What is Proteome-pI - Proteome Isoelectric Point Database?

Proteome Isoelectric Point Database (Proteome-pI) is the collection of data gathering information about isoelectric points and molecular weights for model organism proteomes (over 5,000 organisms). Goals of the database include making statistical comparisons of the various prediction methods freely available to the scientific community (18 algorithms implemented) as well as facilitating biological investigation of protein isoelectric point space.

What isoelectric point?

Isoelectric point is the pH at which a particular molecule carries no net electrical charge. For more information, see:

• Isoelectric point (pI) - wikipedia article
• Theory about isoelectric point
• pK acid dissociation constant - wikipedia article
• Henderson-Hasselbach equation - wikipedia article
• Protein pKa calculations - wikipedia article

Why isoelectric point is important?

Isoelectric point is a important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF) and liquid chromatography-mass spectrometry (LC-MS).

Methods

Currently, isoelectric point in Proteome-pI is predicted using following methods:

• IPC_protein
• IPC_peptide
• EMBOSS
• ProMoST
• Grimsley
• DTASelect
• Solomon
• Sillero
• Rodwell
• Bjellqvist
• Dawson
• Lehninger
• Nozaki_Tanford
• Patrickios
• Wikipedia
• Thurlkill
• Toseland

For the accuracy of individual method check here.

The database has been generated thanks to the use of:

The new version of this software based on deep learning is also available:

Reference Proteomes

pI was predicted for the proteomes provided by UniProt database (Release 2016_04).

The proteomes have been manually and algorithmically selected. They cover well-studied model organisms and other organisms of interest for biomedical research and phylogeny.

Statistics (Total of species = 5029). For more details see here

Other datasets

Apart from the proteomes from model organisms, there are also pI predicted for high-throughput analysis for nr, UniProt and PDB databases:

Isoelectric point for all nr (non redundant) NCBI proteins (86 millions proteins) April 2016. RepOD. http://dx.doi.org/10.18150/repod.2872103
Isoelectric point for all UniProtKB/TrEMBL proteins (63 millions proteins) April 2016 RepOD. http://dx.doi.org/10.18150/repod.9948646
Isoelectric point for PDB proteins (~339,000proteins) Dec 2015. RepOD. http://dx.doi.org/10.18150/repod.1549954

Databases with experimentally derived isoelectric points

• SWISS-2DPAGE - two-dimensional polyacrylamide gel electrophoresis database
• PIP-DB - the Protein Isoelectric Point database

Proteome-pI is available under Creative Commons Attribution-NoDerivs license, for more details see here

Reference: Kozlowski LP. Proteome-pI: proteome isoelectric point database. Nucleic Acids Res. 2016. doi: 10.1093/nar/gkw978

Contact: Lukasz P. Kozlowski