Hello all,

I need a little guidance for an analysis that I am trying to do. For our project we ran a differential analysis between two groups using protein intensity values that we obtained from a private experimentation facility. We have a total of 1300 protein analytes, our univariate group comparison shows at-least 20 statistically significant proteins(P<0.05), after running the Q-value adjustment this significance is lost. Does it make statistically sense to just consider significant proteins by ignoring the Q-value correction and doing a pathway analysis for these protein analytes? Since, I am very new to pathway analysis I wanted to ask if we could use protein names to perform pathway analysis instead of mapping these proteins to gene names? Is there a specific tool just for protein based pathway analysis?