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Re: [proteowizard-developer] msLevel filtering and IntegerSet
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From: Darren K. <da...@pr...> - 2009-09-23 20:47:28
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Hi Chris, (I thought I had responded, but that must have been in my head -- now moving to proteowizard-developer.) Anyway, we have a tool that takes an mzML/RAW file plus a pep.xml file, to visualize the isolation windows of ms2 scans. It's pwiz_tools/commandline/mspicture. You can certainly have a SpectrumList filter take outside data for instantiation. It's probably best to create a separate tool, rather than msconvert, if for no other reason than to be able to give detailed usage information, e.g. dependence on output from another tool. Darren 2009/9/21 Chris Paulse <cp...@sy...>: > Yeah, I saw that, but I was wondering how often this check is important. I > think people like to strip away MS1 scans fairly routinely for protein ID, > independent of the mass analyzer type. I don't mind it being left this way, > but just sayin'. > > On a separate question, I'm trying to figure out a way to integrate calling > of an external binary called Charge Prediction Machine in msconvert. It's a > command line utility that uses as input an ascii file containing data from > ms2 scans. > > So, what I'd like to do in msconvert is to generate one of these ms2 files > as a first pass through a vendor file, run the Charge Prediction Machine > binary on it, gather its output, and merge it with the SpectrumList object > model prior to output to mzML/mzXML. > > I can imagine other situations where making two passes through the data > would be nice to have. Would it be preferred to write the mzML file on the > first pass, and modify it on the second pass? Streaming through mzML files > may be faster than through vendor files. > > Chris > > -----Original Message----- > From: Darren Kessner [mailto:da...@pr...] > Sent: Monday, September 21, 2009 10:06 AM > To: Chris Paulse > Subject: Re: [proteowizard-developer] msLevel filtering and IntegerSet > > Hi Chris, > > stripIT also checks the mass analyzer type -- probably the right thing > to do is to have a general mass analyzer type filter that doesn't care > about ms level, which would then be "orthogonal" to the ms level > filter. > > > Darren > > > > On Mon, Sep 21, 2009 at 9:52 AM, Chris Paulse<cp...@sy...> > wrote: >> Hey Darren, >> Doesn't this overlap functionally with --filter stripIT? We could keep > the >> cmd line option (or even choose not to), but shouldn't the code in >> filterCreator_StripIT be merged with filterCreator_msLevel? >> >> Chris >> >> -----Original Message----- >> From: Darren Kessner [mailto:da...@pr...] >> Sent: Thursday, September 17, 2009 9:49 PM >> To: proteowizard-developer >> Subject: [proteowizard-developer] msLevel filtering and IntegerSet >> >> Hi all, >> >> I added the predicate to SpectrumList_Filter for filtering by msLevel. >> I also made a modification to IntegerSet to be more flexible in its >> parsing of text -- it will now parse lists of closed intervals, where >> the intervals can be in the form [a,b] or a[-][b]. >> >> So the following is now possible: >> >> # extracts ms2 and ms3 scans only >> msconvert file.raw --filter "msLevel [2,3]" >> or >> msconvert file.raw --filter "msLevel 2-3" >> >> # extracts ms1 scans only >> msconvert file.raw --filter "msLevel 1" >> >> # extracts everything but ms2 >> msconvert file.raw --filter "msLevel 1 3- " >> >> This is available in the rest of the command line tools too. >> >> I also attempted to make the usage text more intelligible, but it's >> still a bit confusing -- any suggestions would be welcome. >> >> >> Darren >> >> > ---------------------------------------------------------------------------- >> -- >> Come build with us! The BlackBerry® Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9-12, 2009. Register > now! >> http://p.sf.net/sfu/devconf >> _______________________________________________ >> proteowizard-developer mailing list >> pro...@li... >> https://lists.sourceforge.net/lists/listinfo/proteowizard-developer >> >> > > |