For phosphoproteomics, this has been a by-gone concusion -- you can't get down to the majority of your PTMs without enriching at the peptide level.
Two papers in press now at MCP show the values of these approaches for other PTMS, namely ubiquitination and methylation.
"Peptide level immunoaffinity enrichment enhances ubiquitination site identifications on individual proteins" from Anania et al., and "Immunoaffinity enrichment and mass spectrometry analysis of protein methylation" from Guo and Gu, et al., both support this fact in their PTMS of interest.
Perhaps more importantly, both papers provide a very nice and effective method for identifying high numbers of peptides with these modifications in a complex environment. If you are interested in either of these PTMs, definitely download these papers now!
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