|MIDAS Libraries Questions||roman sakson||2018-10-14|
Hello Skyline team,
thank you very much for the great piece of software that you are developing and maintaining! In our core facility for proteomics in Heidelberg, Germany, I work with a QTrap 5500 and we often use the Sciex MIDAS workflow. Some time ago, you have implemented more support for this in Skyline, which is great. However, I have two general question:
When I import a wiff-file containing MRM traces as well as MS/MS spectra into Skyline, as it is the case for MIDAS experiments, I see the usual MRM XICs and also vertical blue lines with retention times over them. I believe, that this lines indicate the timepoints at which MS/MS spectra were acquired in my wiff-file. Importantly, there is no "ID" word on top of those lines yet, since no "real" spectral library containing a database results output like a dat-file from Mascot is present in the Skyline document at that stage. However, since there is now a "midas" library created by Skyline automatically, I still get to see all the imported MS/MS spectra under "Library Match" with a more or less long list of all those spectra with a corresponding RT in brackets offered to me as a dropdown menu. I appreciate that but I have realized that there is also the peptide sequence and a charge state displayed on top of the library match, just as how it would look like for a "real" spectral library match (see first screenshot). At that point, Skyline probably just imports the peptide sequence from the target list, since it has no database results available yet, and I don't really know what amino acid sequence corresponds to the MS/MS spectrum. Am I missing something here?
The second question concerns the new tab "Library Runs" which I can find under "Manage Results". I believe, that there is an entry created for each MIDAS-experiment that I import (see second screenshot). While the "midas" library is automatically created by Skyline in the same directory in which the Skyline-file itself lives, the path for the Library Run seems to point to the folder where my original wiff-files are stored. I don't have any particular issues with that but would just like to understand whether my wiff-files are now somehow connected to my Skyline-files? What would happen if I made use of the "Remove corresponding runs" check box?