Excellent! Thank you for letting me know. > On Apr 11, 2024, at 9:12 AM, 'Juergen Bartel' via spctools-discuss > <spctools-discuss@googlegroups.com> wrote: > > 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 >> <spctools...@googlegroups.com <>> 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-sulfate >>> mods = {"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 Protein >>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 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: >>>> >>>> >>>> >>>> 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-discu...@googlegroups.com <>. >>> 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. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com > <mailto:spctools-discuss+unsubscr...@googlegroups.com>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/9cae6f2c-dc06-4545-a998-ea33424703aan%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/9cae6f2c-dc06-4545-a998-ea33424703aan%40googlegroups.com?utm_medium=email&utm_source=footer>.
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