Skyline MS1 Filtering and MS1 Quantitation

This paper currently in press at MCP is from a group of researchers at the Buck Institute for Research on Aging.  The paper details a new cross-platform software package for quantitative proteomics that they call Skyline.  (Not to be confused with the legendary Japanese car that was illegal to import into the U.S. due to the engineers focusing so completely on making the car fast that they forgot to include any concern for occupant safety)

(Not this Skyline)

No, this Skyline is an attempt to remove one set of variables from quality control in label free quantitative proteomics experiments.  The Skyline software aims to be a reference system for the analysis and meta-analysis of data generated on any MS platform.  In this text, they demonstrate the analysis of data from a QStar Elite, a TripleTOF 5600, and an LTQ FTICR.  This is accomplished without first converting the RAW data to one of the generic accepted formats.

In order to show the true power of Skyline, the authors investigate two data sets, one generated from the enrichment of lysine-acetylated peptides and a second from TiO2 enriched phosphopeptides.  By walking us through these analyses, the authors show us both the power of Skyline as well as a walkthrough of the software and its features.  

Now, this is a nice paper, and I am looking forward to re-running some label free quant data I previously analyzed against Skyline, but this isn't the most interesting part of this paper for me.

The most interesting part is in the introduction to this paper when the authors describe their unpublished attempts to use iTRAQ to perform quantification of the acetylome.  They found that iTRAQ labeling did not occur (or at least not efficiently) on peptides that were acetylated on lysines.  For that reason, they stopped using iTRAQ and focused on label free quant of the acetylome.  I wonder if the efficiency of iTRAQ labeling could be used as an indirect way to measure global changes in the acetylome the same way we once used cys-TMT to measure the global alkylation of cysteines?