Partially following up to previous issues;
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I am trying to build a library that contains the CCS, drift time(ms), RT, etc. and am running into several issues. The experimental plan was to High pH fractionate the peptides from a sample and do replicate DDA and IMS only (MS1) injections on the Agilent 6560. Then I generated a library from the search results of the DDA run and extract all of the peptides with a narrow retention time window of 1 min. Then I assign the CCS values using the Ion mobility predictor function. I then planned to export a library for each of the high pH-fractions 13 in total and then combine them all to a single library. I have processed each fraction in a seperate skyline document to make sure it was specific just for the peptides in each fraction and keeps the program form integrating for peptides that do not occur in most of the fractions.
1. Ion mobility predictor. I have refined the peptides in my data set and then ->created ion mobility predictor by using the results for each high pH fraction. This produces the predicted region in the ion mobility domain and I can export calculated CCS (A^2) via the export results function. Would like to combine the results from each "ion mobility prediction" into one master prediction. This would not be necessary if I can learn how to export with CCS/ion mobility data as I can then just use the " Use spectral library mobility values when present".
2. Export Spectral Library. When I export the spectral library the file is blank, each file is only 20kb. The plan was to review each fraction form a high pH fractionation of peptides assign the CCS via the ion mobility predictor and then export a spectral library that includes CCS and drift time. Then I was going to combine all of the libraries together, but I had an error that I could not combine more than 10. Could the file be blank because it is all MS1 data ?
Any assistance would be great or if i am going about this incorrectly let me know. Happy to share and collaborate on this.