title: Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects.
abstract: 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.
authors.affiliation: Mass Spectrometry Research Program, Research Triangle Institute, Research Triangle Park, NC, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Cargile
authors.forename: Joel R
authors.initials: JR
authors.lastname: Sevinsky
authors.forename: Amal S
authors.initials: AS
authors.lastname: Essader
authors.forename: Jerry P
authors.initials: JP
authors.lastname: Eu
authors.forename: James L
authors.initials: JL
authors.lastname: Stephenson
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D045744:Cell Line, Tumor; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007525:Isoelectric Focusing / Q000379:methods*; D007526:Isoelectric Point; D008297:Male; D011492:Protein Hydrolysates / Q000737:chemistry*; D051381:Rats; D013737:Testis / Q000737:chemistry; D014357:Trypsin / Q000378:metabolism
chemical_list: D000596:Amino Acids; D011492:Protein Hydrolysates; D014357:Trypsin