Tool:IPC - Isoelectric Point Calculator for proteins and peptides
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4.5 years ago

IPC – Isoelectric Point Calculator is a web service and a standalone program for the estimation of protein and peptide isoelectric point (pI) using different sets of dissociation constant (pKa) values, including two new, computationally optimized pKa sets.

Input: amino acid sequence(s)

Output: pI values predicted by >15 methods alongside with virtual 2D-PAGE plot

Isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an critical parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), X-ray crystallography and liquid chromatography–mass spectrometry (LC-MS).

According to the benchmarks, IPC outperformed previous algorithms by at least 14.9% for proteins and 0.9% for peptides (on average, 22.1% and 59.6%, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Peptide and protein datasets used in the study and the precalculated pI for the PDB and SwissProt databases are available for large-scale analysis and future development.

IPC is available at:

Reference: Kozlowski LP (2016) IPC - Isoelectric Point Calculator. Biology Direct 11:55.

Exemplary output of the IPC calculator for the Mycoplasma genitalium G37 proteome (476 proteins).

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The scatter plot (the virtual 2D-PAGE plot) with the predicted isoelectric points versus molecular weight for all proteins is presented at the top. Then, for individual proteins, pI predictions based on different pKa sets are presented alongside the molecular weight and amino acid composition.

isoelectric point proteomics mass spec 2D-PAGE Tool • 3.1k views

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