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michaelmarty / UniDec

Universal Deconvolution of Mass and Ion Mobility Spectra
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Import of mzML files for "Using MetaUniDec to Analyze Chromatograms" not working #39

Closed wendscheck closed 4 years ago

wendscheck commented 4 years ago

Hi michaelmarty, I was trying to import my MS data as you nicely described in your Wiki "Using MetaUniDec to Analyze Chromatograms". My data was acquired on a Synapt G1 with MassLynx V4.1 and i converted it by using MSConvert V3 to mzML with default parameters. Then i followed your description in MetaUniDec (Version 4.1.2): File/Automated Chromatogram Parsing/Auto Import Chromatogram by Scans and used Scan step of 1.0. At this point I receive the following issue:

UniDec Path: D:\UniDec_Windows_Dist_200121\UniDec.exe Display Size (1920, 1080) TESTING: ['D:\Daniel\20200207_P495\rawfiles\SYNAPT01502.mzML'] SYNAPT01502.mzML Reading mzML: D:\Daniel\20200207_P495\rawfiles\SYNAPT01502.mzML 'NoneType' object is not subscriptable Errors: ['D:\Daniel\20200207_P495_subunitxchange\rawfiles\SYNAPT01502.mzML']

Any ideas?

Thanks for your help, Daniel

michaelmarty commented 4 years ago

Hi Daniel, Thanks for getting in touch. I've had issues before with converting Waters files into mzML. Can you send an example of the raw file and the mzML to mtmarty@email.arizona.edu? Also, does the Raw file open with UniDec? Thanks, MTM

wendscheck commented 4 years ago

Hi Michael, I just send you the files via e-mail. I can open the rawfiles in UniDec using file tab -> Open Waters Raw File. Best, Daniel

michaelmarty commented 4 years ago

Resolved with update to pymzml and with try/except clause on getting start time. Fix loaded in Version 4.2. Thanks!