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Several hundred chemical background ions are found in plasma desorption mass spectrometry (PDMS) at
m/z values less than 1000, effectively limiting its full potential for determining the structures of biological materials from their fragmentation patterns and for use in the study of compounds of lower molecular weight. These interfering ions arise from at least three sources: the vacuum pump oil, aluminium oxide cluster ions from the aluminium targets commonly used and fragment ions from the nitrocellulose often applied as a matrix for the analysis of peptides and small proteins. These peaks in both positive and negative ion modes were sorted with respect to sources and identified by mass, relative area, and proposed structure. Methods of reducing or eliminating these interferences are proposed as a first step in extending PDMS to the study of lower molecular weight species and sample fragment ions.