The performance of two proteomic sample preparation methods, "pseudoshotgun" 
(PSG) and filter-aided sample preparation (FASP) were compared in terms of the 
number of identified proteins, representation of cellular component GO (gene 
ontology) categories in the obtained list of proteins, and the efficiency of 
both methods in the proteomic analysis of a very low number of cells. Both 
methods were combined to obtain a proteomic profile of a short-term culture 
(passage 3) of melanoma cells, established in our laboratory from a human 
metastatic melanoma lesion. The data revealed that with FASP, usually more 
proteins are identified than with PSG when analyzing a higher number of cells (≥ 
5000/injection), whereas PSG is favorable when analyzing only a very small 
amount of cells (250-500/injection). PSG and FASP, however, are complementary 
techniques, as combining both methods further increases the number of identified 
proteins. Moreover, we show that it is feasible to identify a substantial number 
of proteins from only 250 cells/injection that is equivalent to 60 ng of 
protein.