The protein class page contains a selection of gene lists used to stratify the proteome. Each table shows the total number of genes as well as the number of genes with antibodies for all classes. Clicking on one of these two links retrieves a search result with the selection of genes belonging to the class, along with additional data. For each class, where applicable, there is also a link to the original source of the gene list. A number of classes contain a selection of subclasses which unfolds when the parent class (shown in bold and with arrows) is clicked. The subclasses contain the same features as the parent class but may have different sources. Some subclasses (marked with an asterisk) are not included in the total number of genes for the parent class.

All protein classes have been categorized into three different tables: "Function and compartment based", "Disease and drug related", and "Evidence based". The "Function and compartment based" table contains functional classes of proteins such as transcription factors and enzymes, as well as proteins located to specific compartments of the cell, such as the mitochondrial proteins or cytoskeleton related proteins. The "Predicted membrane proteins" subclasses have been previously described in more detail in a publication. The class "Secreted proteins predicted by MDSEC" includes proteins not containing transmembrane regions and having a signal peptide predicted by at least two of the three signal peptide prediction methods SignalP4.0, Phobius, and SPOCTOPUS. The "Disease and drug related" table consists of a selection of gene lists related to disease such as cancer and cardiovascular disease as well as genes associated to drug targets according to Drugbank. For the "Evidence based" classes, further information can be found in the more detailed description of the protein evidence as well as on the protein evidence page.