Hey Jason, If you are able to compress the dataset directory and share it I would be happy to troubleshoot this particular issue.
Cheers! -David On Thursday, August 31, 2023 at 12:52:42 PM UTC-7 jwi...@gmail.com wrote: > I am trying to process my data using StPeter and am getting the following > error: > > Extracting peak intensities from 1 spectral files: > 1 of 1: C:\TPP\data\Supernatant\PG_SS_RAW\SS1_Slot2-4_1_789.mzML > 0%ERROR: Could not read spectra. > > The data was collected on a Bruker timsTOF and converted using the > msconvert options "combine ion mobility scans" as well as vendor peak > picking and scan summing. > > I searched the mzML with Comet, then processed those results with > PeptideProphet, iProphet, and ProteinProphet. I am using TPP v6.3.3 Arcus, > Build 202308242222-9003 (Windows_NT-x86_64). Before it crashes, StPeter > appears to be working: > > ****** BEGIN StPeter ANALYSIS ****** > Time at start of analysis: Thu Aug 31 15:39:02 2023 > > Parameters: > degenerate peptides = yes > fdr = 0.01 > minimum probability = 0 > sample load = 0 > tolerance = 0.4 > > Reading protXML: .\ss1_slot2-4_1_789.iproph.prot.xml > Probability at 0.01 FDR: 0.965 > Number of proteins above FDR cutoff: 418 > Number of quantifiable proteins above FDR cutoff: 418 > Number of peptides for proteins: 822 > Extracting true protein lengths for zero length proteins. Database: > uniref_taxonomy_allcombined_DECOY.fasta > Number of proteins fitting criteria for StPeter analysis: 418****** > BEGIN StPeter ANALYSIS ****** > Time at start of analysis: Thu Aug 31 15:39:02 2023 > > Parameters: > degenerate peptides = yes > fdr = 0.01 > minimum probability = 0 > sample load = 0 > tolerance = 0.4 > > Reading protXML: .\ss1_slot2-4_1_789.iproph.prot.xml > Probability at 0.01 FDR: 0.965 > Number of proteins above FDR cutoff: 418 > Number of quantifiable proteins above FDR cutoff: 418 > Number of peptides for proteins: 822 > Extracting true protein lengths for zero length proteins. Database: > uniref_taxonomy_allcombined_DECOY.fasta > Number of proteins fitting criteria for StPeter analysis: 418 > > The mzML files are in the same directory as the protXML file, and the head > of the mzML appears normal: > > <?xml version="1.0" encoding="utf-8"?> > <indexedmzML xmlns="http://psi.hupo.org/ms/mzml"; xmlns:xsi=" > http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation=" > http://psi.hupo.org/ms/mzml > http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd";> > <mzML xmlns="http://psi.hupo.org/ms/mzml"; xmlns:xsi=" > http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation=" > http://psi.hupo.org/ms/mzml > http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"; > id="SS1_Slot2-4_1_789" version="1.1.0"> > <cvList count="2"> > <cv id="MS" fullName="Proteomics Standards Initiative Mass > Spectrometry Ontology" version="4.1.56" URI=" > https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> > <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI=" > https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo > "/> > </cvList> > <fileDescription> > <fileContent> > <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" > value=""/> > > I also checked within the mzML file to confirm that it does contain MS2 > scan information. > Any advice? > > Jason > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f75403d9-fdee-4ac2-8ddf-19003969beb5n%40googlegroups.com.
