Our lab has recently conducted a proteomic study on a plant species we do research on. We asked the company doing the mass spec to also do the preliminary data analysis which included normalising the data. The data returned to me shows only the significantly abundant proteins (already annotated) and has the log fold change values as well as the normalised abundance values for each replicate. I am having some difficulty in performing routine analysis since most of the tutorials or R scripts I have found starts with the raw sequencing data. I am not very proficient in R so am having trouble navigating how best to deal with the data I have. Any recommendations on software or web-tools that does not require the input of raw sequencing data would be greatly appreciated.