2008/07/01 by Benjamin J. Cargile, Joel Sevinsky, Amal S. Essader +2 · 3 citations
Chemistry · Biochemistry, Genetics and Molecular Biology · #Mass Spectrometry Techniques and Applications #Advanced Proteomics Techniques and Applications #RNA and protein synthesis mechanisms
paper · pdf · doi:10.1002/elps.200700701
openalex publication_date 2008/07/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22
Current algorithms for the calculation of peptide or protein pI, based on the charge associated with individual amino acids, can calculate pI values to within +/-0.2 pI units. Here, we present a new pI calculation algorithm that takes into account the effect of adjacent amino acids on the pI value. The algorithm accounts for the effect of adjacent amino acids+/-3 residues away from a charged aspartic or glutamic acid, as well as effects on the free C terminus, and applies a correction term to the corresponding pK values. The correction increments are derived from a 5000-peptide training set using a genetic optimization approach. The accuracy of the new pI values obtained with this method approaches the error associated with the manufacture of the IPG strip (<+/-0.03 pI units). The approach is demonstrated for cytosolic cell extracts derived from the breast-cancer cell line DU4475, and from membrane preparations from human lung-tissue samples. One potential application of a more highly accurate pI calculation is data filtering of MS/MS outputs that will allow for more complex database searches including gene finding, and validation, and detection of coding single-nucleotide polymorphisms in their expressed form.