Hey AAlpert thanks for such a careful reading of the paper

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Regarding the Wang study from 2011, I think that comparison is hard to make because 1) they use a different column for their reverse phase fractionation 2) different instrument to analyze them 3) different cell line under different conditions and lastly 4) they don't perform an enrichment step for phosphopeptides.
You're correct that there is a difference in the SCX column used between our studies and our SCX fraction method could definitely be optimized further. But as we mention on page 10, our purpose wasn't to use SCX since it's "the method to beat" but merely provide a reference point since it's a widely adopted protocol and had been used in our lab previously many times. Infact we cite several papers including some of the references you provide(such as ERLIC) which show other methods outperforming SCX. However I disagree that the SCX column is totally unsuitable for the comparisons. In fact, Zarie et al 2013 JPR (
http://pubs.acs.org/doi/full/10.1021/pr200092z ) do a comparision and found SCX (on the exact same Resource S column as ours, with similar gradient) outperformed HILIC and ERLIC for phosphopeptide detection.
I couldn't locate the X. Chen paper but in the Boichenko and Hao studies, the comparisons are between non-phosphorylated peptides which was not the goal of our study. You're correct that our statement was in relation to traditional charged based separations such as IEF, SCX and SAX and not HILIC or ERLIC per say.
I would say the focal point of the manuscript wasn't to show how much better our method is compared to SCX (although it is much better) but to show it's usefulness in a off-line 2D setup, how it can be optimized along with phospho enrichment (if using TiO2) and more importantly the importance of "sensitive" detection parameters in relation to phosphoproteomics analysis with Orbitrap systems. Taking all these things into account lets you go much deeper into the phosphoproteome and all the other benefits that come with that as we describe in detail.
Thanks for the questions. feel free to ask more!
Cheers,
T