When you have retrieved your sequence into GPMAW you have to perform a mass search on the downloaded protein.

Copy the same mass list that you used for PMF onto the clipboard, select Search | Mass search from the menu or press the search button on the toolbar.

In the ‘Search for mass’ dialog you press the Paste button to copy the mass list into the left-hand table (you can of course also load the list from a disk file - text with one mass value per line). Remember to check that all the settings are correc before pressing the OK button (some of the settings are pre-defined in the Setup dialog (e.g. working in ppm vs. Da), the others are ‘remembered’ between runs).

There are two displays formats: Wide and Short. The Short format gives the best overview - press the fourth button in the toolbar to activate.

The display shows the input mass values (first column) the fits within the sequence (second column) deviation (third column) modifications (fourth column - if a modification file has been defined), sequence position and finally the sequence with the two preceeding and following residues (enables you to check the cleavage specificity).
Peptide terminals that fits the enzyme cleavage specificity are marked with a green < or >. The E button in the toolbar switches between displaying only ‘Exact’ matches to the enzyme cleavage, or showing all possible peptides without regards to cleavage (C).

You are now ready to optimize the search.

Site last updated: April 14, 2024