As the question, I don't know that what difference between spatial proteomics and affinity enrichment (AE) or purification (AP)-MS in interactomics. Anyone can help?
Hello Paul,
for spatial proteomics you first need to separate your sample/tissue of interest in defined subcellular fractions. We have performed this with defined rat brain areas into cytosol, mitochondria, nuclei, synaptosomes, microsomes and myelin by using differential sucrose density gradient centrifugation. Each of this fractions where then analysed by proteomic techniques (2DE - MALDI MS or LC-MS/MS).
In case of affinity purification or interaction proteomics you are only interested in interaction partners with a high affinity to your bait (protein or affinity matrix).
Best, Murat
Hi Paul
Spatial proteomics: what is located in the same portion of the cell as your protein of interest. As Murat has said, one possibility is sucrose gradient fractionation of your cell which I have also used. Other methods include LOPIT or hyperLOPIT. There are also proximity biotinylation-based methods such as bioID or APEX2. Whats important is these methods tell you what is in the general vicinity of your protein which will include interaction partners, but they don't conclusively show an interaction.
Interaction proteomics: what binds your protein. These can be direct or indirect interactions.
Best
Ed
+1 for Ed. Paul, define 'spatial proteomics' please. What exactly is the question you are trying to answer? This will determine the choice of method (Organelle proteomics/LOPIT, proximity proteomics, AP-MS - all of these have a multitude of variantes based on where you are fishing, and what it is you would like to see).
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