pepxml file generate

pepxml file generate pucci biagio  2020-04-23

i'm working with bruker tof and I'm use mascot as engine software...I'm not able to generate pepxml file to use for MS1 DDA analysis..
help me!!

Nick Shulman responded:  2020-04-23
Skyline can read your Mascot .dat file directly.
You do not need to create a .pepxml file from your Mascot search results.

This web page has the list of which peptide search result file types Skyline can use to create BiblioSpec spectral libraries:

-- Nick
pucci biagio responded:  2020-04-23
thanks Nick!

another question: skyline read .d file generated from bruker ion trap? is it possible to analyze large file from shotgun ms experiment and what is the dimension of each file supported by the software ?
thanks al lot!!!
matt.chambers42 responded:  2020-04-26
If it has an analysis.yep file then the answer is unfortunately no. But you can convert that file with the MSconvert to MzML and then feed that to skyline.

I'm afraid I don't really understand the next two questions.