. Author manuscript; available in PMC: 2014 Feb 1.

Published in final edited form as: J Proteome Res. 2013 Jan 18;12(2):763–770. doi: 10.1021/pr300840j

Table 1 (panels A, B).

Panel A: Average numbers of identified Pyrococcus furiosus proteins, peptides, and spectra in four categories of experimental setups and instruments. False discovery rates are estimated to be below 0.5%.

	Number of identified proteins	Number of identified peptides	Number of identified spectra
Single phase-LTQ	628	3,316	6,880
MudPIT-Orbitrap-CID	1,263	14,846	102,314
Directed MS/MS (TCA-DDA)^a	932	6,085	9,880
Directed MS/MS (acetone)^a	624	3,343	5,433
^aDetailed results of directed MS/MS combining the two protein precipitation approaches are listed in Table S2 and Figure S7..

Panel B: Average numbers of identified Pyrococcus furiosus proteins, peptides, and spectra in three categories of experimental setups and instruments. In each case the results show averages and standard deviations (in parentheses) over three replicate experiments. False discovery rates are estimated to be below 0.5%.
	Number of identified proteins	Number of identified peptides	Number of identified spectra
MudPIT-LTQ	1,279 (9)	11,004 (522)	105,215 (12,210)
MudPIT-Orbitrap-ETD	1,015 (23)	7,548 (1,611)	52,992 (10,370)
QTOF-fractionation	1,024 (47)	9,328 (962)	35,492 (7,205)