Hi Emma, I have definitely converted some RAW data files to truly massive mzML files (around 40+ GB). Not fun, but it definitely works. You might consider using features to reduce the size of the output, like compression and peak picking (centroiding), which you probably want for X! Tandem (or any peptide spectrum matching tool) anyway. You could also convert only the MS2 scans for X! Tandem, which would greatly reduce the size not to carry around the MS1 scans, which I don't think X! Tandem uses.
In the end, I would be willing to bet that the reason you are experiencing difficulty is that you are either running a 32-bit system or your file system is FAT32, which will limit your file sizes to just 2 GB. How big are the mzML files you see msConvert creating? Look for a way to do this on a 64-bit OS with NTFS or similar 64-bit file system. --Brendan On Tuesday, April 5, 2016 at 10:50:20 AM UTC-7, Emma Whittington wrote: > > I am trying to run msconvert on raw files that are ~1.5gb each and it > seems to stop part way through in that the output mzml files are not > complete. Because of this when I try to run the mzml files through Tandem I > get a 'syntax error parsing XML' error. Is there a way of splitting the raw > files before running msconvert (or during) so I get multiple smaller output > files? > > Thanks > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
