what are the basic steps you do when wanting to analyse proteins

[protein dunce]

I have two homologouse proteins within an organism. One is mitotic specific and the other is meiotic specific. These proteins are conserved through evolution. If i was wanting to study just the proteins what are the types of things i should be thinking about to do this? For e.g. i have people giving suggestions such as conserved domains, protein folding, post translational modifications - i'm not a protein biologist / nor a biochemist so what are the things i need to know. These suggestions although very welcome mean little to me.

[danfive]

You may try mutant studies. Categorize the mutations at genetic level then follow through to observed functional/structural differences at the protein or cell cycle level. Your mutations may lead you to defining protein motifs' interactions, if you can observe knock out or deviant effects in vivo. I believe this is called the Forward Genetics approach.