生物质谱结合IMAC亲和提取和磷酸酶水解分析蛋白质磷酸化修饰

蛋白质磷酸化是生物体内非常重要的翻译后修饰方式 ,对磷酸化蛋白质的分析及磷酸化位点的确定有助于理解与其相关的生物功能。基质辅助激光解吸 /电离飞行时间质谱和电喷雾 四极杆 飞行时间质谱这两种生物质谱仪在蛋白质鉴定和翻译后修饰分析中发挥着重要作用。固相金属亲和色谱可选择性亲和提取肽混合物中的磷酸肽 ,结合磷酸酶水解实验和基质辅助激光解吸 /电离飞行时间质谱分析可确定肽混合物中的磷酸肽 ,最后用电喷雾 四极杆 飞行时间串联质谱分析磷酸肽的序列 ,结合数据库检索确定磷酸化位点。     

急性盐度胁迫对军曹鱼稚鱼渗透压调节的影响

研究了环境盐度急性胁迫对军曹鱼(Rachycentron canadum)稚鱼鳃Na⁺-K⁺ATPase(NKA)活性及血清渗透压、Na⁺、K⁺和Cl^-离子调节的影响.结果表明:将稚鱼从盐度37中直接转移至盐度0、5、15、25、37（对照）和45的水体中,12 h后仅盐度0处理出现死亡(死亡率100％).各处理鳃NKA活性和血清渗透压在最初3 h内出现一定波动,随后变化平稳.试验结束时(12 h), NKA活性与盐度梯度呈“U”型分布,盐度5处理酶活性显著高于其它处理(P<0.05),盐度15处理活性最低,而各处理的血清渗透压大小(293～399 mOsmol·kg^-1)与盐度呈正相关;在3～12 h内稚鱼血清Na⁺和Cl^-浓度随盐度升高而升高,但增幅较小,血清K⁺浓度则与盐度呈负相关;12 h稚鱼的等渗点为328.2 mOsm·kg^-1,相当于盐度11.48,而Na⁺、K⁺和Cl^-等离子点分别为155.2、6.16和137.1 mmol·L^-1,分别相当于盐度10.68、20.44及8.41.军曹鱼在生理上具有广盐性鱼类的“低渗环境高NKA活性”特征,有较强及迅速的渗透压和离子调节与平衡能力.     

高等植物自交不亲和性的分子生物学

自交不亲和性是大多数高等植物防止近亲繁殖的一种遗传屏障。它涉及受精时雄配子（花粉）和雌蕊之间的相互作用。目前,已经分离获得了编码控制雌蕊自交不亲和性的Ｓ基因。在孢子体型自交不亲和的芸苔属中,雌蕊Ｓ基因编码Ｓ位点糖蛋白（ＳＬＧ）和Ｓ受体激酶（ＳＲＫ）。它们可能与磷酸化和去磷酸化参与了的某种信号传递有关,最后导致自交花粉生长的抑制。在配子分配体型自交不亲和的茄科中,雌蕊Ｓ位点糖蛋白为一种核糖核酸酶,称为Ｓ－核酸酶（Ｓ－ＲＮａｓｅ）。自交不亲和反应与Ｓ－核酸酶引起的花粉管ＲＮＡ降解有关,并且可能通过花粉管特异性地摄入Ｓ－核酸酶或者花粉管内存在的特异性的核酸酶抑制剂的作用,达到对自交花粉生长的抑制。另外,从配子体型自交不亲和的罂粟中,分离到了与芸台属和茄科不同的雌蕊Ｓ基因,其作用机理可能与Ｃａ＋＋参与的信号传递有关。     

水杨酸对高温强光胁迫下小麦叶绿体D1蛋白磷酸化及光系统Ⅱ功能的影响

为了研究水杨酸（SA）对高温强光胁迫下小麦叶片类囊体膜D₁蛋白磷酸化和PSⅡ功能的影响,用0.5 mmol·L^-1 SA溶液预处理灌浆期小麦叶片,以水预处理为对照,然后将预处理植株进行高温强光（35 ℃,1 600 μmol·m^-2·s^-1）处理,测定胁迫处理过程中小麦旗叶光合电子传递速率、净光合速率、叶绿素荧光参数及D₁蛋白的变化.结果表明：SA预处理有效抑制了高温强光下D₁蛋白的净降解,保持了较高的D₁蛋白磷酸化水平、全链电子传递速率和PSⅡ电子传递速率,维持了较高的PSⅡ原初光化学效率（F_v/F_m）、实际光化学效率(Ф_PSⅡ)、光化学淬灭系数（q_P）和净光合速率（P_n）.表明外源SA通过调节小麦叶绿体D₁蛋白的周转,减轻了高温强光胁迫对叶片光合机构的损伤,有利于PSⅡ的正常运转.     

“一江两河”中部流域植被净初级生产力估算

基于中分辨率成像光谱仪（MODIS）的遥感数据以及地面实际观测资料,采用数学模型方法,对西藏“一江两河”中部流域地区2000和2006年的植被净初级生产力（NPP）进行了估算.结果表明：研究区NPP由河谷向山脊逐渐递减,这与该区的水热梯度基本一致;该区单位面积年NPP平均为86.8 g C·m^-2·a^-1,2006年比2000年高2.15 g C·m^-2·a^-1,不同植被类型的单位面积年NPP以农田(243.1 g C·m^-2·a^-1)最大,荒漠(35.6 g C·m^-2·a^-1)最小;研究区两年平均总NPP为512.8×10¹⁰ g C·a^-1,2006年比2000年高12.7×10¹⁰ g C·a^-1,不同植被类型的总NPP以草甸(194.4×10¹⁰ g C·a^-1)最高,荒漠(30.3×10¹⁰ g C·a^-1)最低.研究期间,人类活动强烈区域（道路缓冲区0～4 km）的植被NPP呈下降趋势,而人类活动较难到达区域的植被NPP呈增加趋势.     

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.     

森林和沼泽对溪流水化学特征的影响

以小兴安岭北部公别拉河上游为研究区,于2004年7～9月对森林溪流和沼泽溪流水样进行水化学特征对比分析.结果表明,森林和沼泽溪流水化学类型均为重碳酸盐类钙组Ⅰ型水(C^Ca_Ⅰ).森林溪流水的pH、矿化度、总硬度、HCO₃^-、SO₄^2-、Ca²⁺、Mg²⁺、Fe均低于沼泽溪流,而总氮、总磷、Cl^-、K⁺、Na⁺则高于沼泽溪流.森林溪流和沼泽溪流中重金属元素Fe、Mn、Cu、Zn、Cd、Hg和Pb含量较低,均未超过我国Ⅰ类地表水环境质量标准.森林溪流中总氮含量为（0.27±0.04） mg·L^-1、总磷含量为（0.040±0.005） mg·L^-1,明显高于沼泽溪流中总氮含量(（0.21±0.02） mg·L^-1)和总磷含量(（0.025±0.004） mg·L^-1),沼泽湿地对N、P有较强的储存和吸附能力,且对NH₄⁺-N的吸附作用远大于对NO₃^--N的吸附.沼泽溪流中Fe含量为（0.26±0.05） mg·L^-1,显著高于森林溪流Fe含量,沼泽湿地对Fe起到还原释放作用.     

盐胁迫下构树幼苗各器官中K+、Ca2+、Na+和Cl-含量分布及吸收特征

将当年生构树幼苗置于含有不同浓度（04、1、2、3、4 g·kg^-1）NaCl的土壤中,研究其生物量积累、叶片细胞质膜透性和K⁺、Ca²⁺、Na⁺、Cl^-等离子的吸收、分布及运输,并观察盐害症状.结果表明：构树幼苗的叶片质膜透性随着NaCl浓度的增加和胁迫时间的延长而升高,根冠比随NaCl浓度的升高而增加,大于3 g·kg^-1的土壤盐胁迫对构树叶片的质膜透性及植株的生物量积累影响显著.构树幼苗各器官中Na⁺和Cl^-含量随土壤NaCl浓度升高而显著增加,K⁺和Ca²⁺则随之降低,叶片各离子含量均明显高于根和茎.说明盐胁迫影响根系对K⁺和Ca²⁺的吸收,并抑制了它们向地上部分的选择性运输,使叶和茎的K⁺和Ca²⁺含量下降.构树通过吸收积累Na⁺和Cl^-抵御土壤盐分带来的渗透胁迫,但过量的Na⁺和Cl^-积累会造成单盐毒害.作为抗盐性较高的非盐生植物,构树地上部分的拒盐作用不显著.     

盐胁迫对桑树幼苗生长、叶片水分状况和离子分布的影响

以黑龙江省两个桑树品种（秋雨桑和泰来桑）为试验材料,研究了不同盐浓度下桑树幼苗生长、叶片水分关系和不同器官中离子的分布.结果表明：盐胁迫明显降低了桑树幼苗的植株高度和每株干物质量,且对新生叶片干质量的影响大于老叶片.随着盐胁迫的加重,两个品种桑树的叶片水势、渗透势、压力势和相对含水量明显下降,根、茎中Na⁺浓度明显增加,当外界NaCl浓度达到或超过150 mmol·L^-1时,各器官中Na⁺浓度达到饱和.盐胁迫明显降低了两个品种桑树根、茎和叶片中K⁺ 和 Ca²⁺浓度,以及茎和叶片中Mg²⁺浓度,而对根中Mg²⁺浓度影响不大.Na⁺在根、茎和老叶中的区域化分布是两个品种桑树生长过程中表现出耐盐性的机理之一,而盐胁迫使叶片中的Ca²⁺、K⁺和Mg²⁺浓度降低,导致植株体内的离子亏缺,从而限制了植株的生长.     

马蔺体内主要阳离子含量月变化及分布

在自然盐碱生境下,通过测定不同月份土壤和马蔺体内主要阳离子Na⁺、K⁺、Ca²⁺、Mg²⁺的含量,研究了主要阳离子的吸收、转运变化及其在马蔺体内的分布.结果表明: 不同月份马蔺体内阳离子含量变动很大.在6月以后,随着马蔺的生长, Na⁺、K⁺、Ca²⁺和Mg²⁺4种离子在植物体内累积量逐渐增加.其中,根中Ca²⁺、Na⁺含量峰值出现在7月,分别为2.30%和0.51%,K⁺、Mg²⁺的含量峰值分别出现在9、10月,分别为0.27%和0.28%;叶片中Na⁺含量在7月达到最大值(0.57%);K⁺、Ca²⁺和Mg²⁺在8月分别达到1.30%、2.69%和0.47%.与Na⁺相比, 7、8月时马蔺对K⁺的选择吸收能力较低,但转运能力较强.马蔺对所测离子有很强的富集能力,各种离子在植物体内的含量都明显高于土壤背景值,且不同部位对离子的利用和累积能力不同,马蔺对各阳离子的累积主要集中在地上30 cm到地下40 cm范围内.马蔺地上部分平均单株K⁺、Na⁺、Ca²⁺和Mg²⁺含量分别是地下部分的9.11、4.07、0.98和2.27倍.     

基于质谱的BLAST方法在金鱼胚胎蛋白质鉴定中的应用

未知基因组及蛋白质序列数据库有限的物种的蛋白质组学分析是当前一些非模式生物物种蛋白质组学研究领域的瓶颈之一.基于同源性搜索的BLAST方法（MS BLAST）,是近年新发展起来的一种用于未知基因组的蛋白质鉴定的搜索工具,已成功应用于许多未知基因组物种的蛋白质鉴定.SPITC化学辅助方法是本实验室建立的一种改进的de novo质谱测序方法.采用MS BLAST方法对经Mascot软件数据库搜索未能鉴定到的19个金鱼胚胎蛋白质进行鉴定,其中12个蛋白质是直接测序后进行MS BLAST搜索得到的结果,另外7个蛋白质是联合MS BLAST和SPITC衍生方法得到的鉴定结果.实验结果证明,采用MS BLAST方法进行蛋白质的跨物种鉴定具有可行性和可靠性,给蛋白质的跨物种鉴定提供了一条新的途径.     

Highly informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry

Recently, various chemical modifications of peptides have been incorporated into mass spectrometric analyses of proteome samples, predominantly in conjunction with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), to facilitate de novo sequencing of peptides. In this work, we investigate systematically the utility of N-terminal sulfonation of tryptic peptides by 4-sulfophenyl isothiocyanate (SPITC) for proteome analysis by capillary reverse-phase liquid chromatography/tandem mass spectrometry (cRPLC/MS/MS). The experimental conditions for the sulfonation were carefully adjusted so that SPITC reacts selectively with the N-terminal amino groups, even in the presence of the epsilon-amino groups of lysine residues. Mass spectrometric analyses of the modified peptides by cRPLC/MS/MS indicated that SPITC derivatization proceeded toward near completion under the experimental conditions employed here. The SPITC-derivatized peptides underwent facile fragmentation, predominantly resulting in y-series ions in the MS/MS spectra. Combining SPITC derivatization and cRPLC/MS/MS analyses facilitated the acquisition of sequence information for lysine-terminated tryptic peptides as well as arginine-terminated peptides without the need for additional peptide pretreatment, such as guanidination of lysine amino group. This process alleviated the biased detection of arginine-terminated peptides that is often observed in MALDI MS experiments. We will discuss the utility of the technique as a viable method for proteome analyses and present examples of its application in analyzing samples having different levels of complexity.     

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry

Despite a recent surge of interest in database-independent peptide identifications, accurate de novo peptide sequencing remains an elusive goal. While the recently introduced spectral network approach resulted in accurate peptide sequencing in low-complexity samples, its success depends on the chance of presence of spectra from overlapping peptides. On the other hand, while multistage mass spectrometry (collecting multiple MS 3 spectra from each MS 2 spectrum) can be applied to all spectra in a complex sample, there are currently no software tools for de novo peptide sequencing by multistage mass spectrometry. We describe a rigorous probabilistic framework for analyzing spectra of overlapping peptides and show how to apply it for multistage mass spectrometry. Our software results in both accurate de novo peptide sequencing from multistage mass spectra (despite the inferior quality of MS 3 spectra) and improved interpretation of spectral networks. We further study the problem of de novo peptide sequencing with accurate parent mass (but inaccurate fragment masses), the protocol that may soon become the dominant mode of spectral acquisition. Most existing peptide sequencing algorithms (based on the spectrum graph approach) do not track the accurate parent mass and are thus not equipped for solving this problem. We describe a de novo peptide sequencing algorithm aimed at this experimental protocol and show that it improves the sequencing accuracy on both tandem and multistage mass spectrometry.     

Performance evaluation of existing de novo sequencing algorithms

Two methods have been developed for protein identification from tandem mass spectra: database searching and de novo sequencing. De novo sequencing identifies peptide directly from tandem mass spectra. Among many proposed algorithms, we evaluated the performance of the five de novo sequencing algorithms, AUDENS, Lutefisk, NovoHMM, PepNovo, and PEAKS. Our evaluation methods are based on calculation of relative sequence distance (RSD), algorithm sensitivity, and spectrum quality. We found that de novo sequencing algorithms have different performance in analyzing QSTAR and LCQ mass spectrometer data, but in general, perform better in analyzing QSTAR data than LCQ data. For the QSTAR data, the performance order of the five algorithms is PEAKS > Lutefisk, PepNovo > AUDENS, NovoHMM. The performance of PEAKS, Lutefisk, and PepNovo strongly depends on the spectrum quality and increases with an increase of spectrum quality. However, AUDENS and NovoHMM are not sensitive to the spectrum quality. Compared with other four algorithms, PEAKS has the best sensitivity and also has the best performance in the entire range of spectrum quality. For the LCQ data, the performance order is NovoHMM > PepNovo, PEAKS > Lutefisk > AUDENS. NovoHMM has the best sensitivity, and its performance is the best in the entire range of spectrum quality. But the overall performance of NovoHMM is not significantly different from the performance of PEAKS and PepNovo. AUDENS does not give a good performance in analyzing either QSTAR and LCQ data.     

Differentially isotope-coded N-terminal protein sulphonation: combining protein identification and quantification

Most proteomic labelling technologies intend to improve protein quantification and/or facilitate (de novo) peptide sequencing. We present here a novel stable-isotope labelling method to simultaneously identify and quantify protein components in complex mixtures by specifically derivatizing the N-terminus of proteins with 4-sulphophenyl isothiocyanate (SPITC). Our approach combines protein identification with quantification through differential isotope-coded labelling at the protein N-terminus prior to digestion. The isotope spacing of 6 Da (unlabelled vs. six-fold 13C-labelled tag) between derivatized peptide pairs enables the detection on different MS platforms (MALDI and ESI). Optimisation of the reaction conditions using SPITC was performed on three model proteins. Improved detection of the N-terminally derivatized peptide compared to the native analogue was observed in negative-ion MALDI-MS. Simpler fragmentation patterns compared to native peptides facilitated protein identification. The 13C-labelled SPITC resulted in convenient peptide pair spacing without isotopic overlap and hence facilitated relative quantification by MALDI-TOF/TOF and LC-ESI-MS/MS. The combination of facilitated identification and quantification achieved by differentially isotope-coded N-terminal protein tagging with light/heavy SPITC represents, to our knowledge, a new approach to quantitative proteomics.     

Algorithms for the de novo sequencing of peptides from tandem mass spectra

Proteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Database search methods are typically employed to identify proteins from complex mixtures. However, databases are not often available or, despite their availability, some sequences are not readily found therein. To overcome this problem, de novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them are detailed in this article. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and, finally, examples are used to construct possible future perspectives of the field.     

De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio

MOTIVATION: Peptide-sequencing methods by mass spectrum use the following two approaches: database searching and de novo sequencing. The database-searching approach is convenient; however, in cases wherein the corresponding sequences are not included in the databases, the exact identification is difficult. On the other hand, in the case of de novo sequencing, no preliminary information is necessary; however, continuous amino acid sequence peaks and the differentiation of these peaks are required. It is, however, very difficult to obtain and differentiate the peaks of all amino acids by using an actual spectrum. We propose a novel de novo sequencing approach using not only mass-to-charge ratio but also ion peak intensity and amino acid cleavage intensity ratio (CIR). RESULTS: Our method compensates for any undetectable amino acid peak intervals by estimating the amino acid set and the probability of peak expression based on amino acid CIR. It provides more accurate identification of sequences than the existing methods, by which it is usually difficult to sequence.     

Evaluation of Chemical Derivatisation Methods for Protein Identification using MALDI MS/MS

In proteomic studies, assigning protein identity from organisms whose genomes are yet to be completely sequenced remains a challenging task. For these organisms, protein identification is typically based on cross species matching of amino acid sequence obtained from collision induced dissociation (CID) of peptides using mass spectrometry. The most direct approach of de novo sequencing is slow and often difficult, due to the complexity of the resultant CID spectra. For MALDI-MS, this problem has been addressed by using chemical derivatisation to direct peptide fragmentation, thereby simplifying CID spectra and facilitating de novo interpretation. In this study, milk whey proteins from the tammar wallaby (Macropus eugenii) were used to evaluate three chemical derivatisation methods compatible with MALDI MS/MS. These methods included (i) guanidination and sulfonation using chemically-assisted fragmentation (CAF), (ii) guanidination and sulfonation using 4-sulfophenyl isothiocyanate (SPITC) and (iii) derivatising the epsilon-amino group of lysine residues with Lys Tag 4H. Derivatisation with CAF and SPITC resulted in more protein identification than Lys Tag 4H. Sulfonation using SPITC was the preferred method due to the low cost per experiment, the reactivity with both lysine and arginine terminated peptides and the resultant simplified MS/MS spectra.*Australian Peptide Conference Issue.**This project was funded by an ARC Linkage grant to Deane supported by TGR Biosciences and facilitated by access to the Australian Proteome Analysis Facility established under the Australian Government’s Major National Research Facilities program.     

Detection of hypoxia-related proteins in medaka (Oryzias latipes) brain tissue by difference gel electrophoresis and de novo sequencing of 4-sulfophenyl isothiocyanate-derivatized peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Two-dimensional fluorescence-based difference gel electrophoresis (DIGE) was used in combination with matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS) to identify a set of hypoxia-related biomarker proteins in medaka (Oryzias latipes) brain tissue. Each of the proteins were identified via de novo sequencing of tryptic peptides derivatized with 4-sulfophenyl isothiocyanate (SPITC), which N-terminally sulfonates peptides and promotes facile post-source decay peptide fragmentation, resulting in greatly simplified spectra consisting mainly of y-series fragment ions. We also report that addition of the non-ionic surfactant n-octyl-beta-d-glucopyranoside significantly improves SPITC-derivatized peptide recoveries. In addition, we found that a MALDI matrix consisting of the sodium-tolerant matrix 2,4,6-trihydroxyacetophenone, diammonium citrate, and alpha-cyano-4-hydroxycinnamic acid also improves ionization of SPITC-peptides, presumably by reducing ionization suppression effects from matrix contaminants, especially sodium cations. The DIGE experiments and analyses resulted in detection of six abundant proteins and related isozymes up-regulated (>1.49, p<0.005) in hypoxic medaka brain tissues, including two hemoglobin beta subunit forms, four carbonic anhydrase 2 forms, calbindin, aldolase, succinate dehydrogenase, and glutathione-S-transferase.