Brendan,
Sorry for the continuing questions.
I generated a spectral library using a Mascot .dat file, which has a high-score match to an 8-residue peptide that contains residue numbers 2-9 in from the protein n-terminus (methionine). When I import the corresponding .raw file, that yielded the .dat file, that peptide is not displayed below the parent protein, despite the peptide settings of 6 AA minimum peptide length and exclude 1 n-terminal AA. This peptide is found in the spectral library explorer, but when I add it from the explorer it appears as a "library" peptide and is not associated with the parent protein (and no RIC is plotted). In addition, this peptide is not included in the long list of possible tryptic peptides shown upon right clicking on the protein in the Targets list. Thank you for any advice you can provide to have that peptide included with the other peptides of that same protein.
Mark