Are those proteins missing in the msmsScans low abundant proteins? I think it is most likely a matter of protein "grouping". If a peptide is identified which matches to several proteins, not all matching protein ID´s are finally listed because other peptides are identified which make it more likely that only several of all of those possible proteins are identified. You may check if those peptides are razor peptides and if they are present in the ProteinGroups file.

Another possibility might be that the spectrum matches are not of high quality and they are excluded in the end again due identification thresholds.

Hope this was helpful.

Best Sebastian

I've run into similar problems. Did you post the question on their Google groups?