Support for exporting transition reports for parallel peptide monitoring. This approach uses a set of reference peptide peak areas to normalize target peptide peak areas from the same run, allowing target peptide comparisons between runs label-free. This has proven useful in monitoring changes in immunoprecipitated phosphoproteins by MRM.

To achieve a suitable transition report sum transition peak areas of target peptides divided by user defined sum transition peak areas for reference peptides is needed. This could be achieved by adding an additional peptide report type called “Parallel Peptide Monitoring”. Users would be provided an interface to define target peptides and reference peptides from the peptides in the Skyline method and an interface (likely in the same window) to specify names for each target and reference peptide. To generate the report, Skyline would then divide sum peak areas of each target peptide by each reference peptide and report each value in separate column with the column labeled “user name for target”/ “user name for reference”. If names are not specified column would be labeled peptide sequence of target/peptide sequence of reference. In exported report each target peptide would be listed for each run, along with ReplicateName, PrecursorMz, PrecursorCharge, one column for each “target/reference” sum transition peak area. Peak Areas for each reference peptide for each run should also be exported either at the bottom of the report or as separate report, so that user can evaluate the reproducibility of each reference peptide between runs.

JM

2009-09-19    Brendan
Hi Jeremy,
We have talked about this in the past, and it just hasn't reached the top of the priority list yet. But thanks for adding the issue. When it does get done, it will be more than just the reports. The ratios will show up in the UI too, as they do for labeled synthetic peptides today.

Still can't say when, but it will get done.

--Brendan

This was implemented in v2.5.