Issue 523: Make it easy to connect raw data file sample information to annotations in Skyline

issues
Status:resolved
Assigned To:Brendan MacLean
Type:Todo
Area:Skyline
Priority:2
Milestone:4.3
Opened:2017-06-11 by Brendan MacLean
Changed:2019-05-08 by matt.chambers42
Resolved:2019-05-08 by matt.chambers42
Resolution:Duplicate
Duplicate: 628
Closed:
2017-06-11 Brendan MacLean
Title»Make it easy to connect raw data file sample information to annotations in Skyline
Assigned To»Nick Shulman
Notify»jjaffe
Type»Todo
Area»Skyline
Priority»3
Milestone»4.1
Found this near the bottom of my inbox (way beyond what I was actually looking at). So, I thought I would add it to the issues list to keep from losing it. About 2 years ago (ouch) Jake suggested that it would be helpful it Skyline could automatically extract sample information from raw data files and make that information available as Skyline annotations.

Maybe we could have some way when defining Replicate annotations (though, these are really file annotations, but very frequently replicates have only one file) to specify that they are linked to a raw data file sample annotation. Maybe this would have to be by name? i.e. both the data file annotation and the Skyline document annotation would have to have the same name... Or maybe it could just be possible to specify a linked name, which would default to being the same.

Anyway, this does seem like it would be pretty cool. Here is what Jake said originally:

For LINCS, we are embedding a "sample id" in Thermo rawfiles using the aptly named "Sample ID" field in XCalibur sequence tables. It would be great if we could expose this property for report views in Skyline. I realize that this is a vendor specific property, but it is important for tracking data provenance in LINCS....

Actually, Vial Position (or Well) might be another good one to expose. I have found that tracking performance by plate location can be useful. We currently input this manually (we have a metadata item called "det_well") but there's no reason we couldn't pull this directly from a Sequence Table.

2018-11-01 Brendan MacLean
Priority3»2
Milestone4.1»4.3

2019-01-15 Brendan MacLean
Assigned ToNick Shulman»matt.chambers42@gmail.com
Assigning to Matt to get the RAW data file annotations into the mzML interface.

2019-05-08 matt.chambers42
resolve as Duplicate of 628
Statusopen»resolved
Assigned Tomatt.chambers42@gmail.com»Brendan MacLean
Notifyjjaffe»
Closing as duplicate.