上节课讲到蛋白质组与蛋白质组学蛋白质结构蛋白质相关数据库 ExPASY UniProt InterPro, HMMER PDB Reactome, KEGG PRO ( to be continued) 课件 : lilab.sysu.edu.cn Demo

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摸襄炉俞
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1 李伟忠

2 上节课讲到蛋白质组与蛋白质组学蛋白质结构蛋白质相关数据库 ExPASY UniProt InterPro, HMMER PDB Reactome, KEGG PRO ( to be continued) 课件 : lilab.sysu.edu.cn Demo

3 蛋白质相关数据库 Protein Ontology Resource (PRO)

4 蛋白质相关数据库 Protein Ontology Resource (PRO) Reference:Natale DA, et al, Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res ;45(D1):D339-D346.

5 蛋白质相关数据库 Gene Ontology defines concepts/classes used to describe gene function, and relationships between these concepts Three categories: molecular function: molecular activities of gene products cellular component: where gene products are active biological process: pathways and larger processes made up of the activities Demo -

6 蛋白质相关数据库 Protein family databases A protein family is a group of evolutionarily-related proteins Pfam A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models (by HMMer). Reference: Finn, et al, The Pfam protein families database: towards a more sustainable future, Nucleic Acids Research (2016)

7 蛋白质相关数据库 Pfam & xfam Xfam: Pfam: protein families Rfam: RNA families Dfam: repetitive DNA element sequence alignments, hidden Markov models (HMMs) TreeFam: phylogenetic trees inferred from animal genomes ipfam: protein family interactions, including domain and ligand interactions, calculated from known structures

8 蛋白质相关数据库 Protein structure databases Protein structure classification database based on the evolutionary relationships of protein domains CATH, a classification of protein structures downloaded from the Protein Data Bank, groups protein domains into superfamilies. Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Reference: Sillitoe I, et al, CATH: comprehensive structural and functional annotations for genome sequences, Nucleic Acids Res. 2015, doi: /nar/gku947

9 蛋白质相关数据库 Protein structure databases Structural Classification of Proteins (SCOP) database a manual classification of protein structural domains based on similarities of their structures and amino acid sequences.

蛋白质相关数据库 Protein-Protein Interaction (PPI) Example: The horseshoe shaped ribonuclease inhibitor (shown as wireframe) forms a protein protein interaction with the ribonuclease

10 蛋白质相关数据库 Protein-Protein Interaction (PPI) Example: The horseshoe shaped ribonuclease inhibitor (shown as wireframe) forms a protein protein interaction with the ribonuclease protein. The contacts between the two proteins are shown as coloured patches. Demo: dfj 0%93protein_interaction

11 蛋白质相关数据库 Protein-Protein Interaction (PPI) ExPASy STRING: a database of known and predicted proteinprotein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections.

12 蛋白质相关数据库 PPI - STRING Demo -

13 蛋白质相关数据库 PPI other databases IntAct Molecular interactions Demo: Biomolecular Interaction Network Database (BIND) Molecular Interaction Database (MINT) MIPS Mpact BioGRID

14 第二课 : 蛋白质组数据什么是蛋白质谱 (MS Mass Spectrometry)? HUPO, HPP, HPM PRIDE & its tools

15 MS 数据蛋白质谱 (MS Mass Spectrometry) 一种将质谱仪用于研究蛋白质的技术完整的蛋白质通过酶切作用后, 分解成多肽混合物, 进入质谱仪后, 通过多肽指纹图谱或串联质谱的方法进行鉴定实现从多肽水平对蛋白质的分析和鉴定

16 MS 数据 Source: Trap_XL-Thermo_Scientific_1.jpg

17 MS 数据蛋白质谱原理在质谱仪中肽段混合物电离形成带电离子质谱分析器的电场磁场将具有特定质量与电荷比值 ( 即质荷比,M/Z) 的肽段离子分离开来检测器收集分离的肽段离子, 确定每个离子的 M/Z 值质量分析器分析得到蛋白质所有肽段的 M/Z 图谱, 即蛋白质的一级质谱峰图离子选择装置自动选取强度较大肽段离子进行二级质谱分析, 输出选取肽段的二级质谱峰图通过和理论上的一级质谱峰图和二级质谱峰图进行比对而鉴定蛋白质

18 MS 数据 Source: ctrometer_schematic.svg

19 第二课 :MS 数据及分析各多肽片段的保留时间各质荷比片段的相对丰度

20 MS 数据蛋白串联质谱 (Tandem Mass Spectrometry) 碰撞诱导解离, 离子分子反应, 光解 Source:

21 蛋白质组数据库 HUPO - Human Proteome Organization an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. HUMAN PROTEOME PROJECT (HPP)

22 蛋白质组数据库 HUMAN PROTEOME PROJECT (HPP) By HUPO to revolutionize our understanding of the human proteome via a coordinated effort to map the entire human proteome in a systematic effort n-proteome-project/

23 蛋白质组数据库 HUMAN PROTEOME PROJECT (HPP)

24 蛋白质组数据库 HUMAN PROTEOME MAP an interactive resource by integrating the massive peptide sequencing result from the draft map of the HPP based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry

25 蛋白质组数据库 HUMAN PROTEOME MAP

26 蛋白质组数据库 PRIDE - Proteomics IDEntification Database Powered by EBI A centralized, standards compliant, public data repository for proteomics data A public-domain repository for mass spectrometry based proteomics data Including protein and peptide identifications, posttranslational modifications and supporting spectral evidence A core member in the ProteomeXchange (PX) consortium Datasets are handled by expert biocurators

27 蛋白质组数据库 PRIDE Datasets 8852 projects assays Reference: Vizcaíno JA, et al, 2016 update of the PRIDE database and its related tools, Nucleic Acids Res. 2016; 44: D447 D456.

28 蛋白质组数据库 PRIDE supports (Proteomics Standards Initiative) data standard formats (mzml and mzidentml) implements the data requirements and guidelines of the ProteomeXchange Consortium the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange PRIDE Cluster and PRIDE Proteomes

29 蛋白质组数据库 PRIDE Ecosystem

30 蛋白质组数据库 PRIDE submission process

31 蛋白质组数据库 PRIDE Demo Submit data Browse data Use tools

32 蛋白质组数据库 PRIDE Inspector Toolsuite the handling and visualization of different experimental output files spectra (mzml,mzxml, and the most popular peak lists formats) peptide and protein identification results (mzidentml, PRIDE XML, mztab) quantification data (mztab, PRIDE XML) freely available at Toolsuite/ Ref: Molecular & Cellular Proteomics 15: /mcp.O , , 2016

33 蛋白质组数据库 PRIDE Inspector Toolsuite

34 第三课蛋白质序列比对检索 (1) generation of mass spectrometers output files (2) peptide/protein identification step (3) peptide/protein quantification step (4) data deposition (PRIDE, MassIVE) (5) private access (6) public access

35 蛋白质组数据库 ProCon PROteomics CONversion tool a conversion tool written in Java for conversion of proteomics identification data into standard formats mzidentml and Pride XML It allows the conversion of Sequest /Comet.out files, of search results from the popular and often used ProteomeDiscoverer 1.x software, and search results stored in the LIMS systems ProteinScape 1.3 and 2.1 into mzidentml and PRIDE XML Ref: Journal of Proteomics 129 (2015) 56 62

36 第三课

37 蛋白质序列检索 Sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.

38 蛋白质序列检索 Use of sequence alignment Finding homologous or similar sequences Finding consensus sequence Variation analysis Conservation and evolution Functional analysis of gene and protein

39 蛋白质序列检索 Homology V.S Similarity Sequence homology is the biological homology between protein or DNA sequences, defined in terms of shared ancestry in the evolutionary history of life. Sequence similarity Homology among proteins or DNA is typically inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution of a common ancestor

40 蛋白质序列检索 Ortholog V.S. paralog Two segments of DNA can have shared ancestry either because of a speciation event (orthologs), or because of a duplication event (paralogs). Image source:

《中国科学》A、E、G与F小开本版式设计

《中国科学》A、E、G与F小开本版式设计 222 E 2006, 36(2): 222~234 * 1** 1,2 1,2 1,2 1,2 3 3 1 1 1,2 (1., 100080; 2., 100039; 3., 200031),. ;,,.. 20 90 (human genome project, HGP), ; HGP 2003, 21. (proteomics) ; (computational proteomics),,,

上节课讲到 蛋白质组与蛋白质组学 蛋白质结构 蛋白质相关数据库 ExPASY UniProt InterPro, HMMER PDB Reactome, KEGG PRO ( to be continued) 课件 : lilab.sysu.edu.cn Demo

上节课讲到蛋白质组与蛋白质组学蛋白质结构蛋白质相关数据库 ExPASY UniProt InterPro, HMMER PDB Reactome, KEGG PRO ( to be continued) 课件 : lilab.sysu.edu.cn Demo