Table 2. PSM Counts for Each Data Set at 1% FDR, Phosphopeptide PSM Counts at 1% FDR, Site Counts (Excluding pA Decoy Sites) for all PSMs Collapsed by Peptidoform Position and at Each of the FLR Thresholds; 1%, 5%, and 10%.

Data set	1% FDR PSM count	1% FDR Phospho-peptide count	Peptidoform-site count	1% FLR Peptidoform site count	5% FLR Peptidoform site count	10% FLR Peptidoform site count
PXD002222	39092	29086	6762	1935	2951	3649
PXD004939	81254	62935	10701	2156	4094	5348
PXD005241	127696	106459	26190	1701	4687	8872
PXD004705	80741	61029	10258	2050	3989	5133
PXD002756	69232	18203	9734	1421	3708	5581
PXD012764	45184	14020	5600	695	1269	1677
PXD000923	14852	12167	5965	2366	3708	4221
PXD019291	31094	30764	22128	4072	11034	13984