Hi I am trying to put together a processing pipeline from Waters MSe data to spectrast. I can process data with Waters own tools to generate a spectral library, and then use skyline and blib to convert to .ms2 format. I would like to put that as an input to spectrast to make a .sptxt / .splib file. However, when I do that the retention time information is not carried through to .sptxt file.
Is there a way to propagate retention time into the spectrast data files? I wondered if the retention time is not labelled the way spectrast expects in my .ms2 file. In which case I could fix it with a program like sed. Alternatively I wondered if I used the wrong switch. Any help would be very welcome. The command line I used was essentially: spectrast.exe -V -cNmyBaseName mySpectra.ms2 The first spectra in my .ms2 and .sptxt files is below showing the presence and then absence of the retention time information. ###### .ms2: H CreationDate Mon Jan 18 22:01:43 2021 H Extractor BlibToMs2 H Comment Library D:/Repositories\p20_05_HaloSpecLibPaper_SciData\splib\halo.blib S 1 1 1278.65 *I RTime 84.7206* Z 2 2481.75 D seq AAAANPGSAKAIADLGGAEGALTQAMGR D modified seq AAAANPGSAKAIADLGGAEGALTQAM[+15.99492]GR 693.35 39.0 822.42 85.0 1006.53 48.0 1209.62 100.0 679.31 36.0 792.40 52.0 863.41 67.0 1049.49 76.0 1031.49 66.0 1120.54 67.0 1103.50 67.0 1330.66 84.0 #### .sptxt: Name: AAAANPGSAKAIADLGGAEGALTQAM[147]GR/2 LibID: 0 MW: 2557.2908 PrecursorMZ: 1278.6454 Status: Normal FullName: K.AAAANPGSAKAIADLGGAEGALTQAM[147]GR.L/2 (CID-QTOF) Comment: AvePrecursorMz=1279.4240 BinaryFileOffset=308 FracUnassigned=0.00,0/5;0.00,0/20;0.00,0/12 Fullname=X.AAAANPGSAKAIADLGGAEGALTQAM[147]GR.X/2 Mods=1/25,M,Oxidation NAA=28 NMC=1 NTT=2 Pep=Tryptic PepContext=1/AGLK_LNVV Prob=1.0000 Protein=1/fig|2745.389.peg.2815 ScanNum=1.1 Spec=CREATE NumPeaks: 12 679.3100 3600.0 y6/-0.009 693.3500 3900.0 b9-18/0.019,b9-17/-0.965 792.4000 5200.0 y7/-0.003,y17-64^2/0.487 822.4200 8500.0 b10-17/0.010,b10-18/0.994 863.4100 6700.0 y8/-0.030 1006.5300 4800.0 b12-17/-0.002,b12-18/0.982 1031.4900 6600.0 y10-18/-0.004,y10-17/-0.988,y22^2/0.467,b24-44^2/-0.558,b24-45^2/-0.042,b24-46^2/0.450 1049.4900 7600.0 y10/-0.014,b13-45/-0.084 1103.5000 6700.0 y11-17/-0.015,y11-18/0.969 1120.5400 6700.0 y11/-0.002,y24-35^2/1.487 1209.6200 10000.0 b14/-0.002 1330.6600 8400.0 y14-17/0.018 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/409253a3-ee5f-470a-a356-7c7935ecf151n%40googlegroups.com.
