Hello Juergen, Thanks for providing the test data. I was able to modify the code to allow Lib2HTML to also read the user modifications and display the from the HTML page. The prerelease installer that has this feature is available here:
https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/TPP_Setup_7.0.x.exe/download Let me know if you have any other questions. Cheers! -David T On Fri, Apr 5, 2024 at 1:45 AM 'Juergen Bartel' via spctools-discuss < [email protected]> wrote: > Dear David, > > to generate my library I have done a couple of steps: > 1) modified the file utils.py from seq2ms to contain my modifications: > > > > > > > > *# C H N O S P# mods = {"ox" : [0,0,0,1,0,0], ## changed this line to > enable sulfatase modification prediction se=serine; > al=formylglycine-aldehyd; do=formylglycine-diol; ds=diol-sulfate; > ss=serine-sulfatemods = {"ox" : [0,0,0,1,0,0], "se" : [0,0,1,0,-1,0], "al" > : [0,-2,1,0,-1,0], "do" : [0,0,2,0,-1,0], "ds" : [0,-1,5,0,0,0], "ss" : > [0,0,4,0,0,0], "ph" : [0,1,0,3,0,1], "cam" : [2,3,1,1,0,0] , > "ac": [2,2,0,1,0,0], "me": [1,2,0,0,0,0], "hy": [0,0,0,1,0,0], "gly": > [4,6,2,2,0,0], "bi" : [10,14,2,2,1,0], "cr": [4,4,0,1,0,0], "di": > [2,4,0,0,0,0], "ma": [3,2,0,3,0,0], "ni": [0,-1,1,2,0,0], "bu" : > [4,6,0,1,0,0], "fo": [1,0,0,1,0,0], "glu": [5,6,0,3,0,0], "hyb": > [4,6,0,2,0,0], "pr": [3,4,0,1,0,0], "su" : [4,4,0,3,0,0], "tr": > [3,6,0,0,0,0], "ci": [0,-1,-1,1,0,0]}* > > 2) I run the prediction by executing 'predict.py' with the a modified > input.tsv and (I think) the pretrained_model. The input file looked like > the following but contained more peptides: > > > > > > > > > > > > > > > > > > > *Sequence Charge Mass Modified sequence Modification > ProteinDILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3332.613578 > _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_ Unmodified > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3332.613576 > _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_ Unmodified > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3332.613576 > _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_ Unmodified > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3316.636422 > _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_ Serine (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3316.636422 > _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_ Serine (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3316.63642 > _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_ Serine (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3314.620772 > _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_ FGAldehyd (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3314.62077 > _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_ FGAldehyd (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3314.620772 > _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_ FGAldehyd (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3332.631336 > _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_ FGDiol (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3332.631336 > _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_ FGDiol (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3332.631336 > _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_ FGDiol (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3411.580326 > _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_ DiolSulfat (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3411.580326 > _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_ DiolSulfat (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3411.580324 > _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_ DiolSulfat (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3396.593236 > _DILTPELDNLAQNGSIFTSAYVAHPFC(ss)GPSR_ SerinSulfat (C) > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3396.593235 > _DILTPELDNLAQNGSIFTSAYVAHPFC(ss)GPSR_ Unmodified > DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3396.593236 > _DILTPELDNLAQNGSIFTSAYVAHPFC(ss)GPSR_ Unmodified * > > 3) I imported the generated .msp file into spectraST format using the > command line and the following options: > *C:\TPP\bin\spectrast.exe -cNPredicted_Sec2MS.splib -MSec2MS.usermods > Predicted.msp* > > 4) I tried to visualise this library by Lib2HTML from the within Petunia > > For the files I will send you a link via the ISB contact form to our > university's nextcloud where I have uploaded them. > > Best regards, > Juergen > > > Juergen Bartel schrieb am Montag, 22. Januar 2024 um 18:22:49 UTC+1: > >> 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/dd0ac502-dde9-495c-ac48-58340707b5b9n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/dd0ac502-dde9-495c-ac48-58340707b5b9n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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