. 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 7.

Comparison of Variable Modification and Directed PTM Searches.

sample^a	search type^b	spectra	peptides	hh:mm:ss^c
"Rat Liver" (QTOF)	TR-DPTM-FT	37864	9388	00:18:46
	TR-DPTM-ST	41076	10406	01:06:50
	MM-VAR-FT	29224	8745	27:21:10
"THP1 Cell Lines" (LTQ)	TR-DPTM-FT	20243	18141	00:16:51
	TR-DPTM-ST	21822	19602	00:59:39
	MM-VAR-FT	19654	17739	00:55:41

^(a)

Refinement searches were configured to match 148,528 “Rat Liver” spectra against 3942 proteins and 160,064 “THP1 Cell Lines” spectra against 7522 proteins, while looking for a total of seven possible modifications in each sample.

^(b)

Each row indicates an algorithm and configuration employed for refinement searches of the samples. TR reports the use of TagRecon and MM reports the use of MyriMatch. DPTM reports the use of directed PTM search mode and VAR reports the use of variable modification search mode. FT reports the use fully tryptic search as opposed to ST for semitryptic search.

^(c)

Time measurements were taken on a cluster equipped with 32 dual-core Intel 1.5GHz nodes.