I have encountered the same problem. My search has Acetylation modifications, but spectrast gives error on such modification as follows,
Can anyone help? ----------------------------------------------- Total Run Time = 3.056e+004 seconds. SpectraST finished at Sat Jun 30 19:26:22 2012 with 60305 error(s): PEPXML IMPORT: Peptide ID has unknown modification: "n[42]SETAISFAK". Skipped query "G_110924_01_Zebrafish_band1_C01.21189.21189.2". PEPXML IMPORT: Peptide ID has unknown modification: "n[42]SETAISFAK". Skipped query "G_110924_01_Zebrafish_band1_C01.21422.21422.2". ........ On Friday, December 3, 2010 12:26:38 AM UTC+8, lgillet wrote: > > Hi, > I have been searching yeast N15 datasets. Sequest search went all fine > (after defining the individual aa modifications) and so did the > peptide prophet. > But when I try to compile a spectra library with spectrast, Spectrast > has problems to handle the modifications: > > 1) First test > > > command: spectrast -cNDP-N15-IDA -cP0.9 interact-CommandLine.pep.xml > > > output: > SpectraST started at Thu Dec 2 17:05:42 2010. > Importing all spectra with probability >= 0.9... > Processing "interact-CommandLine.pep.xml"...DONE! > Importing spectra...DONE! > > Library file (BINARY) "DP-N15-IDA.splib" created. > Library file (TEXT) "DP-N15-IDA.sptxt" created. > M/Z Index file "DP-N15-IDA.spidx" created. > Peptide Index file "DP-N15-IDA.pepidx" created. > > Total number of spectra in library: 0 > Total number of distinct peptide ions in library: 0 > Total number of distinct stripped peptides in library: 0 > > CHARGE +1: 0 ; +2: 0 ; +3: 0 ; +4: 0 ; +5: 0 ; >+5: 0 > TERMINI Tryptic: 0 ; Semi-tryptic: 0 ; Non-tryptic: 0 > PROBABILITY >0.9999: 0 ; 0.999-0.9999: 0 ; 0.99-0.999: 0 ; > 0.9-0.99: 0 <0.9: 0 > NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 0 > MODIFICATIONS None > > Total Run Time = 4 seconds. > SpectraST finished at Thu Dec 2 17:05:46 2010 with 7227 error(s): > PEPXML IMPORT: Peptide ID has unknown modification: > "E[130]D[116]S[88]V[100]Y[164]L[114]A[72]K[130]". Skipped query > "N15-1.0.00966.00966.2". > ...................... > > > Second try: specifying a spectrast.usermods file > > command: > spectrast -cNDP-N15-IDA -cP0.9 -Mspectrast.usermods interact- > CommandLine.pep.xml > > > output: > SpectraST started at Thu Dec 2 17:08:35 2010. > Importing all spectra with probability >= 0.9... > Processing "interact-CommandLine.pep.xml"... > 500...1000...1500...2000...2500...3000...3500...4000...4500...DONE! > Importing spectra...10%...20%...30%...40%...50%...60%...70%...80%... > 90%...DONE! > > Library file (BINARY) "DP-N15-IDA.splib" created. > Library file (TEXT) "DP-N15-IDA.sptxt" created. > M/Z Index file "DP-N15-IDA.spidx" created. > Peptide Index file "DP-N15-IDA.pepidx" created. > > Total number of spectra in library: 4675 > Total number of distinct peptide ions in library: 2720 > Total number of distinct stripped peptides in library: 2443 > > CHARGE +1: 0 ; +2: 3370 ; +3: 1305 ; +4: 0 ; +5: 0 ; >+5: 0 > TERMINI Tryptic: 4642 ; Semi-tryptic: 33 ; Non-tryptic: 0 > PROBABILITY >0.9999: 1325 ; 0.999-0.9999: 1609 ; 0.99-0.999: > 1062 ; 0.9-0.99: 679 <0.9: 0 > NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 4675 > MODIFICATIONS A,USM_A_72.034145: 3156 > C,Carboxymethyl: 340 > D,USM_D_116.023975: 2545 > E,USM_E_130.039625: 2959 > F,USM_F_148.065445: 2077 > G,USM_G_58.018495: 2861 > H,USM_H_140.050015: 625 > I,USM_I_114.081095: 2906 > K,USM_K_130.089030: 2872 > L,USM_L_114.081095: 3408 > M,USM_M_132.037525: 762 > N,USM_N_116.037000: 2431 > P,USM_P_98.049795: 2426 > Q,USM_Q_130.052650: 1911 > R,USM_R_160.089250: 1968 > S,USM_S_88.029065: 2735 > T,USM_T_102.044715: 2733 > V,USM_V_100.065445: 3273 > W,USM_W_188.073380: 431 > > Total Run Time = 17 seconds. > SpectraST finished at Thu Dec 2 17:08:52 2010 with 2541 error(s): > PEPXML IMPORT: Peptide ID has unknown modification: > "E[130]D[116]S[88]V[100]Y[164]L[114]A[72]K[130]". Skipped query > "N15-1.0.00966.00966.2". > .................. > > My spectrast.usermods was as follows: > G|+0.99703497| > A|+0.99703497| > S|+0.99703497| > P|+0.99703497| > V|+0.99703497| > T|+0.99703497| > C|+58.0184989| > I|+0.99703497| > L|+0.99703497| > D|+0.99703497| > E|+0.99703497| > M|+0.99703497| > F|+0.99703497| > T|+0.99703497| > N|+1.99406994| > Q|+1.99406994| > K|+1.99406994| > W|+1.99406994| > H|+2.99110491| > R|+3.98813988| > > > I even tried one like this: > G[58]|+0.99703497| > A[72]|+0.99703497|... > > > But without any success. > > Am I doing something wrong? > How to specify the modifications such that spectrast proceeds? > > Thanks in advance for your help > > Ludovic > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/uotSlqwd2h8J. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
