Table 3.

Summary of sequence based clustering results for PILOT_PROTEIN. For each data set, the total number of peptide spectrum matches (PSMs) identified by the clustering routine is listed along with the fraction of those spectrum that were reassigned to another peptide. The decrease in the number of both true positive and false positive proteins reported by the algorithm is also listed for a 2% false discovery rate

Data Set	Clustered PSMs	Reassigned PSMs	Missed Proteins
			True	False
Data Set C - Orbitrap	217	59	6	23
Data Set C - QTOF	773	387	6	47
Data Set C - LTQ-FT	830	398	25	111
Data Set D - Salt Pellet	115	47	1	46
Data Set D - Salt Supernatant	211	76	29	40
Data Set D - MNase Pellet	123	38	17	66
Data Set D - MNase Supernatant	123	50	45	80
Data Set D - Total Extraction	134	34	38	40