Fasta file converter and validator. Protein Digestion Simulator can be used to read a text file containing protein or peptide sequences (FASTA format or delimited text) then output the data to a tab-delimited file. It can optionally digest the input sequences using trypsin or partial trypsin rules, and can add the predicted normalized elution time (NET) values for the peptides. It can also validate a FASTA file, testing it against a set of rules that identify common formatting errors. Lastly, the program can calculate the number of uniquely identifiable peptides within an input file using only mass, or both mass and NET, given user-defined tolerances.

As an alternative to digesting the peptides, one can read in a fasta file and create a new fasta file with all of the protein sequences reversed or even randomized. This new file can be the equivalent length of the original file, or can include just a subset of the original file.

The third key feature of this software is the ability to calculate the number of uniquely identifiable peptides within the input file (digested or undigested), using only mass, or both mass and NET, with appropriate tolerances.

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