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-discuss@googlegroups.com <spctools-discuss@googlegroups.com>
*On Behalf Of *Ankit Balhara
*Sent:* Tuesday, January 29, 2019 1:22 AM
*To:* spctools-discuss <spctools-discuss@googlegroups.com>
*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.
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