中的应用

随着技术的进步,蛋白质组学的研究重心由最初旨在鉴定细胞或组织内基因组所表达的全部蛋白质转移到从整个蛋白质组水平上阐述包括蛋白翻译后修饰、生物大分子相互作用等反映蛋白质功能的层次。多种质谱离子化技术的突破使质谱技术成为蛋白质组学研究必不可少的手段。质谱技术联合蛋白质组学多角度、深层次探索生命系统分子本质成为现阶段生命科学研究领域的主旋律之一。本文简要综述了肽和蛋白质等生物大分子质谱分析的原理、方式和应用,并对其发展前景做出展望。     

Mass mortality of Japanese macaques in a western coastal forest of Yakushima

The mass mortality of wild Japanese macaques (Macaca fuscata Blyth) was observed in a warm temperate forest of Yakushima, southern Japan. Demographic changes of eight troops between August 1998 and August 1999 were studied and 56% of macaques disappeared from the five intensively studied troops. Mortality varied among troops: two troops became extinct, while another troop did not decrease in size. The rate of mortality of the other troops was between 33 and 80%. The variation in mortality among the troops was either the outcome of local concentrations of mortality or of intertroop competition. The rate of mortality decreased with increasing distance from the two extinct troops and with increasing troop size; these two factors could not be separated statistically. The direct cause of death was diagnosed as pneumonia for four out of five fresh carcasses. The fleshy fruit production in autumn 1998 was the lowest in 14years, and macaques had relied on leaves earlier than in usual years. It was exceptionally hot and dry in the summer of 1998. The exceptionally poor fruit production and hot summer of this year, with the resulting shortage of high-quality foods, was consistent with the scenario that mass mortality was due to the poor nutritional conditions. However, the possibility that epidemics caused the mass mortality cannot be ruled out. Our findings proved that primates in a seemingly stable habitat experience fluctuations in demographic parameters under natural conditions.     

Probing the Influence of Mutations on the Stability of a Ferredoxin by Mass Spectrometry

Hydrogen/deuterium exchange, which depends on solvent accessibility, can be probed by mass spectrometry (MS) to get information on protein conformation or protein–ligand interaction. In this work, the conformational properties of the cyanobacterium Anabaena wild-type ferredoxin as well as of two single-site mutants (Phe 65 Ala and Arg 42 Ala) were studied. After incubation of the wild type and mutant proteins in deuterated water and quenching of the exchange at low pH, the proteins were rapidly digested at high enzyme-to-substrate ratio using immobilized pepsin, and the resulting peptides were characterized using ESI-MS. We have identified specific regions for which the H-bonding or solvent accessibility properties were perturbed by the mutations. These results show that this approach can provide local information on the influence of mutations, even for a highly structured protein like ferredoxin, and sometimes in regions distant from the mutation point.     

Accurate Mass Measurements Using MALDI-TOF with Delayed Extraction

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry is now an essential tool in biopolymer analysis. Sensitivity and mass range are unsurpassed, but mass measurement accuracy and resolution have been limited. With delayed extraction and a reflecting analyzer, mass measurements using MALDI-TOF can be made with an accuracy of a few parts per million (ppm). It is possible to distinguish Lys from Gln in peptides, and to determine the elemental composition of smaller molecules (mass 100–500). In database searching strategies, a smaller mass window, resulting from an increase in mass accuracy, greatly decreases the number of possible candidates. Mass measurement accuracy with errors less than 5 ppm is demonstrated on a mixture of 12 peptides ranging in mass from ca. 900 to 3700 Da. Mass measurements on 13 peaks in an unseparated tryptic digest of myoglobin gave results with an overall average error less than 3.5 ppm, with a maximum error of 7 ppm.     

小菜蛾群体繁殖技术

小菜蛾是世界性十字花科蔬菜的主要害虫 ,也是迄今研究认为抗药性发展最快、最为严重的农业害虫。害虫抗药性以及蔬菜害虫防治技术等方面的研究使小菜蛾成为重要的实验昆虫。本文讨论小菜蛾室内群体繁殖技术的几种方法     

电热蒸发-催化热解-原子吸收法直接测定茶叶中镉

重金属镉（Cd）一直是茶叶产品质量安全关注的重点。本研究基于电热蒸发-催化热解-原子吸收光谱仪（SS-ETV-AAS）,使用镍材质样品舟,在300 mL/min空气条件下,350 ℃干燥20 s,350~725 ℃灰化55 s;引入300 mL/min氢气与空气反应形成氮氢混合气氛,在725~800 ℃（50 s）下完成Cd的蒸发;之后,在高岭土填料催化热解炉800 ℃和准直管700 ℃条件下,氮氢火焰原子吸收测定镉的含量。方法检出限（LOD）为0.3 ng/g、定量限（LOQ）为1.0 ng/g,R2>0.998,多次测定的相对标准偏差（RSD）为1.8%~8.6%,多种茶叶样品中Cd的测定值与微波消解石墨炉原子吸收光谱法（GFAAS）无显著性差异（P>0.05）,Cd的回收率在92%~107%之间。试验结果表明,该方法灵敏度高、稳定性好、简单高效,且无需消解处理,样品分析时间仅为3min,适用于茶叶中Cd的快速检测。     

Mass spectrometry of trimethylsilyl derivatives of gibberellin glucosides and glucosyl esters

The mass spectra of trimethylsilyl ethers of six gibberellin-β-d-glucopyranosyl ethers and five gibberellin-β-d-glucopyranosyl esters are discussed. The fragmentation patterns are shown to be affected by the structural variations of the aglycones.     

种子重量与海拔的相关性分析：

种子重量与海拔的关系是植物生态学中重要而尚存争议的问题。本文对中国123科853种2879份野生植物种子的重量在海拔上的变化特点以及二者之间的相互关系进行了深入研究,结果显示：种子重量总体上与海拔呈负相关,种子重量级别多样性和生活型多样性随海拔上升呈阶梯状下降。但7级种子中,只有10。级种子的重量与海拔呈负相关;7种生活型中,只有灌木和匍匐草本的种子重量与海拔呈负相关;在种水平上,只有8．2％的物种种子重量与海拔存在相关性。本研究揭示了我国种子重量与海拔之间的复杂关系,以及遗传和环境对种子重量的影响,对植物育种、森林管理以及入侵植物的防治具有一定指导意义。     

种子重量与海拔的相关性分析

种子重量与海拔的关系是植物生态学中重要而尚存争议的问题。本文对中国123科853种2879份野生植物种子的重量在海拔上的变化特点以及二者之间的相互关系进行了深入研究,结果显示：种子重量总体上与海拔呈负相关,种子重量级别多样性和生活型多样性随海拔上升呈阶梯状下降。但7级种子中,只有100级种子的重量与海拔呈负相关;7种生活型中,只有灌木和匍匐草本的种子重量与海拔呈负相关;在种水平上,只有82%的物种种子重量与海拔存在相关性。本研究揭示了我国种子重量与海拔之间的复杂关系,以及遗传和环境对种子重量的影响,对植物育种、森林管理以及入侵植物的防治具有一定指导意义。     

Quality Assessment of Tandem Mass Spectra by Using a Weighted K-Means

Introduction  The tandem mass spectrometer is a powerful tool with which to generate peptide (tandem) mass spectrum data for the analysis of complex biological protein mixtures in genomic-related disease cell lines. However, the majority of experimental tandem mass spectra cannot be interpreted by any database search engines. One of the main reasons this happens is that majority of experimental spectra are of quality too poor to be interpretable. Interpreting these “un-interpretable” spectra is a waste of time. Therefore, it is worthwhile to determine the quality of mass spectra before any interpretation. Objectives  This paper proposes an approach to classifying tandem spectra into two groups: one with high quality and one with poor quality. Methods  The proposed approach has two steps. First, each spectrum is mapped to a feature vector which describes the quality of the spectrum. Then, a weighted K-means clustering method is applied in order to classify the tandem mass spectra. Results and Conclusion  Computational experiments illustrate that one cluster contains the majority of the high-quality spectra, while the other contains the majority of the poor-quality spectra. This result indicates that if we just search the spectra in the high-quality cluster, we can save the time for searching the majority of poor-quality spectra while losing a minimal amount of high-quality spectra. The software created for this work is available upon request.