If the signal is saturated then it isn’t possible to accurately compare different protein abundances. Before trying to take any quantitative measurements it is critical to make sure that the signal is not saturated and is in its linear range (figure 2).Crucially this technique can only inform of relative changes in abundance between samples therefore without known standards, cannot be used to give exact concentrations. Protein expression can be quantitatively compared within a immunoblot using densitometry. How to quantify protein expression from a Western blot A high R2 value indicates increased accuracy in interpretation of the unknown proteins MW. Example standard curve of log(MW) against relative migration (Rf). The actual protein molecular weight as determined by mass spectrometry is likely to differ from the estimated through western blotting due to differences in glycosylation status, experimental inaccuracies and some proteins not being amenable to full denaturation by SDS.įigure 1.The general equation is: which in figure 1 simplifies to: Use the equation of the best fit line to calculate the mass of the target using its Rf.This should be linear if the samples are fully denatured and the gel percentage was adequate for sufficient separation. Plot the log(MW) of the protein standards against relative migration distance (Rf) on a graph and generate a curve of best fit.This can either be measured using a ruler or within appropriate software. Calculate the relative migration distance (Rf) of each protein standard and the target protein using the equation below.Run the gel using a molecular weight ladder, transfer to the membrane and then visualise the proteins using a dye such as Coomassie blue or Ponceau.The molecular weight of a protein can be estimated by comparing the migration of proteins of known molecular weight (such as in a protein ladder) and the target protein. Measuring the molecular weight of proteins Western blots are essential for comparing protein expression between experimental conditions and for working out the molecular weight of proteins. P.S: I incubated these membranes with primary antibody A, read it, then primary antibody B, read it, then lastly with housekeeping gene.Western blots are a key technique where antibodies are used to probe immobilised proteins on a membrane in order to visualise them. Thus, I am now very confused of which program is more reliable. And my PI does not agree that ImageJ makes more sense than Odyssey. This time the numbers are much similar to each other, but I still don't understand how the area and percent work and what they really mean. Then I tried using ImageJ to re-do all measurements. If even the housekeeping gene readings are so different, how can we expect the soluble protein readings to be accurate? (this is a question) For example, I ran 40ug of proteins for all samples, but I would get an average intensity reading of 80 on one membrane and 120 on another for the housekeeping gene. However, no matter how similar the procedures were, there was still some huge difference in band expression. We are trying to compare between 2 sets of 8 samples, so I ran 2 western blots simultaneously all the time. Not sure if many people are familiar with the Odyssey software, but we use it to scan our membrane and to quantify the bands. I am currently using IR-dye secondary antibodies purchased from LI-COR to detect some soluble proteins. Hi all, this is my very first project and I hadn't have any experience at all.
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