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-discuss@googlegroups.com <spctools-discuss@googlegroups.com> *On Behalf Of *RS *Sent:* Tuesday, July 7, 2020 10:36 AM *To:* spctools-discuss <spctools-discuss@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-discuss+unsubscr...@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-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/658cee33ae9c07f387d02e891524708e%40mail.gmail.com.
