Hi Chris, You'll want to use a newer msconvert. The one you can download from http://downloads.sourceforge.net/proteowizard/pwiz-1.5.2-tools-windows-i386.zip 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 -~----------~----~----~----~------~----~------~--~---
