Hi David, Thank you for modifying the code so quickly! I have just tested Lib2HTML with the new prerelease and it works perfectly fine now.
Cheers! Juergen David Shteynberg schrieb am Donnerstag, 11. April 2024 um 02:28:19 UTC+2: > 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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