Hi Chris, Just a reminder that the masswolf centroid mode is experimental, as noted in the "usage" statement.
Matt, how is PWIZ centroiding? Can msconvert be used to apply this signal processing and output a processed mzXML file? -Natalie On Wed, Jul 15, 2009 at 11:57 AM, 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 -~----------~----~----~----~------~----~------~--~---
