Hi Eric, Thanks Eric. I haven't used any use any probability threshold value. Moreover, I also tried with loose parameters values, but still getting only two iRT peptides present in the library. I am attaching the parameter file, could you please suggest anything? Also, does the way in which the sequence of iRT peptide are fused to be put into the fasta sequence influence the search?
Thanks in advance. Regards Ankit On Tuesday, 29 January 2019 14:51:58 UTC+5:30, Ankit Balhara wrote: > > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
comet_1.params
Description: Binary data
