GPMAW™ General Protein Mass Analysis Program Features
The sequence window is the default view of a sequence. From here you can call most of other sequence related functions (either through the menu, the toolbar, or the pop-up menu).
The display can be configured in various ways, 1- or 3-letter display, average mass/monoisotopic mass, fixed residue width, sidebar with sequence information, show disulfide bridges etc. By highlighting part of the sequence you can easily obtain the mass of the given section. For easy navigation you can color specific residues (three different colors and underlining are available).
Most of the settings can easily be pre-set.
The sequence window is the parent window from which a large number of derived daughter windows can be created:
- Peptide window
- Ms/ms window
- Mass search, composition search
- Secondary structure
- Charge vs. pH
- Alpha-helical wheel
The peptide window is normally called from the sequence window through the automatic digest commend. However, there are alternative methods like manual or semi-automatic cleavage.
The peptide window lists all the peptides that will be generated from the given protein along with a large number of physical-chemical parameters (charge single/multiple/negative, peptide number, location, HPLC index, theoretical pI, Bull & Breese index, sequence - 1/3-letter etc.).
Peptides can be generated with partial cleavages, modified termini, modified residues (even partial modifications are supported in a limited way). Specific residues may be colored for easier referencing.
The actual parameters presented can be configured by the user.
Sorting and reverse sorting can take place on any column by clicking on the header.
Through the toolbar and/or the pop-up menu (right mouse click) you can access a large number of additional functions related either to the digest (like the simulated HPLC reversed phase chromatogram) or to the currently selected peptide (ms/ms cleavage, peptide information, charge vs. pH graph).
User Defined pI Values
How are these pKa values then used by GPMAW? For the modifications, it is quite simple, as the pKa values are taken into the calculations of pI and charge whenever they are defined in a sequence (i.e. whenever a residue is modified with the relevant modification).
However, for the mass file GPMAW has a user-defined table, as GPMAW has four different tables.
The first and third are values taken from the literature (references in the on-line help and the manual). The second option is based on the values for free amino acid residues. The fourth and last option is based on the definitions in the currently selected mass file and has to be checked in order to use these values.