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.
蛋白质组是蛋白质的完整补充，包括由生物体或系统产生的对特定蛋白质组的修饰。这将随着时间和细胞/有机体经历的不同要求或压力而变化。

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?

为什么在基因组序列以及大量的工具的情况下，转录组和蛋白质组学很重要？
不仅要从基因水平上进行分析，还有研究mRNA level(e.g. Microarray/ RNAseq/Ribosome profiling)/ Protein Level.

ribosome profiling:
provides data about which mRNAs are actively translated.
通过RNA酶处理细胞裂解物，把不受核糖体保护的RNA降解掉，然后分离被核糖体保护的mRNA片段。通过这一实验处理可得到30个核苷酸左右的"Footprints"，可将其直接map到原始的mRNA，用于确定翻译中的核糖体的准确位置。

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.

Naively, we could state if we know how much RNA is, we know how much of the protein

So why proteomics??

After mRNA production, many events can occur before an active protein is produced!

见456步

1 gene -> 1 messenger -> 1 protein dogma is not addressing nature's complexity!

need to address protein abundance, but also modifications, turn over, ...

• protein structure and localization defines the function
• moonlighting proteins (兼职protein)

• 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?
  某种特定细胞的蛋白质是什么？

• 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