Table 3. Counts at pX FLR for 1, 5, and 10% Using Each Decoy Method, Searching PXD008355 (Arabidopsis Data Set) (TPP, Fully Tryptic, 1% FDR) Showing all PSMs (Not Collapsed) and Collapsing Multiple PSMs to One Row per Modified Peptide, Sorting by Combined Probability and Count of the Supporting PSMs.

	count at 1% FLR		count at 5% FLR		count at 10% FLR
	not collapsed	collapsed	not collapsed	collapsed	not collapsed	collapsed
pAla	23,104	1570	40,541	4704	44,556	5815
pGly	18,872	1469	35,939	3654	38,885	4990
pLeu	17,943	1017	42,157	4964	45,875	6068
pAsp	13,490	234	32,595	4151	39,262	5130
pGlu	21,923	2766	34,949	4385	40,532	5607
pPro	23,696	2771	35,170	4483	38,226	5221