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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): enter image description here

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. enter image description here

Label min. ratio coun -- should this be 1? I am not sure what this means. enter image description here

Should the following fields be checked? enter image description here

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