Proteome-pI: proteome isoelectric point database

Abstract

Proteome-pI is an online database containing information about predicted isoelectric points for 5029 proteomes calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography-mass spectrometry and X-ray protein crystallography. The database, available at http://isoelectricpointdb.org allows the retrieval of virtual 2D-PAGE plots and the development of customised fractions of proteome based on isoelectric point and molecular weight. Moreover, Proteome-pI facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life. For instance, using Proteome-pI data, it is clear that Eukaryotes, which evolved tight control of homeostasis, encode proteins with pI values near the cell pH. In contrast, Archaea living frequently in extreme environments can possess proteins with a wide range of isoelectric points. The database includes various statistics and tools for interactive browsing, searching and sorting. Apart from data for individual proteomes, datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated and made available in CSV format.

Figure 1.

Proteome-pI example report for Salmonella enterica. At the top, the average isoelectric point, precalculated fractions of proteins according to isoelectric point and virtual 2D-PAGE plot for the proteome are shown. In the next section, the user can retrieve a subset of proteins within specified isoelectric point and molecular weight ranges calculated using a particular method. Next, proteins with minimal and maximal isoelectric points are presented along with some general statistics.

Figure 2.

Isoelectric points and molecular weights across kingdoms of life. Data for the proteomes of 135 Archaea, 127 viruses (>50 proteins), 3775 bacteria and 614 eukaryotes.