1.What is proteomics?
proteome = protein + genome
The proteome is the entire complement of proteins, including modifications made to a particular set of proteins, produced by an organism or system. This will vary with time and distinct requirements or stresses that a cell/organism undergoes.
蛋白質(zhì)組是蛋白質(zhì)的完整補(bǔ)充愧驱，包括由生物體或系統(tǒng)產(chǎn)生的對特定蛋白質(zhì)組的修飾。這將隨著時間和細(xì)胞/有機(jī)體經(jīng)歷的不同要求或壓力而變化留瞳。
Central dogma
2. why transcriptomics and proteomics important if we have full genome sequence info and have a lot of bioinformatics tools to analyze them?
為什么在基因組序列以及大量的工具的情況下摸柄，轉(zhuǎn)錄組和蛋白質(zhì)組學(xué)很重要？
不僅要從基因水平上進(jìn)行分析碍舍，還有研究mRNA level(e.g. Microarray/ RNAseq/Ribosome profiling)/ Protein Level.
ribosome profiling:
provides data about which mRNAs are actively translated.
通過RNA酶處理細(xì)胞裂解物柠座，把不受核糖體保護(hù)的RNA降解掉，然后分離被核糖體保護(hù)的mRNA片段片橡。通過這一實驗處理可得到30個核苷酸左右的"Footprints"妈经，可將其直接map到原始的mRNA，用于確定翻譯中的核糖體的準(zhǔn)確位置捧书。
ribosome profiling原理
- The same genome leads to different phenotypes due to differences in the genes that are actively expressed, the amount of expression products, and way of which they interfere with each others.
So why proteomics??
After mRNA production, many events can occur before an active protein is produced!
1 gene -> 1 messenger -> 1 protein dogma is not addressing nature's complexity!
- protein structure and localization defines the function
- moonlighting proteins (兼職protein)
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the proteomic line in systems biology
proteomics can aid in functional genomics at different levels
expression proteomics: what are proteins in a cell type, organelle, supramolecular assembly?
某種特定細(xì)胞的蛋白質(zhì)是什么吹泡？differential expression analysis: how is the proteome(gene expression) affected upon a trigger?
Protein localization analysis: where is my protein?
protein interaction mapping:
what are the partners of my protein? in which network is it involved?
3. What is not proteomics?
- study of structure and function of individual proteins, even they use methods like MS in proteomics.
- enzymology(enzyme kinetics)
4. proteomics challenge:
- genome size: for human 23000 protein-coding genes
- proteome size: deal with 100,0000s of protein compounds
- dynamic range: analyze the protein abundance in different plasma
j - physicochemical diversity:
mRNA 4 building blocks, for protein, is 20 building blocks, side chains have very different properties(polarity, charge, hydrophobicity)... we can't simply extract protein sufficiently, no method to amplify proteins
