Hi Eric, Thanks for helping. Actually I used 11 iRT peptides (all are present in iRT.txt file), but unfortunately only two are present in the library. So do I need to repeat the experiment or there is another way out?
Regards Ankit On Tuesday, 29 January 2019 22:10:38 UTC+5:30, Eric Deutsch wrote: > > Hi Ankit, I suppose the first question to ask is: how many iRT peptides > are in your iRT.txt file and how many of those have a corresponding entry > in the library? > > > > Regards, > > Eric > > > > > > *From:* spctools...@googlegroups.com <javascript:> < > spctools...@googlegroups.com <javascript:>> *On Behalf Of *Ankit Balhara > *Sent:* Tuesday, January 29, 2019 1:22 AM > *To:* spctools-discuss <spctools...@googlegroups.com <javascript:>> > *Subject:* [spctools-discuss] Problem during spectrast library generation > > > > Hi, > > > > I am trying to build the spectral library using the SpectraST. I have > analyzed the DDA data upto the Mayu FDR determination step, also got the > IPP/PP values corresponding to 1%FDR. After that I am using following > command, but got the error that "Too few landmarks with distinct iRTs to > perform RT normalization". Could anybody please help me out? > > > > c:\TPP\bin>spectrast -cNSpecLib -cICID-QTOF -cf "Protein! ~ 'rev_'" > -cP0.891383 -c_IRTc:\TPP\data\iRT.txt -c_IRR > c:\TPP\data\params\interact.ipro.pep.xml > > SpectraST started at Tue Jan 29 14:38:13 2019. > > Processing > "c:\TPP\data\params\interact.ipro.pep.xml"...500...1000...1500...DONE! > > Importing all spectra with P>=0.891383 ...INFO: Reading file: > c:/TPP/data/HLM_27_DDA.mzXML > > 10%...20%...30%...40%...50%...60%...70%...80%...90%...DONE! > > > > Library file (BINARY) "SpecLib.splib" created. > > Library file (TEXT) "SpecLib.sptxt" created. > > M/Z Index file "SpecLib.spidx" created. > > Peptide Index file "SpecLib.pepidx" created. > > > > Total number of spectra in library: 1661 > > Total number of distinct peptide ions in library: 1560 > > Total number of distinct stripped peptides in library: 1429 > > > > CHARGE +1: 0 ; +2: 1187 ; +3: 450 ; +4: 24 ; +5: 0 ; >+5: 0 ; > Unk: 0 > > TERMINI Tryptic: 1654 ; Semi-tryptic: 7 ; Non-tryptic: 0 > > PROBABILITY >0.9999: 1347 ; 0.999-0.9999: 147 ; 0.99-0.999: 89 ; > 0.9-0.99: 76 ; <0.9: 2 > > NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 1661 > > MODIFICATIONS C,Carbamidomethyl: 288 ; C,Pyro-carbamidomethyl: 2 > > M,Oxidation: 12 > > Q,Gln->pyro-Glu: 4 > > n,Acetyl: 5 > > > > Total Run Time = 24 seconds. > > SpectraST finished at Tue Jan 29 14:38:37 2019 with 1 error(s): > > PEPXML IMPORT: Too few landmarks with distinct iRTs to perform RT > normalization. > > > > -- > 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 <javascript:>. > To post to this group, send email to spctools...@googlegroups.com > <javascript:>. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
