How to browse proteomaps

What do the proteomaps show?

All maps show measured protein abundances, weighted by protein chain lengths. Links in the top line take you to the four hierarchy levels (level 1, 2, 3, and the protein level).

Each protein or protein category occupies a certain area, i.e. a certain mass-certain fraction of the total proteome. To see the numerical values, move the mouse pointer over a region of interest: after a short while, the value will be visible. The mass abundance (measured abundance times protein chain length) is given as a percentage value. Currently, this feature is only available in some of the proteomaps.

The estimated copy (molecule) number is obtained by scaling the measured abundances to the total protein number per cell. We note that growth conditions can change cell volume several fold and thus affect the copy numbers accordingly. We use a generic value of ~3 million proteins per micron cubed of cell volume (Milo, Bioessays 2013) and characteristic reported cell volumes. This leads us to the following total protein number per cell type:

Mycoplasma pneumoniae	5 * 10⁴ molecules/cell
Escherichia coli	3 * 10⁶ molecules/cell
Saccharomyces cerevisiae	1 * 10⁸ molecules/cell
Schizosaccharomyces pombe	3 * 10⁸ molecules/cell
Arabidopsis thaliana	1 * 10¹⁰ molecules/cell
Mus musculus	1 * 10¹⁰ molecules/cell
Homo sapiens	1 * 10¹⁰ molecules/cell

Information in the protein-level maps

In the protein-level maps, systematic gene names or Uniprot IDs (as used inthe original proteome data) are shown in brackets, and most proteins are linked to pages from the KEGG database, showing detailed information about the protein. Click on a tile to access the corresponding page.

How to use the zoom

The "Zoom" version of the protein map has no links, but allows you to zoom in and out easily (using mouse wheel or page up/down keys) and to move within the map (using the cursor keys).