Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects.

@article{citeulike:2996920, 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.}, address = {Mass Spectrometry Research Program, Research Triangle Institute, Research Triangle Park, NC, USA.}, author = {Cargile, Benjamin J J. and Sevinsky, Joel R R. and Essader, Amal S S. and Eu, Jerry P P. and Stephenson, James L L. }, citeulike-article-id = {2996920}, doi = {10.1002/elps.200700701}, issn = {0173-0835}, journal = {Electrophoresis}, keywords = {bioinformatics, electrophoresis, modeling, proteomics}, month = {July}, number = {13}, pages = {2768--2778}, posted-at = {2008-07-13 01:07:20}, priority = {2}, title = {Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects.}, url = {http://dx.doi.org/10.1002/elps.200700701}, volume = {29}, year = {2008} }

TY - JOUR ID - citeulike:2996920 L3 - citeulike-article-id:2996920 TI - Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects. JF - Electrophoresis VL - 29 IS - 13 SP - 2768 EP - 2778 AD - Mass Spectrometry Research Program, Research Triangle Institute, Research Triangle Park, NC, USA. SN - 0173-0835 N2 - 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. KW - bioinformatics KW - electrophoresis KW - modeling KW - proteomics AU - Cargile, Benjamin J AU - Sevinsky, Joel R AU - Essader, Amal S AU - Eu, Jerry P AU - Stephenson, James L PY - 2008/07/10/ UR - http://dx.doi.org/10.1002/elps.200700701 ER -