Note that the X!Tandem that ships with TPP only speaks mzML1.0 - we're working hard with the ProteoWizard crew to get 1.1 support without losing 1.0, we're soooo close now...
Brian -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Chris Hughes Sent: Thursday, July 16, 2009 1:10 PM To: spctools-discuss Subject: [spctools-discuss] Re: XTandem Error on non-centrioded files To add to that previous post. What I had mentioned before was converting the files to mzML format. The option to do this within the TPP petunia interface already uses msconvert. However, if I can do it with only centroiding the MS/MS functions, that would be preferred. It looks like I can only do this from within the command line interface. Chris On Jul 16, 4:04 pm, Chris Hughes <[email protected]> wrote: > Natalie, > > I am trying the msconvert way as well, then I can compare the two. Am > I correct in thinking, that in msconvert, using the command > > msconvert myfile.raw --filter "nativeCentroid [2,5]" > > this will only centroid my MS/MS data if I have 5 functions (5 scans), > survey and 4 ms/ms? I assume thats what the ms level means. > > Thanks, > > Chris > > On Jul 16, 1:13 pm, Natalie Tasman <[email protected]> > wrote: > > > Hi Chris, > > > The centroid option for mzXML output through the Petunia interface should > > have been marked as "experimental option". I don't recommend it. Instead, > > why not give Matt's suggestions a try and let us know how it goes. > > > Natalie > > > On Thu, Jul 16, 2009 at 8:39 AM, Chris Hughes <[email protected]> wrote: > > > > I see that the mzML converter in the TPP offers the centroid option in > > > the Petunia interface. I assume this also uses Masswolf for > > > centroiding? At this point the masswolf centroid is my only real > > > option, except for converting the files to pkl, at which point I am > > > not sure if I can run them through the TPP, correct me if I am wrong > > > here. > > > > Chris > > > > On Jul 16, 10:52 am, Matthew Chambers > > > <[email protected]> wrote: > > > > 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 -~----------~----~----~----~------~----~------~--~---
