Hi Matt, I think you have helped to clarify another issue which i posted earlier: http://groups.google.com/group/spctools-discuss/browse_frm/thread/6aa0ae195b29adde?hl=en
My data was also not centroided, since it is not working in MassWolf 4.2.1. Hence I believe what you said about XTandem not designed to run on profile mode data, explains why my Xtandem searches assigns certain doubly charged peptides as +1 or +3 charge states. This should occur for those lower intensity hits. Thanks, guys! Bernt On Jul 16, 2:46 am, 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 -~----------~----~----~----~------~----~------~--~---
