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!!!
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.