Most frequently, the components that fail composite scoring are low-abundance components. To overcome this, you can exclude low-abundance isotopes from composite scoring by selecting this option in the Filtering area of the Composite Scoring page and by selecting an appropriate threshold.
As another frequent issue, a charge state cannot pass composite scoring if not detected. Consequently, the entire master peptide cannot pass composite scoring. To overcome this problem, you can enforce integration even if a peak is not present, replacing undetected peaks with peaks that have zero area (or height). To do this, use the Set Detection Reference XIC option to enforce the integration start and end of a different charge state. After that, the master peptide can pass composite scoring even if some charge states are missing.