Proteome-pI 2.0

Proteome-pI 2.0 provides pre-computed isoelectric points (pIs) and molecular weights for proteins and peptides derived from model organism proteomes to support analysis of protein charge and mass properties across over 61 million protein sequences from 20,115 proteomes.

Key Features:

• pI predictions: Isoelectric points are predicted using 21 different algorithms for proteins and peptides.
• pKa values: Dissociation constant (pKa) values for proteins are provided, inferred through a single method.
• Dataset size: Covers over 61 million protein sequences across 20,115 proteomes.
• In silico digestion: Individual proteomes are digested in silico using five proteases: trypsin, chymotrypsin, trypsin+LysC, LysN, and ArgC.
• Peptide collection: In silico digestion yields over 9.58 billion peptides with calculated pIs and molecular weights.
• 2D-PAGE and fractions: Provides virtual two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) plots and customized proteome fractions based on pI and molecular weight.

Scientific Applications:

• Bottom-up proteomics: In silico digestion with five proteases supports peptide-centric experimental design and analysis for bottom-up proteomics.
• Experimental planning and interpretation: Virtual 2D-PAGE plots and customized pI/MW fractions aid planning and interpretation of electrophoretic separations.
• Protein charge analysis: Combined pI and pKa data enable analysis of protein charge properties across proteomes at different pH values.

Methodology:

Isoelectric points are computed using 21 different algorithms; protein pKa values are inferred via a single method; individual proteomes are digested in silico with trypsin, chymotrypsin, trypsin+LysC, LysN, and ArgC producing over 9.58 billion peptides for which pIs and molecular weights are calculated; virtual 2D-PAGE plots and proteome fractions are generated based on pI and molecular weight.