On 2014 Feb 01, David Simpson commented:

I'm intrigued by the concept discussed here that larger modifications might be inherently more difficult to identify using current search software. Comparing TMT 6-plex with the newer TMT 10-plex, which has the same mass shift, might shed some light on this problem.

On 2014 Jan 31, David Simpson commented:

A minor question, but I noticed that a different composition was given for the 4-plex iTRAQ 115 label here in Figure 3 than was given in the classic iTRAQ paper: Ross et al., Mol. Cell. Proteomics 2004, 3, 1154–1169. Has the 4-plex iTRAQ 115 label composition been changed by the manufacturer since the first report was published?

EDIT: To be clear, I'm not doubting the composition given here (it's supported elsewhere: Phanstiel et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1255–1262). I'm just curious about the change from the earliest report.

On 2014 Jan 31, David Simpson commented:

A minor question, but I noticed that a different composition was given for the 4-plex iTRAQ 115 label here in Figure 3 than was given in the classic iTRAQ paper: Ross et al., Mol. Cell. Proteomics 2004, 3, 1154–1169. Has the 4-plex iTRAQ 115 label composition been changed by the manufacturer since the first report was published?

EDIT: To be clear, I'm not doubting the composition given here (it's supported elsewhere: Phanstiel et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1255–1262). I'm just curious about the change from the earliest report.

On 2014 Feb 01, David Simpson commented:

I'm intrigued by the concept discussed here that larger modifications might be inherently more difficult to identify using current search software. Comparing TMT 6-plex with the newer TMT 10-plex, which has the same mass shift, might shed some light on this problem.