I've some a list of protein Ids derived by proteomics experiment and for two samples, Normal and Cancer cells. However NO quantitative data,relative or absolute is available.
Can I upload these Ids to some functional enrichment analysis tool like GO term over representation analyzer to have a ROUGH Idea of what functional categories are enriched /non-enriched in cancer cell lines compared to Normal. Say, the p-value of cell-division process is 0.05 for normal tissue data and that of cancer is 0.0001, so I can tell that Cell-division proteins are enriched in cancer cells.
How bad theoretically is this method when I don't have any list of differentially expressed proteins both up and down regulated?