Analysis Of Shotgun Proteomics Data

Question

[9921]

Hi everyone, I have 3 samples (Cell) with 3 replicate. In shotgun proteomics 1750 protein with variable expression identified for each sample . How can I found up and down regulation protein between 3 samples? How can I do ANOVA analysis for them? Thanks

[Devon Ryan]

You say "3 sample (Cell) with 3 replicate", by that do you mean "3 cell-types with 3 biological replicates each"? I assume that's what you mean, but figured I'd ask before incorrectly answering. BTW, you probably just want pairwise t-tests, since I suspect you'll want p-values for each of the 3 comparisons.

[Michael]

Please be more specific (I think that's the most used request on scientific forums?). It is very hard to answer your question, because we do not know what your problem really is. Also, I find it rude to have two obvious typos in the tags, couldn't you take a little more care if the answer means anything to you?

Answer 1

[Devon Ryan]

Given the N of 3 per group, you're likely to want to share information across proteins. In that case, you could actually just use limma in R/Bioconductor. There happens to be a thread on the Bioconductor list discussing analysing proteomics data here. That thread also discusses possible data transformation methods that you might pursue, since you've not otherwise mentioned anything about the form your data takes.