特邀专家
11月10日和11日两天全天为邀请专家作大会报告，本次会议不征文，只设邀请报告。确认参会的专家名单（截止到2010年10月22日上午12：00，按照报告顺序排名）如下。
杨芃原 复旦大学 |
报告题目：糖蛋白结构的质谱数据库 ════════════════════════════════ 摘要：糖蛋白的结构分析需要借助于糖链结构数据库， 但由于糖链结构的复杂性， 构建一个理论的糖链结构数据库似乎是不太可行的方法。因此，通过各种技术构建专业性强、针对性明显的糖链结构数据库已经引起了关注。 我们的研究基于生物质谱的数据分析， 建立了蛋白质糖基化位点以及糖链结构数据库。通过自己开发的一种对比实验方法，先鉴定去糖链结构的糖基化肽段序列，建成理论糖肽库，为后期在实际样品中的快速鉴定糖肽组成提供数据基础。 开发了一套糖蛋白鉴定和糖链结构确立的理论算法，并将理论算法在我们创建的软件GRIP: Glycopeptide Reveal & Interpretation Platform中全部实现。 实际的分析表明， 我们的新方法可以有效的进行通量化的糖蛋白结构质谱分析， 展现了比较好的应用前景。 
Fig.1 Topo-strucure of GRIP for exp MS tree |
应万涛 北京蛋白质组研究中心 |
报告题目：核心岩藻糖化蛋白质特异性发掘的系统解决方案 Establishment of a systematic method coupling consecutive MSn and software tools for charactering core-fucosylated glycoproteins ════════════════════════════════ Abstract: Core-fucosylated glycoproteins have been known to involve a variety of biological and pathological processes, especially in hepatocellular carcinoma, TGF-β1 and EGF signaling pathways, pancreatic cancer and so on. Current methods, such as lectin blotting, could map core-fucosylated glycoproteins. However, when dealing with the glycosite information, it is hard to discriminate core-fucosylated ones from general glycosites. A more efficient and targeted approach is needed to screen core-fucosylated glycoproteins. Here, we simplified carbohydrate parts of three core-fucosylated glycopeptides, following with LTQ-FT analysis under MS2 and MS3 mode. Several special fragments signal appear to be particular and helpful to identify core fucosylated N-linked glycopeptides, which may be useful in its large scale identification by mass spectrometer and searching engine directly. The most obvious characteristic in the MS2 spectra of CID model in ion trap was that the intensity of the highest fragment peak was about ten times higher than that of the second one. These peaks were attributed to mass of the peptide parent ion mass and a GlcNAc residue, which resulted from neutral loss of the fucose unit. In a consecutive MS3 analysis, a neutral loss of GlcNAc appears to be the most strong peak (about two times higher than other peaks), and the peaks’ intensity in MS3 distribute much more even than that in MS2. Standing on these characteristics summarized from the three glycopeptides’ data, we are developing software tools to identify core fucosylated glycopeptides automatically, and design a strategy to determine core-fucosylated glycoproteins from normal and cancer individual. This strategy will be aim to establish a high confident core fucosylated glycopeptides database for biomarker discovery. |
张凯中 加拿大西安大略大学 |
报告题目：利用串联质谱技术解析多糖结构 Glycan Structure Sequencing with Tandem Mass Spectrometry ════════════════════════════════ Abstract: Glycosylation which adds carbohydrate moieties to a protein is one of the important post-translational modifications. The carbohydrates in glycoproteins are commonly referred as glycans which are assembled from simple sugars. Since each sugar can have up to five linkage sites, glycans are assembled in a tree-like structure. The structural variation in glycans is fundamental to their biological activity. The glycan structure sequencing problem is to determine the tree-like structure. We study glycan de novo sequencing with tandem mass spectrometry. We show results concerning complexity and algorithm of the problem. Some experimental results based on a heuristic algorithm will also be presented. |
汪迎春 中国科学院遗传与发育生物学研究所 |
报告题目：解码细胞迁移过程中的信号通路网络 Deciphering the Signaling Network in the Leading Edge of the Migrating Cells ════════════════════════════════ Abstract:Cell polarization to form a dominant pseudopodium in the leading edge is necessary for sustained directional cell migration, a process that plays a central role in many important physiological and pathological pathways including wound healing and cancer metastasis. However, the mechanism underlying polarization of migratory cells is still unclear because it has not been possible to biochemically isolate the front and the back compartments for large-scale protein analysis. Here we use microporous filters to differentially isolate the pseudopodium and cell body compartments for large-scale (> 3000 proteins) quantitative proteomic analysis. We found that proteins involved in the regulation of actin cytoskeleton, focal adhesion dynamics, and MAPK signaling are highly enriched and/or differentially phosphorylated in the pseudopodium, whereas proteins involved in nuclear functions and metabolism are highly enriched and/or differentially phosphorylated in the cell body. Importantly, several hypothetical phosphoproteins were also differentially distributed and phosphorylated in polarized cells, including the novel tyrosine kinase (PEAK1, pseudopodial-enriched atypical kinase one). Functional analysis of PEAK1 revealed that PEAK1 colocalizes with actin cytoskeleton and focal adhesions, and is necessary for cell migration and tumor progression. Our findings provided novel insight into the spatial organization of complex signal transduction pathways that control directional cell migration and cancer cell metastasis and reveal PEAK1 is a new tyrosine kinase that regulates the cell migration and invasion machinery. |
王 通 暨南大学 |
报告题目：信号通路分析辅助的功能蛋白质组学研究策略 Pathway analysis-assisted study strategy in functional proteomics ════════════════════════════════ Abstract: Major breakthroughs in proteomics, particularly in mass spectrometry and computational proteomics, are continuously increasing the capacity of identifying low abundance proteins as well as acquiring more relative quantification information. As a result, new ways of experimental designs and the amount of valid data are expanding at an extremely high rate. As one of the greatest challenges, functional interpretation of these data is a crucial link between proteomic profiling and biological probing, turning investigations from descriptive into mechanistic. Regarding this tough job, numerous pathway analysis tools, including both public and commercial ones, are available. Among them, Ingenuity Pathway Analysis (IPA) is one of the concentrated and specialized biological function mining tools. In this talk, IPA-assisted functional proteomic investigations performed by our group will be presented as examples. These include a proteomic modeling study of HIV infected astrocyte-microglia crosstalk, addressing the protection effects of astrocytes in containing HIV infection in central nervous system, as well as a lung cancer cell proteomic model, defining new endpoints of epithelial to mesenchymal transition (EMT). These studies employed the strategy of proteomic profiling--pathway analysis--biological validation, successfully identifying target pathways and nodes of regulation by computational pathway analysis, as well as directing downstream biological investigations and validating, in turn, the accuracy of pathway analysis. |
关慎恒 加州大学旧金山分校 |
报告题目：利用稳定同位素代谢标记研究哺乳动物动态蛋白质组的数据处理平台 A data processing platform for mammalian proteome dynamics studies using stable isotope metabolic labeling ════════════════════════════════ Abstract: Mammalian in vivo heavy metabolic labeling using heavy isotopes such as 15N allows for proteome scale investigations of protein dynamics in various tissues. These proteomic dynamics studies can provide a deeper understanding of healthy development and well-being of complex organisms, as well as the possible causes and progression of diseases. An essential and enabling component of these large scale investigations is a robust data processing platform, which is capable of reduction of a large set of LCMSMS raw data files into the desirable protein turnover rate constants. The data processing platform described here is the integration of a variety of software modules into a workflow. This software platform consists of some established software tools such as the database search engine and several novel data processing modules specifically developed for 15N metabolic labeling, such as (1) cross-extraction of 15N-containing ion intensities from raw data files of varying biosynthetic incorporation times, (2) computation of peptide 15N incorporation distributions, (3) aggregation of multiple peptide relative isotope abundance curves into a protein curve. In order to reduce the propagation errors in a long chain of the processing steps, processing parameter optimization and noise reduction procedures are performed in some necessary processing modules. |
徐 平 北京蛋白质组研究中心 |
报告题目：大规模SILAC标记定量蛋白质组学研究中的数据分析 Data analysis in large scale quantitative proteomics study with SILAC approach ════════════════════════════════ Abstract: Protein ubiquitination is a highly conserved modification that plays a central regulatory role in eukaryotic cells. Ubiquitin (Ub) is covalently attached to protein substrates by a cascade of enzymatic reactions involving activating enzymes (E1), conjugating enzymes (E2), and ligases (E3). These reactions generally form an isopeptide bond between the carboxyl group of the C terminus of Ub (G76) and the 3-amino group of a lysine residue within the substrates. All seven lysines in Ub contribute to the assembly of polyUb chains, thereby producing a variety of structures with diverse lengths and linkages. On the other hand, ubiquitinated substrates may be sorted into different pathways based on diverse polyUb structures. Canonical K48-linked polyUb chains are believed to be the principal signal for targeting substrates for degradation by the 26S proteasome, whereas K63-linked chains act in a range of other processes, including protein trafficking, DNA repair, and inflammation. However, the prevalence of other polyUb topologies and their roles in biological processes are not well known. Recent proteomics developments in mass spectrometry will facilitate functional study on ubiquitinated proteins. However large scale identification of heterogeneously ubiquitinated protein and quantification for low abundant proteins is still remaining challenge. Large-scale analyses of ubiquitinated proteins are usually performed by combining affinity purification strategies with mass spectrometry. Here, we provide a strategy for differentiating ubiquitinted proteins from co-purified unmodified components by reconstructing virtual Western blots for proteins analyzed by gel electrophoresis and mass spectrometry. Because protein ubiquitination, especially polyubiquitination, causes a dramatic shift of molecular weight, the difference between experimental and expected molecular weight was used to confirm the status of ubiquitination. Experimental molecular weight of putative yeast ubiquitin-conjugates was computed from the value and distribution of spectral counts in the gel using a Gaussian curve fitting approach. Unmodified proteins in yeast cell lysate were also analyzed as a control to assess the accuracy of the method. Multiple thresholds that incorporated the mass of ubiquitin and/or experimental variations were evaluated with respect to sensitivity and specificity. Furthermore, by profiling both the entire yeast proteome and ubiquitinated proteins in wild-type and ubiquitin K11R mutant strains using mass spectrometry, we identified K11 linkage-specific substrates. In order to study K11 chain function, we applied quantitative proteomics analysis through SILAC approach. Both biological and technical replicates have been utilized for evaluating the variation in large scale quantitative proteomics study. By combining all of these strategies, we found that Ubc6 primarily synthesizes K11-linked chains, and K11 linkages function in the ERAD pathway. |
陆豪杰 复旦大学 |
报告题目：体内终端氨基酸标记在定量蛋白质组学中的应用 In vivo termini amino acid labeling for quantitative proteomics ════════════════════════════════ 摘要：定量蛋白质组学已经成为当今科学研究的一个热点和挑战，在多种定量分析策略中，细胞稳定同位素标记（SILAC）方法已被广泛而有效的应用于各种重要的生物学过程和医学问题的研究中。在这里，我们建立了一个新的定量策略---体内终端氨基酸标记方法，重精氨酸-6和重赖氨酸-6稳定同位素分别培养细胞，蛋白混合后经过Lys-N和Arg-C酶解，使肽段两端分别含有轻重精赖氨酸，这样在一级质谱中为同一质荷比，但在串级质谱中可以观察到成对的b, y碎片离子，通过直接比较对峰的强度可以得到肽段和蛋白的定量信息。相比传统的SILAC，由于一级质谱中肽段母离子质量相同，这样降低了样品分析的复杂度，而且提高了一级质谱分析的灵敏度，同时克服了iTRAQ方法低端报告离子的抑制效应，可以在全质量范围内提供多对碎片离子的定量信息，为准确的肽段和蛋白定量提供了可靠的依据。 |
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邓宁 浙江大学 |
报告题目：利用基于肽段计数的无标记定量技术揭示线粒体蛋白质组的功能特性 Quantitative Analysis of Mitochondrial Proteomes using Normalized Spectral Abundance Factor ════════════════════════════════ Abstract: As double-membrane organelles in the cell, mitochondria are essential for cell metabolism, transport, biosynthesis, and signaling. Quantitative proteomics has been increasingly recognized as an essential
proteomics tool to generate significant insight in biomedical research. In this study, we used the normalized spectral abundance factor (NSAF) to quantitatively analyze the mitochondrial proteome for human
heart, mouse heat and mouse liver samples. In this approach, the spectral counts of a protein were divided by its length and normalized to the total sum of spectral counts / length in a given LC-MS/MS analysis. |
邵 晨 中国协和医科大学 |
报告题目：尿液蛋白质疾病标志物数据库 The urinary protein biomarker database ════════════════════════════════ 摘要：尿液是重要的疾病标志物来源。目前的尿蛋白质组疾病标志物研究面临着两个问题：（1）当前技术手段的限制和正常人个体间较大的差异，降低了候选标志物的可信度；（2）由于实验时未对所有可能影响尿蛋白质组的疾病同时比较，很多候选标志物不具有疾病特异性。通过实验手段改善这两个问题必须大幅度增加工作量，而通过对已有研究结果进行数据整合和对比分析，可以以最小的代价获取最多的信息，指导后续的实验工作。 本研究通过收集、整理目前已发表的蛋白质组研究文献，建立了尿液中的蛋白质标志物数据库。以互联网平台的形式展现出来，使得相关领域的研究者可以通过这个平台方便、快捷、全面地对自己的数据进行分析，研究泌尿系统的生理功能，或选取最有可能成为疾病标志物的蛋白质分子进行下一步的验证，从而降低实验耗费，提高研究效率。 研究还通过对不同实验条件和手段、不同疾病类型的数据进行整合和对比分析，以及对建立的疾病—蛋白质标志物的网络图结构进行分析，对数据库收集的潜在疾病标志物的可信度和疾病特异性进行了评价。 |
谢 鹭 上海生物信息中心 |
报告题目：基于质谱数据发现小鼠基因组新蛋白质编码区域 The discovery of novel protein-coding features in mouse genome based on mass spectrometry data ════════════════════════════════ Abstract: Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. Proteogenomics strategy has been employed in many eukaryotes to validate protein-coding genes directly on protein level in large scale and has provided valuable complementary information in genome annotation.We applied a proteogenomics method to detect un-annotated protein-coding regions in mouse genome. Two searchable proteomic datasets were constructed, one with all possible encoded exon junctions (EJCT dataset) for the discovery of novel exon splice events, and the other with all putative encoded exons (ORF dataset) for finding uninterrupted novel protein-coding regions. The two datasets were combined with a public full-length protein dataset (competitive dataset) respectively and queried against 496 high-accuracy tandem mass spectrometry (MS/MS) RAW files from diverse mouse samples. By setting a strict spectra false discovery rate threshold at close to 0, thirty two unique peptides (matching 149 spectra) from EJCT dataset were discovered which straddle novel exon junctions, and 104 unique peptides (matching 450 spectra) from ORF dataset were located in 99 unique protein-coding regions. Aligning backwards from these peptides to the parent genome could classify them into seven distinct new protein coding categories based on their genome loci relative to adjacent previously annotated genes or exons. Some of the novel peptides were under cross validation by RT-PCR. Our work discovered a number of novel mouse protein-coding regions directly at the translational product level, which implied that proteogenomics strategy could be performed to provide substantial evidences for genome annotation in encoded genes and help novel gene identifications. |
张 勇 华大基因 |
报告题目： 从新一代测序技术的组学到基于质谱仪的蛋白质组学 -- 华大基因的生物信息学 From NGS Genomics to Ms-based Proteomics -- BGI's bioinformatics activities ════════════════════════════════ 摘要： 1999年9月9日，随着“国际人类基因组计划1%项目”的正式启动，华大基因在北京正式 成立。过去11年，先后完成了若干具有国际领先地位的大型基因组项目，在《Nature》 和《Science》等国际一流的杂志上发表多篇论文。2007年，华大基因主力南下深圳， 基因组领域迎来第二代测序浪潮，新型测序仪使得基因组从物种水平上升到个体水平。 一直以来，测序和生物信息学堪称华大基因的两大核心竞争力。对于海量数据的信息分
析和挖掘成为华大基因立足世界基因组领域的根本。新一代测序技术被广泛用于DNA, RNA测序，针对动植物、人，华大基因与许多科学家合作，一起启动并完成了若干项目。
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赵 屹 中科院计算技术研究所 |
报告题目：腾冲嗜热菌的多温度条件下的蛋白质组基因组学研究 ════════════════════════════════ 摘要：蛋白质组基因组学是近几年诞生的一门用蛋白质组数据信息，也是结合转录组数据来解析基因组的新兴学科。MS/MS 质谱实验辅助基因组注释已经在多种物种中成功运用。这里我们整合腾冲嗜热菌的多温度条件下的蛋白质组质谱数据及转录组深度测序数据进行分析。结果显示：(1)转录组数据可以覆盖70%以上的2588核酸库基因；(2) 74%以上的质谱鉴定肽段可以寻找到转录组证据。此外，通过基因的定量表达分析，我们比较了不同温度条件下基因转录表达的差别：初步得出在四种温度条件下都有表达的基因359条，而每个温度条件下都有自己特异表达的基因；结合两种独立来源的组学数据互相验证研究，发现其中有80多个不属于2588范围内的转录区，其中2个区域强烈支持质谱鉴定得到的新基因区域，21个区域属于可能的新非编码RNA。我们还对于腾冲嗜热菌基因组中预测的2588条基因进行了注释修正。这种系统的数据整合分析方法无疑对于生物学的研究，尤其是基因组学，将起到非常大的辅助作用。 |
董梦秋 北京生命科学研究所 |
报告题目：基于HCD谱图的肽段从头测序 De novo Sequencing of Peptides Using HCD Spectra ════════════════════════════════ Abstract: Previous de novo sequencing efforts could correctly interpret only 30% of high- and medium-quality tandem mass spectra generated by collision-induced dissociation (CID). This compares poorly to database search, and hence, de novo sequencing did not find any practical use in biological research. Our study shows that higher-energy collisional dissociation (HCD) is much more superior to CID for de novo sequencing. This is because HCD produces high mass accuracy tandem mass spectra, the majority of which contain complete ion series. Besides, abundant internal and immonium ions in the HCD spectra can help differentiate between similar sequences. Based on the characteristics of HCD spectra, an algorithm called pNovo was developed for efficient de novo sequencing. Tested with HCD data of tryptic digests of either a simple protein mixture or a highly complex C. elegans whole-worm lysate, pNovo correctly assigned peptide sequences to at least 80% of the HCD spectra that were independently identified by database search. The number of correct full-length peptide sequences generated by pNovo was comparable with that obtained by database search. A distinct advantage of de novo sequencing is that deamidated peptides and peptides with amino acid mutations can be identified efficiently without extra cost in computation. In short, by taking advantage of the HCD characteristics, pNovo makes an excellent tool for de novo peptide sequencing. |
王全会 中科院北京基因组研究所 |
报告题目：从未知基因组到可测定的蛋白质组：通过从头测序来研究依赖于pH值的N10细菌蛋白质组 From an unknown genome to a measurable proteome: Studying on the pH-dependent proteomes in N10 bacteria by denovo sequencing ════════════════════════════════ Abstract: It is very important to understand why alkaliphiles could survive from alkaline environment, which is still poorly understood yet. Alkalimonas amylolytica N10 is such a kind of alkaliphilic bacteria found in China, which could survive from pH 7.5 to 11.0. Till now, only limited numbers of proteins were found in alkaliphiles, which are involved in regulation of pH homeostasis and play important roles in the adaptive mechanism. More proteomic surveys are highly expected to explore the pH-dependent proteins in alkaliphilic bacteria. Being absent of genome data of N10, a combined strategy, including derivative with 4-sulfophenyl isothiocyanate (SPITC) and non-derivative de novo peptide sequencing were used to interpret proteome data. The protein identification rate was highly improved from 18.1% to 73.6%, and approximately 40 pH-dependent proteins were identified from the 72 differential spots. This study give us the confidence that mass data could be directly interpreted but not dependent upon genomics. |
马 斌 加拿大滑铁卢大学 |
报告题目：利用质谱和同源数据库进行全蛋白测序 Complete Protein Sequencing with MS/MS and a Homologous Database ════════════════════════════════ Abstract: Protein identification with database search and peptide de novo sequencing are routinely carried out with tandem mass spectrometry (MS/MS) today. However it is still a challenging problem to use MS/MS to sequence a complete protein that is not in a sequence database. Such possibility has been demonstrated by biochemists with human interpretation of the data. We present a novel algorithm and automated software, named CHAMPS, for sequencing the complete protein from MS/MS data and a homologous protein database. Experiments with two standard proteins showed that our automated method yields greater than 99% sequence coverage and 100% sequence accuracy on these two proteins. |
孙瑞祥 中科院计算技术研究所 |
报告题目：电子转运裂解质谱:特征发现与鉴定应用 Electron Transfer Dissociation: Characterization and Applications in Protein Identification ════════════════════════════════ Abstract: In recent years, electron transfer dissociation (ETD) has enjoyed widespread applications from sequencing of peptides with or without post-translational modifications to top-down analysis of intact proteins. However, peptide identification rates from ETD spectra compare poorly with those from collision induced dissociation (CID) spectra, especially for doubly charged precursors. This is in part due to an insufficient understanding of the characteristics of ETD and consequently a failure of database search engines to make use of the rich information contained in the ETD spectra. In this study, we statistically characterized ETD fragmentation patterns from a collection of 461,440 spectra, and subsequently implemented our findings into pFind, a database search engine developed earlier for CID data. From ETD spectra of doubly charged precursors, pFind 2.1 identified 63~122% more unique peptides than Mascot 2.2 under the same 1% false discovery rate. For higher charged peptides as well as phosphopeptides, pFind 2.1 also consistently obtained more identifications. Of the features built into pFind 2.1, the following two greatly enhanced its performance: 1) refined automatic detection and removal of high-intensity peaks belonging to the precursor, charge-reduced precursor, or related neutral loss species, whose presence often set spectral matching askew; 2) a thorough consideration of hydrogen-rearranged fragment ions such as z+H and c-H for peptide precursors of different charge states. Our study has revealed that different charge states of precursors result in different hydrogen rearrangement patterns. For a fragment ion, its propensity of gaining or losing a hydrogen depends on (1) the ion type (c or z) and (2) the size of the fragment relative to the precursor, and both dependencies are affected by (3) the charge state of the precursor. In addition, we discovered ETD characteristics that are unique for certain types of amino acids (AAs), such as a prominent neutral loss of SCH2CONH2 ( 90.0014 Da) from z ions with a carbamidomethylated cysteine at the N-terminus and a neutral loss of histidine side chain C4N2H5 (81.0453 Da) from precursor ions containing histidine. The comprehensive list of ETD characteristics summarized in this paper should be valuable for automated database search, de novo peptide sequencing, and manual spectral validation. |
叶明亮 中科院大连化学物理研究所 |
报告题目：基于质谱的蛋白质组学数据处理新方法和平台发展 Development of Methods and Platform for Data Processes in Mass Spectrometry Based Proteome Research ════════════════════════════════ 摘要：在基于质谱的蛋白质组学研究中，高可信度的肽段和蛋白的鉴定信息是蛋白质组学研究的目的和后续生物信息分析挖掘的源头。我们在蛋白质组学数据处理方法和平台方面，分别发展了针对非修饰肽段和磷酸化肽段鉴定的数据筛选方法，并建立了一个磷酸化蛋白质组学数据处理专用平台以促进蛋白质组学研究。 对于非修饰肽段的鉴定，发展了一种基于遗传算法的数据筛选门槛优化方法以克服基于模型的鉴定结果筛选方法的高风险性和大部分数据筛选标准仍基于经验筛选标准的问题[1]。通过结合正伪数据库检索，该方法可以安全快速的针对每个数据集得出指定可信度下的最优筛选门槛，在不降低可信度的前提下提高了肽段和蛋白鉴定的数目。
对于非修饰肽段的鉴定，还发展了一种基于实例的肽段鉴定概率的计算方法[2]。该方法基于Shannon信息熵和k近邻算法，利用局部假阳性率实现对肽段鉴定正确概率进行计算。计算得到概率可以很好的与实际概率相匹配。由于该方法不基于假设模型，因而可以安全的应用于各种具有不同特点的数据处理。该方法通过合理的结合多个具有判别能力的参数值，大大提高了肽段和蛋白鉴定的数目，并且计算得到的概率可以直接应用于蛋白鉴定概率的计算。
针对磷酸化蛋白质组学中磷酸化肽段鉴定难，假阳性率高，主要依赖于人工验证的现状，发展了一种结合MS2和MS3图谱以及正伪数据库检索的自动磷酸化肽段鉴定方法[3]。该方法结合了MS2和MS3的鉴定信息，提高了磷酸化肽段鉴定的灵敏度和可信度，可以自动的对磷酸化肽段进行鉴定而无需进一步的人工验证。进而发展了一种基于分类筛选的磷酸化肽段鉴定方法，该方法结合了MS2/MS3方法的高可信度，并且考虑了部分不易发生中性丢失的磷酸化肽段的鉴定，进一步提高了磷酸化肽段鉴定的灵敏度[4]。此外发展了一种利用小库进行正伪检索，实现对单个蛋白质磷酸化的深度分析[5]。
建立了一个跨平台，支持多个数据库检索软件的磷酸化蛋白质组学数据处理平台，克服了目前磷酸化蛋白质组学数据处理中的繁琐性，大大加快了磷酸化蛋白质组学数据处理的速度，提高了鉴定结果的灵敏度和可靠性。并且该平台可以同时适用于非修饰和具有其他修饰的肽段和蛋白数据处理[6]。
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余维川 香港科技大学 |
报告题目：基于优化的肽质量指纹谱方法鉴定蛋白质混合物 Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification ════════════════════════════════ Abstract: In current proteome research, the most widely used method for protein mixture identification is probably peptide sequencing. Peptide sequencing is based on tandem Mass Spectrometry (MS/MS) data. The disadvantage is that MS/MS data only sequences a limited number of peptides and leaves many more peptides uncovered. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins from single-stage MS data. Unfortunately, this technique is less accurate than the peptide sequencing method and can not handle protein mixtures, which hampers the widespread use of PMF technique. In this talk, we tackle the problem of protein mixture identification from an optimization point of view. We show that some simple heuristics can find good solutions to the optimization problem. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF-based protein mixture identification. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures, especially in the identification of low-abundance proteins which are less likely to be sequenced by MS/MS scanning. |
付 岩 中科院计算技术研究所 |
报告题目：基于相关谱图对的非限制性修饰检测 Unrestrictive modification detection based on related spectral pairs ════════════════════════════════ Abstract: Identification of proteins and their modifications via liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an important task for the field of proteomics. However, due to the complexity of tandem mass spectra, the majority of the spectra cannot be identified. The presence of unanticipated protein modifications is among the major reasons for the low spectral identification rate. Efficient and comprehensive detection of protein modifications has become one of the most important and challenging problems in MS/MS-based proteomics. In this report, I will introduce two new computational approaches for unrestrictive detection of modifications. Both of them are based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample. The first approach takes full advantage of the precursor information and can detect abundant modifications in a very fast speed. The second approach is by open spectral library searching and can detect lower-abundance modifications. On various datasets, our methods successfully detected many anticipated modifications, yielding deep insights into the data. The spectral identification rates were significantly increased, and many modified peptides were identified. |
朱云平 北京蛋白质组研究中心 |
报告题目：评价诱饵库设计，搜索策略，匹配误差和质量控制对鸟枪法蛋白质组学中肽段鉴定精确性的影响 Evaluation of the effect of decoy design, search strategy, mass tolerance and quality control method on the accuracy of peptide identifications in shotgun proteomics ════════════════════════════════ Abstract: In the last decade, a large number of quality control methods have been developed to improve the sensitivity of peptide identifications. False discovery rate (FDR) and q-value have been widely used to estimate/control false positive identifications based on target-decoy strategy. However, the accuracy of q-value estimation and its influence factors need to be carefully examined. Using a widely used standard protein dataset with high mass accuracy, we found that decoy database of reversing tryptic peptides, composite database search generated significant lower deviation from actual q-values across various parent mass tolerance and quality control methods and that parent mass tolerance could significantly affect q-value accuracy when separate search was applied. This analysis offered an important clue as to how to find the optimal decoy design, search strategy, search parameters, and quality control method to achieve sensitive and accurate peptide identifications in shotgun proteomics. |
盛泉虎 上海生命科学院 |
报告题目：BuildSummary : 一个基于目标-诱饵策略的蛋白质鉴定整合软件 BuildSummary: A software tool for assembling protein ════════════════════════════════ Abstract:Target-decoy database search strategy has been widely accepted as a standard method for evaluating the confidence of peptide/protein identifications in high throughput shotgun proteomics. In order to maximize the number of confident proteins above a threshold of false discovery rate (FDR), a post-processing procedure is often used to integrate results from different peptide search engines for the same dataset. Specifically, three issues should be addressed in the post-processing procedure: 1) how to maximize the number of peptide-spectrum matches (PSMs) above a given peptide FDR? 2) how to maximize the number of confident proteins above a given protein FDR? and 3) how to integrate results from different search engines? We show that the PSMs with different charges, different number of missed internal cleavage sites, different modification states, different number of protease termini should be grouped into different categories for filtering PSMs above an FDR threshold. We also developed an iterative procedure that simultaneously assigns FDRs to identified peptides and corresponding proteins in each group of protein. Finally, we build a general framework to integrate results from different peptide search engines (or the same engine by using different parameters) based on the post-processing procedure. The framework allows a user to combine many independent PSM scoring algorithms including de novo sequencing and spectrum library search algorithms, as long as the same peptide FDR is applied to each of them by using target-decoy search approach. We implemented the methods described above in user-friendly software called BuildSummary, which report a list of identified proteins under a user-defined protein FDR as well as a list of identified peptides under a low peptide FDR in these proteins. The software is tested by using several shotgun proteomics datasets acquired by multiple LC/MS instruments from two different biological samples, and shows satisfactory performance. BuildSummary can be downloaded as part of software suite ProteomicsTools freely from http://www.proteomics.ac.cn/software/index.htm. |
张 法 中科院计算技术研究所 |
报告题目：冷冻电镜中的计算方法：图像数据处理和三维重构 Computational methods in cryo-electron microscopy: image data processing and 3D structure reconstruction ════════════════════════════════ Abstract: Cryo-electron microscopy (cryoEM) has emerged as a method of choice for determining the three-dimensional (3D) structures of biological complexes towards atomic resolution. It has the potential of revealing structural details of large macromolecular machines at near atomic scale without requiring crystallization, and unlike other techniques, can examine structural changes occurring during operation of the molecule. To obtain a high resolution structure using cryoEM, large numbers (104~105) of individual images of the structure is combined to form an average three-dimensional electron density map. Particle selection has becoming a significant bottleneck in cryoEM. Moreover, each of individual images requires a complex series of computing to obtain the final result. So the needs for computational power are constantly growing with the increasing complexity of algorithms and the amount of data needed to push the resolution limits. In this report, I will present some research progresses of computational methods of our group in cryoEM, which includes: 1) Picker, an automated particle selection algorithm, 2) ParaEMAN, a high efficient parallel strategy for 3D structure reconstruction of cryoEM and 3) ISAFRS, a new 3D structure reconstruction system in cryoEM. |
江 瑞 清华大学 |
报告题目：DomainRBF: 一种对疾病相关蛋白质结构域进行优先排序的贝叶斯回归方法 DomainRBF: a Bayesian regression approach to the prioritization of associations between protein domains and human complex diseases ════════════════════════════════ Abstract: Domains are basic units of proteins, and thus exploring associations between protein domains and human inherited diseases will greatly improve our understanding of the pathogenesis of human complex diseases and further benefit the medical prevention, diagnosis and treatment of these diseases. Based on the assumption that domain proximities in a domain-domain interaction network imply phenotype similarities between human diseases, we propose in this paper a Bayesian regression approach named "domainRBF" (domain Rank with Bayes Factor) to prioritize associations between candidate domains and human diseases. Using a compiled a dataset that contains 1,614 associations between 671 domains and 1,145 phenotypes, we demonstrate the effectiveness of this approach through three large-scale leave-one-out cross-validation experiments (random control, simulated linkage interval, and genome-wide scan) in terms of three criteria (precision, mean rank ratio, and AUC score). Results show that the approach can effectively rank susceptible domains among the top of a few candidates. We further show that the proposed approach is robust to parameters involved and the underlying domain-domain interaction network through a series of permutation tests. With the validity of this approach being accessed, we show the possibility of ab initio inference of domain-disease associations and gene-disease associations, and we illustrate the well agreement of our inference with evidence of genome-wide association studies for four common diseases (type 1 diabetes, type 2 diabetes, Crohn's disease, and breast cancer). Finally, provide a precalculated genome-wide landscape of associations between 5,490 protein domains and 5,080 human diseases and offer free access to this resource. |
卜东波 中科院计算技术研究所 |
报告题目：蛋白质结构“字母表”设计 Designing Succinct Structural Alphabets ════════════════════════════════ Abstract: The three dimensional structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence, \cite{Sim97,Levitt2002}. For each small sequence segment, there are only a few more likely substructures. We call them the "structural alphabet" for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments. Integer linear programming technique is applied to derive the best combination of these sequence and structural information items. This approach generates significantly more accurate and succinct structural alphabets with more than 50\% improvement over the previous accuracies. With these novel structural alphabets, we are able to construct more accurate protein structures than the state-of-art Ab Initio protein structure prediction programs such as ROSETTA. We are also able to reduce the Kolodny's library size by a factor of 8, at the same accuracy. |
张红雨 华中农业大学 |
报告题目：蛋白质作为分子化石 Proteins as molecular fossils ════════════════════════════════ Abstract: On the stage of evolution, fossils are central players. Fossils not only refer to preserved body remains of ancient organisms, but also include molecules that are durable during the geological history. The latter are also known as molecular fossils. Traditionally, molecular fossils are small-molecule metabolites, including biomarkers (e.g., porphyrins, hopanoids, biphytanes and sterols), and very conserved coenzymes (e.g., ATP, NAD, NADP and FAD). Recently, accumulating evidence indicated that proteins can also serve as molecular fossils, which include protein remains of ancient organisms, such as collagen peptides in dinosaurs, and extremely conserved protein features, such as protein folds. Using a phylogenomic structural census in hundreds of proteomes, we build phylogenies and timelines of domains at fold and fold superfamily levels of structural complexity. These timelines correlate approximately linearly with geological timescales and can be used to date some crucial events in life history, such as planet oxygenation and organism diversification. |