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
Modifications:
Groups/condition: Diabetic vs. Control
Diabetic mice
FL0408_MSQ911_MariaRohm_554_F30
FL0408_MSQ911_MariaRohm_545_F11_544_F33
FL0408_MSQ911_MariaRohm_554_M3
FL0408_MSQ911_MariaRohm_582_M1
Control mice
FL0408_MSQ911_MariaRohm_544_F13
FL0408_MSQ911_MariaRohm_544_F31
FL0408_MSQ911_MariaRohm_582_M13
FL0408_MSQ911_MariaRohm_544_M1
Modifications: Fixed: Oxidation(M) Deamidation NQ
Variable: Carbamidomethyl(C)
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.
Abundance (shown in the paper):
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.
Label min. ratio coun -- should this be 1? I am not sure what this means.
Should the following fields be checked?
