The Annotated Modifications page is associated with the Proteins page when the consensus workflow includes the Protein Annotation node. It displays the details of the modifications that you selected to be annotated. For more information, see Protein Annotation node.
The Found Modifications page is associated with the PSMs and Decoy PSMs pages. On the PSMs page, it displays the found modifications of the PSMs. On the Decoy PSMs page, it displays the found modifications of the decoy PSMs. The modifications themselves are shown in the Modifications column of the PSMs and Decoy PSMs pages, but the Found Modifications page shows more details about them, such as the delta mass or the formula of the substitution.
The Unknown Modifications page is associated with the PSMs page and the Decoy PSMs page. The PSMs page displays unknown modifications of the PSMs, which are modifications found by error-tolerant searches. In these searches, the search engine does not use a fixed set of modifications for the search, but rather systematically adds a range of masses one by one. If it identifies a peptide by assuming an additional mass, it considers this mass a modification. However, the output is only a mass without any indication of which modification it might be, so these modifications are called unknown modifications and given an automatically created name. The Decoy PSMs page displays unknown modifications of the decoy PSMs.