Hello again, as I described before (topic: *What happens during consensus building?*) I have a problem with some messed up spectra in my spectral libraries. I combined four spectral libraries and built consensus spectra. Afterwards I reimported the combined consensus spectral library in MRM format and converted it in an assay library. When I checked the SPTXT file I found some *slightly changed spectra* and new *"ion types" m*. Please see my example of an old, normal spectrum and the corresponding new one below:
Name: DIETIIQK/2 *(old entry, original library)* LibID: 4160 MW: 960.5481 PrecursorMZ: 480.2740 Status: Normal FullName: X.DIETIIQK.X/2 (CID-QTOF) Comment: AvePrecursorMz=480.5611 BinaryFileOffset=23385298 FracUnassigned=0.09,1/5;0.23,11/20;0.06,7/31 MassDiff=-0.0014 Mods=0 NAA=8 NISTProtein=Id_02 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=11 Parent=480.274 Pep=Tryptic PrecursorIntensity=0 Prob=1.0000 Protein=1/Id_02 RawSpectrum=file_02_04.69683.69683 RetentionTime=2745.2,2745.2,2745.2 Sample=1/sample_02,1,1 Se=1^C1:pb=1.0000/0,fv=2.7040/0 Spec=CREATE TotalIonCurrent=8.9e+003 iRT=33.4,33.4,33.4 NumPeaks: 31 308.1581 226.5 ? 309.0826 359.4 ? 325.6734 1596.8 b6-35^2/0.000,b6-36^2/0.492 329.1945 141.2 a6^2/0.000 343.1920 668.4 b6^2/0.000,y3-45/-0.042,y6-45^2/-0.516,y6-46^2/-0.024 353.2183 967.7 y3-35/0.000 354.2183 480.9 y3-35i/0.000 355.2183 481.6 y3-35i/0.000 358.1609 442.5 b3/0.000,y6-17^2/0.456,y6-18^2/0.948 358.1970 96.7 ? 365.2030 293.0 ? 373.2367 296.2 ? 388.2554 1744.6 y3/0.000,b7-36^2/-0.955 424.1714 315.8 b4-35/0.000,b4-36/0.984 442.1820 644.1 b4-17/0.000,b4-18/0.984 457.7633 546.4 p-45^2/0.000,p-46^2/0.492,y4-44/0.414 458.2791 109.5 p-44^2/0.000,b4/-0.929 471.7608 110.9 p-17^2/0.000,p-18^2/0.492 472.2608 111.1 p-17^2i/0.000 477.1321 111.6 ? 480.2740 336.0 p^2/0.000 484.3130 224.9 y4-17/0.000,y4-18/0.984 501.3395 523.5 y4/0.000 553.1674 240.4 ? 567.3501 487.3 y5-35/0.000 584.3766 247.1 y5-18/0.000 602.3872 2935.1 y5/0.000 696.3927 205.5 y6-35/0.000,y6-36/0.984 714.4032 2211.4 y6-17/0.000,y6-18/0.984 731.4298 10000.0 y6/0.000 732.4298 414.9 y6i/0.000 Name: DIETIIQK/2 *(new entry, combined library)* LibID: 4673 MW: 960.5481 PrecursorMZ: 480.2740 Status: Normal FullName: X.DIETIIQK.X/2 (CID-QTOF) Comment: AvePrecursorMz=480.5611 BinaryFileOffset=20613807 FracUnassigned=0.09,1/5;0.25,13/20;0.17,13/31 MassDiff=-0.0014 Mods=0 NAA=8 NISTProtein=Id_02 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=11 Parent=480.274 Pep=Tryptic PepContext=1/NTPR_DIHE PrecursorIntensity=0 Prob=1.0000 Protein=1/Id_02 RawSpectrum=file_02_04.69683.69683 RetentionTime=2745.2,2745.2,2745.2 Sample=1/sample_02,1,1 Se=1^C1:pb=1.0000/0,fv=2.7040/0 Spec=CREATE TotalIonCurrent=8.9e+003 iRT=33.4,33.4,33.4 NumPeaks: 31 308.1581 226.5 ? 309.0826 359.4 ? 326.1680 1596.8 ? 328.2231 141.2 m4:6/0.000 344.1816 668.4 m3:5/0.000 353.2183 967.7 y3-35/0.000 354.2183 480.9 y3-35i/0.000 355.2183 481.6 y3-35i/0.000,m5:7/-0.016 358.1609 442.5 b3/0.000 358.1970 96.7 ? 365.2030 293.0 ? 373.2367 296.2 ? 388.2554 1744.6 y3/0.000 424.1714 315.8 b4-35/0.000 441.1980 644.1 b4-18/0.000 457.2713 546.4 p-46^2/0.000,m3:6/0.006 459.2086 109.5 b4/0.000 471.2688 110.9 p-18^2/0.000 472.2512 111.1 ? 477.1321 111.6 ? 480.2410 336.0 ? 484.3130 224.9 y4-17/0.000 501.3395 523.5 y4/0.000 553.1674 240.4 ? 568.3124 487.3 ? 584.2763 247.1 ? 602.3872 2935.1 y5/0.000 695.4087 205.5 y6-36/0.000 713.4192 2211.4 y6-18/0.000 731.4298 10000.0 y6/0.000 732.4675 414.9 ? I assumed before, that it was an issue with the consensus building, but I figured out that it took action during the *import via spectraST into MRM format*. Now, I just saw that I don't have this problem when I use the single libraries. Even with consensus libraries built with with an older spectraST version the MRM import works just fine. Maybe there is the *problem in the combination of the spectral libraries?* I already got them as single consensus libraries and combined them with the following command spectrast -cNcombined_lib -cd -cu -cr1 -cy1 -cAC -cJU Lib_01.splib Lib_01 .splib Lib_01.splib Lib_01.splib Could this be an issue here. Do I have to rebuild all libraries before combining them? I would be really happy about any suggestions. Thank you in advance! Kind regards, Kristina ____________________ Kristina Plate, MSc. Biomathematics University of Greifswald Center for Functional Genomics of Microbes Institute for Microbiology Department of Microbial Proteomics Felix-Hausdorff-Str. 8 17489 Greifswald phone: +49 3834 420-5925 fax: +49 3834 420-5902 -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/1573a2bc-1b4a-4ca7-bc88-75579028df95%40googlegroups.com.
