Hi Brendan, thank you for the response. I am using a 64 bit OS system and the zlib compression option. The resulting mzML files are ~ 4gb.
I will be running the files through TPP using both X!Tandem and comet (combining the two later with iprophet). Do you know if either of those use MS1 scans (or where I could find out)? I tried using a computer with more RAM (that was a suggested solution) and ended up getting the following error: [SpectrumWorkerThreads::work] error in thread: [SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=21718": [ThermoRawFile] [RawFileImpl::getMassList(), GetMassListFromScanNum()] Failed call to XRawfile: The system cannot find the file specified. So I'm currently redownloading the raw files in case there was some sort of corruption that I hadn't caught up with previously. These are the largest raw files I've worked with so I haven't come across these problems before. thank you again On Wednesday, 6 April 2016 12:31:32 UTC-4, Brendan MacLean wrote: > > 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.
