. Author manuscript; available in PMC: 2012 Feb 18.

Published in final edited form as: Chem Res Toxicol. 2011 Jan 7;24(2):204–216. doi: 10.1021/tx100275t

Table 2.

Comparison of TagRecon and InsPecT in the Context of “Blind PTM” Searching.

	no. of proteins^a		no. of peptides^a		no. of spectra^a		modified peptide FDR^b
Sample	TagRecon	InsPecT	TagRecon	InsPecT	TagRecon	InsPecT	TagRecon	InsPecT
DNA-Histones	237	126	1,449	1,482	7,402	5,556	1.2%	1.1%
Rat Liver	1,533	1,210	9,994	7,534	50,921	32,504	3.0%	2.4%
THP1 Cell Lines	3,227	2,302	17,000	14,117	56,317	39,577	3.3%	2.9%

^(a)

TagRecon and InsPecT matched the MS/MS against respective subset FASTA databases. IDPicker filtered the PSMs at 2% FDR.

^(b)

Global false discovery rates of peptide identifications containing unanticipated modifications. Overall, TagRecon recovered more proteins, peptides, and spectra than InsPecT.