Hi ! I am new in proteomics and kinda lost about how to analyze the statistics of my proteomic data. So please be patient with me, and if you know any forum specific for proteomics,please let me know.
My experiment is based in two treatments (CON vs RES) with male and female replicates .
The raw data were processed with MaxQuant (v.1.6.3.3) software with parameters set to default values. Label-free quantification (LFQ) was add and only protein ratios calculated from at least two unique peptides ratios (min LFQ ratio count = 2) were considered for calculation of the LFQ protein intensity. The goat reference proteome was used. After that I used the Perseus software (v.1.6.140), log2 transformed the raw data to achieve normality, filtered and removed proteins identified by site, reverse and potential contaminants, and considered the valid values the ones with occurrence in at least 50% of the biological replicates in both experimental groups.
I performed the comparison between treatments using Student’s t-test and differentially abundant proteins (DAPs) were deemed significant when p-value < 0.05 (CON vs RES). However using this comparison in Perseus software I was not able to add the effects of sex in the model , it is just considering treatment.
Thus , I would like to know if can do that in perseus , or if I need to use other program and which method/software should I use to do that. I am trying to evaluated the treatement effects , however the sex effect needs to be considered because the effects can be different between male and females.
Thanks
