Unmatched masses are often observed in the experimental peptide mass spectra 
when database searching is performed with the ProFound program. Comparison 
between theoretical and experimental mass spectra of standard proteins shows 
that contamination accounts for most of the unmatched masses. In this 
retrospective analysis, the top 100 most probable contaminating masses, as 
listed in order of their probability, are statistically filtered out from 118 
different experimental peptide mass fingerprinting (PMF) maps. Most of the 
interfering masses originate from trypsin autolysis and human keratins. 
Subtraction of known contaminants from raw data and using cleaner masses for 
searching can enhance protein identification by PMF.