I am following the OpenMS tutorial using KNIME, but I am using my own LC/MS data. I have downloaded the uniref90 fasta database (from UniProt), and created an index file with NCBI’s makeblastdb -dbtype prot -in uniref90.fastsa. However, I get an error that says "Invalid Character 0xB in line LINE and column COLUMN" in reference to the mzML file I have input.
I have converted my data using MSConvertGUI (from ProteoWizard) and the command line msconvert tool, but each one results in the same error.
I’m not exactly sure where this error is coming from (OpenMS/KNIME or MSConvert), so I thought I would start with OpenMS/KNIME and go from there
My questions are:
Does anyone know why I get this error, and some general steps I might take to fix it?
Is the reference database I have downloaded acceptable, or is there a better known one? This may be user-specific, but I thought I would ask anyway
I appreciate any help!
Edit: I would also like to say this is very new to me, so I apologize for any information not included
Hello, usually pictures of your problems and a workflow (with real or fake data) where we can reproduce the problem helps greatly. So please create a shareable workflow with the minimal information needed to replicate your issue and I can inspect what may be happening.
This is the “Standard output”: Error: Unable to read file (- due to that error of type Parse Error in: C:\jenkins\ws\openms\ntly\TstPkg\9447518b\source\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp@132-void __cdecl OpenMS::Internal::XMLHandler::fatalError(enum OpenMS::Internal::XMLHandler::ActionMode,const class OpenMS::String &,unsigned int,unsigned int) const)
And this is what the “Error output” shows: C:\jenkins\ws\openms\ntly\TstPkg\9447518b\source\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(131): While loading 'C:\Users\joshl\Desktop\Data\PWU1F_P1-C1_1_1003.mzML': invalid character 0xB( in line 209752 column 56085)
I have my workflow/data/reference database on OneDrive, I hope that’s okay Link to data
Hi,
Sorry, I should have specified that I gzipped my data only for upload because my internet speed is not great. I have the data unzipped in my workflow
Usually, you should have a mixture of MS1 and MS2 scans in your data. If you really only have MS1 data, then, for proteomics you can only do quantification, no identification. For metabolomics data, you could do an AccurateMassSearch based on a compound database.
Okay. Neither my supervisor nor I have worked with KNIME/OpenMS before, so I apologize for the naive questions and hand-holding I’m needing.
He said I should be using OpenMS for MS Only Full Scan data for pairwise comparisons of our data, am I able to do this in OpenMS? Or do you happen to know of any papers/writeups of doing something similar to this?
I see from this issue that OMSSAAdapter is not really supported anymore, and should be moved to CometAdapter or MSGFPlusAdapter.
Well, you could use the quantification tools and compare quantities of unknown features. That works with just MS1.
But to annotate peptides and distinguish peptide sequences with the same composition you need MS2 spectra in OpenMS.