This is a follow up to my previous question here.
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic β-cells" (figures from here: link). I want to process RAW files from this proteomics experiment. I'm trying to set up the analysis in MaxQuant and I am looking for some help in defining some parameters.
Sample: PRIDE dataset (https://www.ebi.ac.uk/pride/archive/projects/PXD012979). I want to analyse 8 sample files (please find the file labels and appropriate condition labels below).
Instrument used to generate the data: Orbitrap Fusion Lumos
Method: Label free quantification
Groups/condition: Diabetic vs. Control
Modifications: Fixed: Oxidation(M) Deamidation NQ
My objective is to get the values of the normalized abundance (kindly find the figure below from the article associated with this dataset, for 4 control vs. 4 diabetic samples) from MaxQuant analysis.
MaxQuant setup: I'm not sure what has to be filled in the fields circled in red. Could someone please have a look? Should the fraction be set to 1? I am not sure what has to be filled for the dataset in the link that I shared above.