. Author manuscript; available in PMC: 2013 Sep 12.

Published in final edited form as: Anal Chem. 2012 Oct 25;84(21):9214–9221. doi: 10.1021/ac301962s

Table 1.

Number Comparison of Five-Plex Interference Sample Quantified with the TMT^C Approach or the MS3 Method

	QExactive TMT^C	Orbi Elite TMT^C	Orbi Elite MS3
acquired MS2 spectra	22024	10173	8843
acquired MS3 spectra			7494
identified peptides^a	9390	4511	4063
identified yeast peptides	4029	2046	1879
identified yeast peptides with sufficient ions for quantification^b	1567	1039	1024
filter for agreement bw predicted and observed TMT^C cluster^c	1291	924	1024

1% false discovery rate on peptide level.

At least 1000 TMT^C ions or at least 500 reporter ions for the MS3 method.

Applies only for TMT^C quantification; minDiff < 0.005. (See Materials and Methods for detail.)