![]() ![]() Electrophoresis-based separation of proteins and peptides in both free-flow and gel systems has been adapted to a wide variety of proteomics platforms in order to reduce the complexity of the studied proteome ( Ramos et al., 2008, 2011). ![]() The p I is obtained as essentially incidental information during isoelectric focusing (IEF) experiments, free flow electrophoresis (FFE), capillary electrophoresis, and in-gel electrophoresis experiments using IPG strips ( Audain et al., 2014 Ramos et al., 2008). Protein p I values are amongst the most widely determined and widely reported quantities in all of biochemistry and proteomics. In a titration curve, the isoelectric point (p I) is the value at which the overall net surface charge of a macromolecular polyprotic species equals zero. Supplementary information: Supplementary data are available at Bioinformatics online. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction.Ĭontact: and Implementation: The software and data are freely available at. In general, learning-based p I prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. ![]() We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of p I calculation methods. While such p I calculation is widely used, it remains largely untested, motivating our efforts to benchmark p I prediction methods. Therefore accurate theoretical prediction of p I would expedite such analysis. Peptide fractionation according to their p I is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Motivation: In any macromolecular polyprotic system-for example protein, DNA or RNA-the isoelectric point-commonly referred to as the p I-can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge-and thus the electrophoretic mobility-of the ampholyte sums to zero. ![]()
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