Hi everyone!

I'm trying to answer some questions about protein abundance in healthy/diseased human tissues using mass spec data online. I've got a pipeline planned but because I'm new to proteomic analysis I'm not sure if I am making any glaring errors.

As an example, say I am interested in comparing protein abundance between psoriatic skin and atherosclerotic plaques. I don't have the means to collect this data myself, so I go to PRIDE and use samples from the following datasets:

a) https://www.ebi.ac.uk/pride/archive/projects/PXD021673 (psoriasis)

b) https://www.ebi.ac.uk/pride/archive/projects/PXD035555 (atherosclerotic plaque)

Then, I do the following processing:

1. I convert the .RAW files to .mzML (with peak-picking enabled)
2. For each separate experiment, I use openMS to do feature detection
3. For each separate experiment, I use openMS to do feature map retention time alignment
4. For each separate experiment, I use openMS to do feature linking
5. For each separate experiment, I use openMS to do an accurate mass search
6. For each separate experiment, I do QC (imputation/filtering)
7. I should now have intensities for each protein in each sample in each experiment
8. For each protein, I do a Kruskal Wallis test. Group 1 consists of the psoriasis samples. Group 2 consists of the atherosclerotic plaque samples.
9. Perform FDR and do a volcano plot to find enriched proteins

Does this seem sensible? Am I making any glaring errors?

My main hesitation relates to comparing data from two different experiments. I am also unsure if experiments need to have been performed with the same instrument

Thank you very much for your time - Aay references to exemplar papers that I could consult would be greatly appreciated if you know them.