Notes 20100329.094512 Zhenyu Group Meeting
From SnOwy - Ed's Wiki Notebook
Differential Expression Proteomics
- methods...
- response to stimuli (toxicity, nutrient, mutation, overexpression)
- DIGE: differencing gel electrophoresis: fluorescence dyes (different protein spots)
- limitations exist
- alternatives: quantitative proteomics
- mass spec based quantitative proteomics (2): tagged or label-free
- tagged...
- ICAT: isotope-coded affinity-tag -- labels cysteines, also impacts mass spectroscopy
- iTRAQ -- uses reporter ions
- SILAC
- label-free...
- ...
- Post translational modification-- phosporylation: pTyr pSer pThr mass +80
- labelled: we add an isotope or some other tag that will facilitate differential detection during mass spectrometry
- label-free: we add nothing, but must run mass spectrometry several times for different samples in order to determine mass
- mass spectrometry: this is a more general operational definition: we mean to include all techniques that allow mass determination
- interesting notion of heavy water-- normally, we mean deuterium oxide as heavy water;
- in biology, this term actually means that the oxygen atom is replaced with an 18-oxygen isotope so that it is incorporated into a protein during digestion