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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