"Guidance Needed for Analyzing Quantitative Protein Data Using Perseus Software"

Question

[iqra]

I need help using Perseus software to analyze protein data. Can someone guide me?

[GenoMax]

A forum is not the best place to learn about a complete software package. You must have seen the documentation (which appears to be detailed). That should get you started easily.

If you learn interactively then the lab has a YouTube Channel for tutorials: https://www.youtube.com/channel/UCKYzYTm1cnmc0CFAMhxDO8w

If you have specific questions about steps/things then post them here.

[iqra]

I have three replicates for control and three replicates for KO mouse data. I analyzed raw mass spectrometry data using MaxQuant. By using the ProteinGroup.txt file as the input, I removed identifications by sites, reverse sequences, and potential contaminants. I then transformed the data using log2(x) and normalized it by subtracting the column data and selecting the most frequent values. After this, I aimed to find the differentially expressed proteins between Control and KO groups. When I used a group t-test to get the p-values and differences between Control and KO, the resulting values are different than example data. How can I modify this process to ensure I get the exact values for this analysis? thank you for your time