Previous | Next | See Also

This document gives a brief introduction into how theoretical isoelectric point is calculated in the PRIDE Inspector.

In the PRIDE Inspector, the theoretical isoelectric point is calculated by default for proteins and peptides. The value of the isoelectric point can be used as a filtering technique to validate peptide identifications [1, 2]. The algorithm used to estimate the theoretical isoelectric point was published by Bjellqvist and coworkers [3].

The pI is calculated using pK values of the amino acids as described in Bjellqvist et al.5. These values were defined by examining polypeptide migration between pH 4.5 to 7.3 in an immobilized pH gradient gel environment with 9.2 M and 9.8 M urea. The authors reported a standard deviation of 0.2 units for the entire pH range. Most of the recent isoelectric point calculators implement the Bjellqvist algorithm to compute it [4, 5, 6].

References

1. Cargile, B.J., Talley, D.L. & Stephenson Jr., J.L. Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 25, 936-945 (2004).

2. Heller, M. et al. Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides. Journal of Proteome Research 4, 2273-2282 (2005).

3. Bjellqvist, B. et al. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14, 1023-1031 (1993).

4. Skoog, B. & Wichman, A. Calculation of the isoelectric points of polypeptides from the amino acid composition. Trends in Analytical Chemistry 5, 82-83 (1986).

5. Gasteiger, E. et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31, 3784-3788 (2003).

6. Gauci, S., van Breukelen, B., Lemeer, S.M., Krijgsveld, J. & Heck, A.J.R. A versatile peptide pI calculator for phosphorylated and N‐terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics 8, 4898-4906 (2008).

See Also

Other topics which will help you understand the data you are exporting: