how are you? I am PhD student from Göttingen, DE.
I am using Spectrast to create my library from Sequence Search Results (comet and X!tandem nature protocol Olga T Schubert, 2015).
I did a SEC fractionation MS experimient- 53 fractions- I measured with Q-exactive DDA 12 more intense peptides. And I would like to use my library for SWATH (I will also use Q-exactive for DIA).
The bioinformatic workflow was// seach comet - seach xtamdem// Peptideprophet (hier I got only two files)// then iprophet (hier I got 1 file combined)// and now I want to create my library by SpectraST I got the error when spectra ST goes to the files to extract the peptides, it can not open the files!! (see picture attached).
This happend to me in DOS-windows, but in Ubuntu 20.04 as well.
Do you know what could be the mistake?.
I used Ms convert- I try Creating new mzXML files and I got allways the same error/ My Iprophet file input weigh 550 mb. then files peptideprophet search 1 weight 500 mb and search 2 1,6Gb. the files have of peptides and 4000 proteins predicted (PEP3D). But spectral library is empty.
Thank you for your support, I really try everything I could to make it works.