Is the "Comment:" field is optional? I've seen modification info is mentioned in the comment section differently in NO_DECOY and PLUS_DECOY spectral lib
Example , for different peptides in NO_DECOY and PLUS_DECOY respctively:. Note the Mods=0, Mods=1/8,C,Carbamidomethyl etc. tokens Comment: AvePrecursorMz=375.4312 BinaryFileOffset=229 FracUnassigned=0.00,0/5;0.09,4/20;0.25,1061/1512 Fullname=X.KSDVEAIFSK.X/3 NAA=10 Prob=1.0000 ScanNum=13667.13667 Spec=DECOY Comment: AvePrecursorMz=375.4312 BinaryFileOffset=35971 FracUnassigned=0.00,0/5;0.09,4/20;0.25,1061/1512 Fullname=X.KSDVEAIFSK.X/3 Mods=0 NAA=13 NMC=2 NTT=1 OrigPeptide=X.KSDVEAIFSK.X/3 Pep=Semi-tryp Prob=1.0000 Protein=DECOY_0_Unknown Remark=DECOY_0 ScanNum=13667.13667 Spec=DECOY Comment: AvePrecursorMz=379.7998 BinaryFileOffset=3603257 FracUnassigned=0.28,1/5;0.53,12/20;0.37,482/779 Fullname=X.IGKPHTVPC[160]K.X/3 Mods=1/8,C,Carbamidomethyl NAA=10 NMC=1 NTT=1 OrigPeptide=X.IGKPHTVPC[160]K.X/3 Pep=Semi-tryp Prob=1.0000 Protein=DECOY_0_Unknown Remark=DECOY_0 ScanNum=21336.21336 Spec=DECOY On Saturday, July 11, 2020 at 2:01:17 PM UTC-4 RS wrote: > I've used two modifications, Methionine oxidation and Cysteine > Carbamidomethylation. None of the modifications were imported into PD from > the DECOY-FREE library. > The unmodified peptides worked just fine. > > Thanks > > On Friday, July 10, 2020 at 2:51:47 AM UTC-4 Eric Deutsch wrote: > >> I have never tried this (importing from MS2) myself. So it works for a >> spectrum with no M[147], but it fails for a spectrum with M[147]? >> >> >> >> >> >> *From:* spctools...@googlegroups.com <spctools...@googlegroups.com> *On >> Behalf Of *RS >> *Sent:* Wednesday, July 8, 2020 9:34 AM >> *To:* spctools-discuss <spctools...@googlegroups.com> >> *Subject:* Re: [spctools-discuss] Re: SpectraST: Missing modifications >> in decoy free library import in ProteomeDiscoverer >> >> >> >> I was trying to debug the problem using a single MS2 format Spectra. >> Here's the Pastebin link <https://pastebin.com/3Ju2C4r8> >> However, I'm getting an error message while trying to build the spectrst >> format library: >> >> *C:\TPP\bin>spectrast.exe -cNSingleSpectraMet SingleSpectraMet.MS2* >> >> *SpectraST started at Wed Jul 08 12:20:28 2020.* >> >> *Total Run Time = 2 seconds.* >> >> *SpectraST finished at Wed Jul 08 12:20:30 2020 with 1 error(s):* >> >> *CREATE: Libraries to be imported have illegal formats. Exiting.* >> >> >> Any help? >> >> Thanks >> >> On Wednesday, July 8, 2020 at 2:19:24 AM UTC-4 Eric Deutsch wrote: >> >> I’ve never tried to import into PD, so I can’t help there. Presumably the >> ADD DECOY doesn’t change things like M[147], so I also do not understand >> why PD would recognize M[147] in a library with decoys but not in a library >> without? >> >> >> >> >> >> *From:* spctools...@googlegroups.com <spctools...@googlegroups.com> *On >> Behalf Of *RS >> *Sent:* Tuesday, July 7, 2020 10:36 AM >> *To:* spctools-discuss <spctools...@googlegroups.com> >> *Subject:* Re: [spctools-discuss] Re: SpectraST: Missing modifications >> in decoy free library import in ProteomeDiscoverer >> >> >> >> Thanks Eric, >> Please let me know if you have any remedies for the rest of the problems >> >> On Tuesday, July 7, 2020 at 1:29:08 PM UTC-4 Eric Deutsch wrote: >> >> Yes, M[147] is the TPP notation for oxidized methionine. The total mass >> of oxidized methionine rounds to 147 Da. >> >> >> >> >> >> *From:* spctools...@googlegroups.com <spctools...@googlegroups.com> *On >> Behalf Of *RS >> *Sent:* Tuesday, July 7, 2020 9:38 AM >> *To:* spctools-discuss <spctools...@googlegroups.com> >> *Subject:* [spctools-discuss] Re: SpectraST: Missing modifications in >> decoy free library import in ProteomeDiscoverer >> >> >> >> and I wonder why Methionine oxidation (*15.995* Da) is replaced by M >> [147], is that an internal code to represent that modification or something >> got messed up? >> >> On Tuesday, July 7, 2020 at 12:27:41 PM UTC-4 RS wrote: >> >> Hello All, >> >> I'm trying to create a spectral library from Proteome Discoverer (PD >> )result files to re-import into PD as PD accepts* sptxt* format >> libraries. >> >> My workflow was as follows: >> >> ProteomeDiscoverer 2.3 *msf * format search result files were converted >> to a * blib* file. The filtered *blib* file was converted to *sp2 *format. >> The* sp2* format file was finally converted to *sptxt *format library by >> SpectraST. >> >> While importing the sptxt format file (without adding any decoy) I've >> seen the amino acid modifications used like Methionine oxidation and >> Cysteine carbamidomethylation were not recognized by PD >> >> However if I ADD DECOY to the library, followed by its import to PD , the >> modifications show up in PD (see attached pics) >> >> This is how the header info. of one such modified amino acid peptide >> appears in the decoy-free library: >> >> Name: M[147]ATALPPR/2 >> >> LibID: 329 >> >> MW: 873.4731 >> >> PrecursorMZ: 436.7366 >> >> Status: Normal >> >> FullName: X.M[147]ATALPPR.X/2 (CID) >> >> Comment: AvePrecursorMz=437.0325 BinaryFileOffset=10637539 >> FracUnassigned=0.90,4/5;0.89,17/20;0.66,1314/1631 >> Fullname=X.M[147]ATALPPR.X/2 Prob=1.0000 ScanNum=2539.2539 Spec=Raw >> >> NumPeaks: 1631 >> >> Can somebody let me know how to incorporate these modifications so that >> they can be imported by ProteomeDiscoverer >> Image links: >> >> Decoy library <https://i.imgur.com/Yiz6QLt.png> >> >> >> NO-Decoy library <https://i.imgur.com/1lLKlwt.png> >> >> >> Thanks >> >> >> >> >> >> -- >> 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/913df290-7bbc-4ffe-a6a4-c5eedf6ece6en%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/913df290-7bbc-4ffe-a6a4-c5eedf6ece6en%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-discu...@googlegroups.com. >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/5d70193f-2881-44e8-aa94-0391516f1d00n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/5d70193f-2881-44e8-aa94-0391516f1d00n%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-discu...@googlegroups.com. >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/05b6cc19-440a-46ce-9c8e-65f005534d00n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/05b6cc19-440a-46ce-9c8e-65f005534d00n%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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