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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/464c1ab6-5b58-44b2-a0fa-28a60447c8e9n%40googlegroups.com.
