Apparently SpectraST has added support for retention time information since I first implemented the support for SpectraST libraries to Skyline over 5 years ago. It would be nice to extend the library support for SpectraST libraries to allow access to these retention times.

Here is how the new support has been described by someone interested in seeing Skyline support:

Below is one example of spectrum in .sptxt. (a complete example file of .sptxt is also attached, which contains spectrum from Q1, Q2, and Q3 mzXMLs. FYI, we renamed the T1 as Q1, T2 as Q2, and T4 as Q3 in order to make is consistent with the descriptions in the manuscript) In the "Comment" section of each spectrum, there is "Sample=1/f__Data_AP_MS_3rep_DMSO_SWATH_13979_CDK_WT_BR1_DMSO_SWATH_interact-13979_CDK_WT_BR1_DMSO_SWATH_Q1" to indicate the source file, but I think you don't need this information because .sptxt has all the information including fragment intensity and we can use spectrast to combine three .sptxt into one combined .sptxt.

The retention time information is reported like "RetentionTime=1842.8,1842.8,1842.8" in "Comment" section.


=========================================================
Name: n[43]AAAAAGTATSQR/2
LibID: 0
MW: 1118.5669
PrecursorMZ: 559.2834
Status: Normal
FullName: M.n[43]AAAAAGTATSQR.F/2 (CID)
Comment: AvePrecursorMz=559.5860 BinaryFileOffset=1659 FracUnassigned=1.00,5/5;0.83,15/20;0.75,98/150 Inst=1/UNKNOWN,1,1 MassDiff=-0.0020 Mods=1/-1,A,Acetyl NAA=12 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=13 Parent=559.283 Pep=Semi-tryp PrecursorIntensity=0 Prob=0.7637 Protein=2/sp_Q9Y2Z0-2|SUGT1_HUMAN/sp_Q9Y2Z0|SUGT1_HUMAN RawSpectrum=13979_CDK_WT_BR1_DMSO_SWATH_Q1.73777.73777 RetentionTime=1842.8,1842.8,1842.8 Sample=1/f__Data_AP_MS_3rep_DMSO_SWATH_13979_CDK_WT_BR1_DMSO_SWATH_interact-13979_CDK_WT_BR1_DMSO_SWATH_Q1,1,1 Se=1^X1:pb=0.7637/0,fv=2.9427/0,hs=0/0,ns=0/0,ex=0.0000/0 Spec=Single TotalIonCurrent=2.5e+002
NumPeaks: 150
110.0685    1907.4    ?   
112.0000    252.4    IRB/0.00   
114.5708    458.8    a3^2/0.00   
122.0751    296.8    ?   
128.5682    927.7    b3^2/0.00,IRA/-0.55,y1-46/-0.55,y2-46^2/-0.52   
136.0732    943.3    ?   
141.0987    487.4    ?   
155.5735    527.8    b4-17^2/0.00   
175.1190    1455.5    y1/0.00   
185.0921    683.6    b2/0.00,a5^2/-0.52   
207.0831    240.0    ?   
212.1015    918.3    ?   
213.0849    259.4    ?   
226.1517    1483.8    ?   
237.1270    232.0    y4-18^2/0.00   
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