TABLE 1.

Protein Identifications and False Discovery Rates in SEQUEST Analysis of MudPIT Data

			FDRC
Expt No	Total proteins identifieda	Single peptide proteins identifiedb	Single peptides only	Overall	Two peptides minimum
Y1	532	248	50.4	23.9	1.1
Y2	604	295	51.2	25.5	2.9
Y3	517	262	47.7	25.5	5.7
R1seed	221	155	41.9	29.9	3.1
R2root	258	175	28.6	19.4	0.0
R3leaf	247	169	59.2	40.9	2.6

^a Number of proteins identified in yeast and rice MudPIT protein identifications using SEQUEST cutoff scores of: Xcorr for a 1+ ion = 1.8, Xcorr for a 2+ ion = 2.5, Xcorr for a 3+ ion = 3.5, deltaXcorr = 0.1.

^b Number of proteins identified from single peptides only using SEQUEST with cutoff parameters detailed in footnote a.

^c False discovery rates assessed by searching against a reversed sequence database, calculated using FDR is FP/(TP + FP), where FP is false positives and TP is total positives,²⁴ expressed as a percentage.