Very poor results is what I would expect. I can't explain the crashing but I'm not too familiar with the X! Tandem code. You can batch process pretty much anything with xargs/ls (downloadable from the GnuWin32 project). A command like: ls c:\path\to\waters\sources | grep ".raw" | xargs -n 1 -t masswolf --mzXML <options> should do the trick. The "sources" directory above would contain one or more Waters .raw directories - the grep part is to filter out anything else.
-Matt Chris Hughes wrote: > Also, I just tried it, and as long as I am using the native XTandem > parameters, without k-score, and spectrum conditioning it works, but > it seems to give pretty poor results. > > > On Jul 15, 2:57 pm, Chris Hughes <[email protected]> wrote: > >> Thanks Matt. >> >> That being said, I have a batch of profile data now that I will likely >> use the masswolf centroid option to deal with so I can search it in >> XTandem. Is there any way to batch process using Masswolf with the >> centroiding option? I notice its not part of the TPP. >> >> Chris >> >> On Jul 15, 2:46 pm, Matthew Chambers <[email protected]> >> wrote: >> >> >>> Hi Chris,, >>> >>> AFAIK, X! Tandem isn't designed to run on profile mode data. If you are >>> using the default "total peaks" setting then it will take only the 50 >>> most intense samples (not peaks, because it assumes every data point is >>> a peak). 50 samples are easily consumed by just a few peaks. You can >>> increase the total peaks setting, but I expect that would kill the score >>> discrimination because it's designed to look at peaks instead of >>> samples. You should continue to acquire centroided MS/MS data or at >>> least have some way to centroid it post-acquisition before sending it to >>> X! Tandem. >>> >>> -Matt >>> >>> chr12is wrote: >>> >>>> Greetings, >>>> >>>> I am encountering an error which I dont remember having troubles with >>>> before. I used to acquire my data such that in MS/MS mode it would be >>>> centroided, as in older versions of the TPP, filesizes over 4gb were >>>> problematic. Since I have noticed this isnt a problem anymore in the >>>> newer TPP versions, I am using 4.2.1, I have started acquiring in >>>> continuum mode again for MS/MS. I have MassLynx 4.1 installed, and >>>> have run centroided MS/MS files through the TPP on this computer with >>>> no problems. >>>> >>>> However, if I take one of my new continuum files, it converts in >>>> masswolf with no errors, I am not centroiding in masswolf, or using >>>> gzip. When I take it to XTandem it gives me this error: >>>> >>>> X! TANDEM 2 (2007.07.01.3) >>>> >>>> Loading spectra ... >>>> This application has requested the Runtime to terminate it in an >>>> unusual way. >>>> Please contact the application's support team for more information. >>>> >>>> Any ideas whats happening? >>>> > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
