lazear
commented
11 months ago Hi Karl,
- Sage should work with any of the acquisition windows... not sure if there is a "best", as I haven't extensively tested different m/z windows. Maybe check out one of the GPF papers and run the files through Sage? I would love to know the results!
- MS-X acquisition isn't supported (yet). If you're willing to share a mzML or a PRIDE project containing MS-X data, I can take a look at how it's encoded. At the moment, Sage supports multiple precursors internally (for handling, i.e. SPS data), but only considers the first encoded precursor for searching. I imagine MS-X is encoded as a list of precursors in an mzML so should be feasible...
- I haven't used easypqp yet, but that's what FragPipe is using. It should be possible to tweak Sage outputs into whatever format easypqp is expecting from FragPipe. If you go this route, I would appreciate any knowledge you can share. Talus Bio has kindly open sourced their Sage to .dlib converter, but then I think you need to import into Skyline and convert to blib? I had some issues with this step. I previously asked the Skyline team to add support for importing Sage results directly (since FragPipe, MQ, PD, etc are supported...) but they didn't seem terribly interested (I will not be supporting any XML based formats). Perhaps you can add your voice?
k-p4
Hi @lazear ,
I was hoping to recreate Fragpipe's DIA SpecLib Quant workflow but with Sage and DIA-NN. The idea would be to run 6 X Gas Phase Fractionation injections through Sage by setting
wide_windowthen building a DIA-NN compatible speclib from results. A couple of questions here are:Thank you, Karl