Library versus DDA import for PRM | abrahampe | 2018-02-21 11:30 | |||||||||||||||||||||||||||||||||
Hello, I generated DDA data on a QExactive Pro instrument that I then used to build a spectral library from Crux results. I have created a .ssl file as instructed here (https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats). I imported the .ssl and created a library that appears to be correct. Next, I then imported the results (.mzML) files that were used to generate the library. Interestingly, the peak picking (transition settings: MS/MS filtering, acquisition method=targeted, orbitrap, resolution 60k @ 200 m/z) does not seem to be working properly. I would expect the dot product scores to be a value near 1, given that the library was generated from the same data. Oddly, the peak picking retention times are, in many cases, nowhere near the ID time. For whatever reason, Skyline isn't identifying the transitions near the ID time. I have used the parameters outlined in the webinar document and I've looked through the MS/MS manually and the mass tolerances are well within the set parameters. I'm not quite sure what's happening. I've looked at previous posts regarding this topic and so I've made sure to check file names, for example. Thoughts? I am using Skyline 64bit version 4.1.0.11796. -- Paul to obtain a refined list of precursors that will be used for a PRM approach. I am using the Webinar-17 document as a reference. |
|||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||