The graph (left above) shows all the ‘marked’ peptides in the peptide hit list (In the peptide ‘hit’ list, all perfect matches are initially checked in the left-hand column while other ‘potential hits’ are unmarked).
The orange line shows the best multiple point calibration through the displayed points. Check and uncheck a couple of ‘hits’ in the ‘hit list’ to see how the dots turn on and off and the calibration line changes.
Press the second button to transfer the multiple calibration line to the mass table, and see that another peptide now matches the search, but was outside of the initial precision (above right). You are now within 4 ppm on all the hits. As the calibration line is still angled it means that by pressing the second button we can improve the precision again - this time to 2 ppm.
You may already have found peptides that were not detected in your initial PMF search, as these searches are usually performed using a missed cleavage value of ‘1’ and GPMAW displays all peptides fitting the enzyme cleavage definition (using a higher value in PMF will not increase score as the relative database will increase more than the few extra hits increase the score).
To increase the number of hits and coverage click on the E button in the peptide hit toolbar to change it to a C (check fit). This removes the constraint that peptide hits have to fit the exact enzyme cleavage specifications and will thus show all peptides that fits within the given mass window.