Hi,
I am a relatively new Skyline user, so I apologize in advance if this is a minor issue.
I am working on the detection method for a group of phosphatases using scheduled PRM. I first ran 37 synthetic peptides (SP) to establish retention times (RT). I then ran NK cell samples using those RT along with m/z. The NK raw files were searched using MaxQuant, and the resulting msms.txt file was imported into Skyline to build the spectral library.
Here is where I encounter the issue: According to the MaxQuant results, 25 peptides are identified in the NK samples. However, in Skyline I can only see chromatograms for 18/25 peptides, even though MS/MS spectra for all peptides is present in the spectral library. One example is shown in the attached screenshot: PTN13 ms/ms in N1, N2, N3 samples, but to chromatogram (upper panel).
However, when I import msms.txt from the synthetic peptides first and then add the msms.txt from NK cells, Skyline does display chromatograms for all peptides (In N1, N2, N3 and even in D1, D2, D3 which do not have MS/MS).
My concern is that using synthetic peptide spectra in this way affects (and improves) the dotp values... Additionally, this approach causes Skyline to pick chromatograms (or apparent signal) in samples where these peptides are not detected at the MS/MS level (D1, D2, D3).
My question is: is there an alternative way to visualize or force chromatograms for these peptides using only the NK cell data, without relying on synthetic peptide MS/MS spectra?
Thank you very much for the help!