I just tested and I can run that command on a Waters .raw with the 1.5.2 msconvert. Do you have MassLynx installed? It might be a newer version than the one that msconvert is compiled for. Do you have a small example file I can test locally?
-Matt Bernt wrote: > 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 -~----------~----~----~----~------~----~------~--~---
