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