Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects
Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects
复制标题
DOI：
10.1002/elps.200700701
复制
发表时间：
2008-07-01
期刊：
影响因子：
2.9
通讯作者：
Stephenson, James L., Jr.
中科院分区：
文献类型：
--
作者：
Cargile, Benjamin J.;Sevinsky, Joel R.;Stephenson, James L., Jr.
当前用于计算肽或蛋白质 pI 的算法基于与单个氨基酸相关的电荷，可以将 pI 值计算在 +/- 0.2 pI 单位内。在这里，我们提出了一种新的 pI 计算算法，该算法考虑了相邻氨基酸对 pI 值的影响。该算法考虑了距带电天冬氨酸或谷氨酸 3 个残基的相邻氨基酸的影响，以及对游离 C 末端的影响，并对相应的 pK 值应用了校正项。校正增量是使用遗传优化方法从 5000 个肽训练集得出的。通过此方法获得的新 pI 值的精度接近与 IPG 条带制造相关的误差（< +/- 0.03 pI 单位）。该方法已针对乳腺癌细胞系 DU4475 的胞质细胞提取物以及人肺组织样本的膜制剂进行了验证。更高精度 pI 计算的一个潜在应用是 MS/MS 输出的数据过滤，这将允许进行更复杂的数据库搜索，包括基因查找、验证以及编码单核苷酸多态性表达形式的检测。
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.