I am working on a proteomic analysis project on iPSC-derived neurones. After the protein pellets were collected from cell homogenates I began acetone precipitation. There was a minor spillage while vortexing the acetone-treated pellets in Eppendorf tubes, the labels on 2 tubes were erased but we were certain which tubes they were to a certain extent. Not too much of the solution was spilt but the volume difference compared to other tubes was noticeable. My question is how could I address these biases or any nullified data in quality control of the LC-MS raw outputs at a later stage? Thank you very much for your time and appreciate any help.
By selecting a housekeeping protein and applying normalization through this protein's peak intensity. Like western blot protein normalization approach, you may find a cytoskeleton protein and use it as an inherent internal standard...
Good luck
If we are talking about shotgun proteomics analysis, you also could normalize on the total peptide amount. If you normalize on specific proteins, like İsmail Emir Akyildiz recommended, you could try various housekeeping proteins and check if you get similar results as reliability check.
- Badges
- Science topic
- Similar topics
- Psychology