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Peptide window
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 can take place on any column by clicking on the header. Clicking a second time reverses the sort.
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).
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