I typically acquire all my files on a machine that does only that. The raw data is moved off right away to an external computer which is much faster and is used specifically for processing data. They both have the same version of MassLynx 4.1 installed. I have successfully converted the file which Dr. Li is referring too. My best guess is that it is not working on his machine due to the non-matching version of MassLynx.
On Jul 15, 4:05 pm, Natalie Tasman <[email protected]> wrote: > Hi Chris, > > Yes, especially for MassLynx, it can make a big difference if the versions > don't match. You really want to have the MassLynx version on the conversion > machine exactly match the acquisition version. It's good news that the file > can be opened by MassLynx itself and thus doesn't seem corrupted. I am > curious, though, if you did that test on the conversion or acquisition > machine (that is, which vendor version you tested against?). > > Natalie > > On Wed, Jul 15, 2009 at 11:34 AM, Chris Hughes <[email protected]> wrote: > > > The file is Micromass data. It is not odd for the size to read 0K, > > this is some sort of artifact of it being a .raw folder. The file is > > not corrupt, it opens on MassLynx properly, and can be run through > > PLGS with no troubles to a pkl file. It was acquired in MassLynx 4.1 > > however, might this make a difference as the user is using an older > > version? > > > On Jun 25, 2:36 pm, Natalie Tasman <[email protected]> > > wrote: > > > Thanks, Dave, and just pointing out that there is a description of > > > these options in the usage statement (printed out when running the > > > program with no arguments). > > > > Natalie > > > > On Jun 25, 2009, at 9:36 AM, Dave Trudgian wrote: > > > > > Matt, > > > > > TD filters out data points less than a given intensity, discarding > > > > them. > > > > TZ sets them to zero. You can producecentroidspectra using the > > > > Accurate Mass Measure function in the tools tab within Masslynx, which > > > > can batch process raw files. > > > > > DT > > > > > Matthew Chambers wrote: > > > >> Hi Bernard, > > > > >> What is TD and TZ? MassLynx doesn't provide centroiding capability so > > > >>MassWolfhas a custom centroiding algorithm. I haven't seen any > > > >> comprehensive comparisons between that custom algorithm and the > > > >> MaxEnt > > > >> algorithm available from ProteinLynx Global Server (which is not > > > >> programmatically accessible even if you have access to PLGS!). > > > > >> -Matt > > > > >> Bernt wrote: > > > > >>> Hi Natalie, > > > > >>> I'm also currently trying outMassWolf4.2.1......it works with TD > > > >>> and > > > >>> TZ as well, although TD appears to be a better option at generating > > > >>> smaller mzxml files. But the centroiding function doesn't seem to be > > > >>> working. It gives a "Warning: using EXPERIMENTAL centroiding > > > >>> functionality" error msg in command prompt and Windows pops up a > > > >>> "masswolf.exe has encountered a problem and needs to close" error > > > >>> report. Is the centroiding function still in the process of > > > >>> development? > > > > >>> Bernard > > > > >>> On Jun 25, 5:46 am, Natalie Tasman <[email protected]> > > > >>> wrote: > > > > >>>> Hello, > > > > >>>> First, you might want to check that the file extention is > > > >>>> indeed .raw > > > >>>> and not .RAW. Capitalization might make a difference. > > > > >>>> Can you open this file in the Waters MassLynx application on the > > > >>>> same > > > >>>> computer? This must be installed in order for the converter > > > >>>> (massWolf) to work properly. > > > > >>>> Natalie > > > > >>>> On Jun 24, 2009, at 2:39 PM, Hong wrote: > > > > >>>>> Hi there, > > > > >>>>> I am new to TPP. I have trouble converting the MassLynx .RAW > > > >>>>> directory > > > >>>>> with mzXML. I got the following status report message. What do I > > > >>>>> need > > > >>>>> to change to get it work? I greatly appreciate your inputs. > > > > >>>>> Hong Li > > > >>>>> NJ Med School > > > > >>>>>massWolf-v --mzXML c:/Inetpub/wwwroot/ISB/data/hilo08.raw > > > > >>>>> Settings: > > > >>>>>centroidscans: 0 > > > >>>>> compress scans: 0 > > > >>>>> verbose mode: 1 > > > >>>>> lockspray: 1 > > > >>>>> MS^E: 0 > > > >>>>> threshold: 0 > > > >>>>> mzML mode: 0 > > > >>>>> mzXML mode: 1 > > > >>>>> input filename: c:/Inetpub/wwwroot/ISB/data/hilo08.raw > > > >>>>> output filename: c:/Inetpub/wwwroot/ISB/data/hilo08.mzXML > > > >>>>> output file as gzip: 0 > > > > >>>>> Command FAILED > > > > > -- > > > > Dr. David Trudgian > > > > Bioinformatician in Proteomics > > > > University of Oxford > > > > > Tel: (+44) (01865 2)87807 (CCMP - Mon-Thu) > > > > Tel: (+44) (01865 2)75557 (Dunn Sch - Fri) --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
