Issue 463: Automating Skyline for HT Proteomics with Skyline Runner

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:3
Milestone:3.6
Opened:2016-04-12 by alex apffel
Changed:2016-04-12 by Brendan MacLean
Resolved:2016-04-12 by Brendan MacLean
Resolution:Not Repro
Closed:2016-04-12 by Brendan MacLean
2016-04-12 alex apffel
Title»Automating Skyline for HT Proteomics with Skyline Runner
Assigned To»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»3.6
We are trying to set up an automated pipeline for High Throughput Proteomics. As a first step, we're going to use Skyline Runner to automate the communications. Predictably, I've already run into a few issues (admittedly, I'm not the most expert Skyline User).
My plan was to set up a specific method as a Settings file. So questions:
1. Can I specify a spectral library in a settings file?
2. I'd like to export an isolation list with Skyline's prediction of the best 3 peptides and best 3 fragments for each protein. I managed to limit to the top 3 fragments. How do I limit number of peptides per protein.
Thanks
Alex

2016-04-12 Brendan MacLean
resolve as Not Repro
Statusopen»resolved
Please post to the support board. This is not really the right venue for your questions.

2016-04-12 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest