GPMAW began as a program for the analysis of protein primary structures, particularly using mass spectrometry data. It was designed to answer the question of how many peptides that fit with a mass within the given precision.
The program has since expanded significantly in a number of directions, most characterized by the fact that they are based upon previous knowledge of a known sequence.
GPMAW interfaces to protein databases, addressing the challenges of exponentially growing data-input (from less than 10,000 proteins in 1988 to more than 700,000 proteins today, EMBL non-redundant database).
Load or enter your sequence (GPMAW interfaces to a number of other file formats and hardware) and it can be post-translationally modified and cross-links established. The protein can be cleaved based on a number of parameters (using enzymes or chemicals) and the resulting peptides can be sorted, viewed, and further characterized based on a number of parameters.
Some of the most recent advances in mass spectrometric protein identification are supported, including digest mass search and ms/ms fragmentation.
When performing mass spectrometry on proteins and peptides you are very likely to perform additional protein chemical procedures. For this purpose a number of features have been included: Searching a protein for amino acid composition, displaying the hydrophobicity index, reversed phase retention data of peptides, predicting secondary structure, comparing sequences with dot-plots, charge vs. pH graphs of peptides and proteins, digest HPLC chromatogram and mass spectra of peptide mixtures, etc.