| SWATH Ion Library with controlled Protein FDR% | andrea armirotti | 2018-01-04 07:41 | |||||||||
Hello guys Thanks for the great work you're doing with Skyline. I'm wondering if I can use it to add quality to SWATH ion libraries. I mean the following: I want to 1) Acquire fractionated DDA data on a given proteome 2) Use a NON Protein Pilot software to search for IDs. I want to use a software that gives active control of protein FDR by searching Vs a decoy db (Mascot? MaxQuant?) 3) Retrieve the list of proteins at 1% FDR and import it back into Skyline 4) Export the transition list back into a .txt file that the SWATH microapp in Peakview can read. I recently acquired a set of DDA data that I searched with MASCOT. I then imported it in Skyline as .dat and I now have my Skyline library with my peptide and transition settings. How do I convert it back into a txt? I understand I can't do it directly fron Skyline. I tried the BiblioSpec workflow: BlibBuild to create the library from the .dat, then BlibFilter to remove PSM redundancy, then what? Is this the right path to obtain a .txt list of transitions usable with Peakview? Many many thanks for your support Andrea |
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