Compute predicted normalized elution time values for peptide sequences. The NET Prediction Utility can be used to compute predicted normalized elution time (NET) values for a list of peptide sequences. The elution times are intended for use with reversed phase liquid chromatography (e.g. using C18 coated silica particles) analyses, and are used in our lab for alignment of LC-MS and LC-MS/MS datasets to one another (using the predicted elution times to form a master in-silico dataset to align each dataset to). The predicted elution times are also used by the Protein Digestion Simulator Basic when calculating the number of uniquely identifiable peptides within an input file using both mass and NET.

The NET Prediction Utility reads the peptides from a text file containing one peptide sequence on each line. The output file includes the peptide sequence plus the predicted NET value (and/or predicted SCX value) using one or all of the prediction algorithms:
1. Kangas/Petritis LC retention time model
2. Kangas/Petritis SCX fraction model
3. Krokhin hydrophobicity model
4. Mant hydrophobicity model

The program reads the peptides from a text file containing one peptide sequence on each line. The output file includes the peptide sequence plus the predicted NET value (and/or predicted SCX value) using one or all of the prediction algorithms (Kangas/Petritis neural network trained retention time model, Krokhin hydrophobicity model, Mant hydrophobicity model, or Kangas/Petritis SCX fraction model).

Note that the only modified residues that the program recognizes are alkylated cysteines, which should be notated using an asterisk following a C (for example, LYFSAC*GR)

Requirements:
* .NET Framework

The license of this software is Freeware, you can free download and free use this calculator software.