mRNA splice variants (Isoforms): Through alternative splicing, one gene can generate different proteins with different M.W. Regulation of alternative splicing depends upon cell type, conditions, etc.
Multimerization: Some proteins could form dimers or multimers, increasing the M.W. This phenomenon usually can be found in reducing gel condition; however, strong interactions may still be seen with higher molecular weight proteins even in denaturing gel.
Protein charge: The observed size could also potentially be influenced by the protein charge
Different species Different species likely have different protein sequence and PTM, which can lead to a different protein M.W.