Dear all, I have recently generated an in-silico spectral library for several peptides which may contains different modifications on the same cystein (cystein converted to a serin, formylglycin-aldehyde, ...). For this prediction I used Seq2MS (https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00180) and obtained a library in msp format. In this file the header indicates modifications for examle in the following way:
Name: DILTPELDNLAQNGSIFTSAYVAHPFCGPSR/2_1(26,C,FGAldehyd) Comment: Charge=2 Parent=1657.310386 Mods=1(26,C,FGAldehyd) Protein=nan If I correctly specify the modifications in a .usermods file(*) and import it to spectraST, the resulting sptxt files contain header such as: Name: DILTPELDNLAQNGSIFTSAYVAHPFC[85]GPSR/2 LibID: 6 MW: 3316.6353 PrecursorMZ: 1658.3177 Status: Normal FullName: X.DILTPELDNLAQNGSIFTSAYVAHPFC[85]GPSR.X/2 (CID) Comment: AvePrecursorMz=1659.3531 BinaryFileOffset=19516 Charge=2 FracUnassigned=0.89,4/5;0.83,16/20;0.56,35/60 Mods=1(26,C,FGAldehyd) NAA=31 NISTProtein=nan NMC=0 NTT=1 Parent=1657.310386 Prob=1.0000 Protein=1/nan However, when I want to check the spectra in this file in HTML format using Lib2HTML, the table contains the complete peptide only for the unmodified form and has an identical truncated peptide for all other modified forms: [image: Unbenannt.PNG] Ths does not only affect the truncated amino acids but also results in mis-alignment of the y-ion-series (i.e. due to the modified cystein, y1 is annotated as 122.027 while in this case it should be y5 with a much larger m/z). Again, the annotation in sptxt seems good. Does anyone has an idea how to solve this and/or how I could watch the spectra alternatively? Best, Juergen (*) part of the usermods file: C[se]|-15.977156|Serin C[al]|-17.992806|FGAldehyd ... -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/c568f446-b522-40fe-8e03-27684fd71d1bn%40googlegroups.com.
