Hi Matt, I tried using msconvert from pwiz1.5.2 in the following manner:
msconvert D:\InetpubData\HUO00159S00168GL05B06.raw --mzXML -v -- filter "peakPicking false [1,2]" -o D:\InetpubData But I got this error: format: mzXML (Precision_64 [ 1000514:Precision_64 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) indexed="true" outputPath: D:\InetpubData extension: .mzXML contactFilename: filters: peakPicking false [1,2] filenames: D:/InetpubData/HUO00159S00168GL05B06.raw processing file: D:/InetpubData/HUO00159S00168GL05B06.raw [msconvert] Caught unknown exception. which doesn't really say much..........have you any idea what might be the problem here? Bernt On Jul 17, 4:21 am, Matthew Chambers <[email protected]> wrote: > Hi Chris, > > You'll want to use a newer msconvert. The one you can download > fromhttp://downloads.sourceforge.net/proteowizard/pwiz-1.5.2-tools-window... > should do the trick. The command would be: > msconvert myfile.raw --filter "peakPicking true [2,2]" > The true/false field ("prefer vendor peak picking") is irrelevant in > this case because Waters doesn't provide vendor peak picking, and the > integer range is in the ms level domain, not the function domain. > Msconvert, like MassWolf, will assign a ms level to each function based > on its reported type (i.e. MS, MS/MS, MRM, etc.). > > -Matt > > Chris Hughes 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 -~----------~----~----~----~------~----~------~--~---
