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 produce centroid spectra 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 >> MassWolf has 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 out MassWolf 4.2.1......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: >>>>> centroid scans: 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 -~----------~----~----~----~------~----~------~--~---
