Histones are hard to study via LC-MS. Problems with histones include tons of post-translational modifications around, many of which are isobaric (same mass!) For some reason, however, people want to do it anyway. Like any LC-MS/MS experiment, we can apply the normal tools. Sometimes, however, you want to have the correct tool for the job.
(Thanks Google Images, for exactly the right image!).
Zuo-Fei Yuan et al., would argue in this new paper in press at MCP that the tools they really needed for studying these tough and important modifications did not exist - so they had to write their own.
Epiprofile is the tool they came up with, and from their description it sounds great. Unfortunately, that is all I have to go on since I can't find a download link for it anywhere. This paper is in press, after all!
What does it do? It separates out the isobaric ions from data dependent experiments by use of specific fragment ion peptides. It then refers back to the chromatographic peaks for quantification data. From the description in the paper it seems to work very well with different quantification technologies, SILAC included, and is good at quantifying a modified peptide sequence from its unmodified counterpart.