The pwiz non-vendor centroiding currently available to msconvert is a very crude local maximum algorithm. But I have virtually no doubt that even using that crude algorithm would give better results with any centroid-dependent search engine than using the raw profile data. Whether it performs better than the masswolf centroiding... I have done no comparisons so I can't say. Pwiz also has Savitzky-Golay smoothing which is good to apply to spiky profile data before applying local-maximum peak picking, but it's not accessible from msconvert yet. It is accessible from SeeMS, which allows to adjust the SG window size and polynomial order and also the peak picker window size and immediately see the result.
-Matt Natalie Tasman wrote: > 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] > <mailto:[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] > <mailto:[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 -~----------~----~----~----~------~----~------~--~---
