Moritz, I don't think this is the intended use of the TSV import function. SpectraST expects the following columns:
mzMLFile scanNumber peptideID probability scores protein In other words, you cannot specify the peak list in the TSV. The peak list must be read from an mzML file. The TSV only supplies the "header" of each entry, namely, the peptide, a probability of identification accuracy, any scores you would want to include, and optionally the protein mapped to by the peptide. If you want to create a library out of an SRM transition list (which seems to be what you are trying to do), you may want to format the file like an MSP (NIST's library format, which is also similar to SpectraST's sptxt), and then import via that route. As a general comment though, I'd note that many functions of SpectraST -- e.g. consensus creation, decoy generation, spectral searching, etc -- are designed for full MS2 spectra. It probably won't work as intended if you feed it something else. Henry On Monday, July 16, 2018 at 10:52:56 AM UTC+8, ML wrote: > > Hi all, > > > I’m a bit stuck on importing an existing PeakView library (tsv or txt > format) into SpectraST. > > In the log file from SpectraST it says the following : > > > START: (Mon Jul 16 14:16:51 2018) spectrast -cNimported out.tsv > > GENERAL: File offset size is 8 bytes. Big library supported. > > GENERAL: Pointer size is 8 bytes. > > TSV IMPORT: Peptide ID too short. Skipped spectrum 778.427.427 . > > TSV IMPORT: Peptide ID too short. Skipped spectrum 778.498.498 . > > TSV IMPORT: Peptide ID too short. Skipped spectrum 778.569.569 . > > TSV IMPORT: Peptide ID too short. Skipped spectrum 778.214.214 . > > … > > CREATE: IMPORT FROM TSV > "c:/TPP/data/dbase/speclibs/test/out.tsv"[P=0.9;n=;g=FALSE;o=FALSE;I=;_RNT=0;_RDR=100000;_DCN=0;_NAA=6;_NPK=10;_CEN=FALSE;_XAN=FALSE] > > TSV IMPORT: Total of 0 spectra imported, 3531720 spectra skipped. > > PERFORMANCE: Total Run Time = 54 seconds. > > END: (Mon Jul 16 14:17:45 2018) spectrast -cNimported out.tsv > > > The column formats I've tried are: > > Q1 Q3 RT_detected protein_name isotype > relative_intensity stripped_sequence modification_sequence > prec_z frg_type frg_z frg_nr iRT uniprot_id decoy N > confidence shared > > > and > > > PrecursorMz ProductMz Tr_recalibrated transition_name CE > LibraryIntensity transition_group_id ProteinName GroupLabel > PeptideSequence FullUniModPeptideName UniprotID decoy shared > confidence PrecursorCharge FragmentType FragmentCharge > FragmentSeriesNumber > > > > Any ideas? > > > > Moritz > -- 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.
