From: Brian P. <bri...@in...> - 2013-10-03 17:46:42
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It's not actually about our own filtering capability. The repeated complaint that we don't populate the "filterline=..." attribute of mzXML scans, and there are downstream systems that could use that information (thus forcing the use of ReAdW).. On Thu, Oct 3, 2013 at 9:23 AM, Parag Mallick <spa...@gm...> wrote: > Do we really not have a filter that can handle this? We certainly were > able to split it/ft. > > If not too hard, makes sense to add. > > ~ Parag M ~ > > typos and brevity by iPhone. > > On Oct 3, 2013, at 9:14 AM, Brian Pratt <bri...@in...> wrote: > > This one keeps coming up... much as I'd like to say to folks "it's a sign > from god that its time to dump mzXML for mzML", that's not really helpful - > all it does is prolong the life of ReAdW. Shall I see about at least > writing this info to mzXML, if not reading it? > > > On Thu, Oct 3, 2013 at 6:50 AM, M.L. Pras - Raves <m....@am...>wrote: > >> >> >> Dear Sir/Madam, >> >> >> >> I have recently downloaded the latest version of the Proteowizard >> software package and was very happy to discover that MSconvert is now >> capable of converting RAW files from Positive Specific scan modes to mzXML >> format. In a previous version, this did not work, so I had to use ReAdW to >> convert the RAW files one by one, followed by a JAVA script which split >> each mzXML file into 2 or more mzXML files, one for each scan mode. >> >> >> >> I still haven't worked out how to separate the two scan modes in the >> mzXML files which the new version of MSconvert produces, however. I don't >> see a line called "filterLine" which tells me which piece of data belongs >> to which scan mode (see below for examples). >> >> >> >> Is there a setting in MSconvert that I can use to separate the two scan >> modes? Or is there another way to achieve this? >> >> >> >> I'd appreciate any help you can give me. >> >> >> >> Best regards, >> >> >> >> Mia Pras-Raves. >> >> >> >> >> >> File containing PR184 en CNL141 data, as generated by ReAdW: >> >> <scan num="1" >> >> msLevel="0" >> >> peaksCount="8571" >> >> polarity="+" >> >> scanType="Full" >> >> filterLine="+ p ESI sid=10.00 Full pr 184.100 [400.000-1000.000]" >> >> retentionTime="PT0.32S" >> >> lowMz="400.07" >> >> highMz="1000" >> >> basePeakMz="435.844" >> >> basePeakIntensity="195.338" >> >> totIonCurrent="26552.5" > >> >> <peaks precision="32" >> >> byteOrder="network" >> >> contentType="m/z-int" >> >> compressionType="none" >> >> compressedLen="0" > ** coded data ** >> >> </scan> >> >> <scan num="2" >> >> msLevel="0" >> >> peaksCount="8571" >> >> polarity="+" >> >> scanType="Full" >> >> filterLine="+ p ESI sid=10.00 Full cnl 141.100 [400.000-1000.000]" >> >> retentionTime="PT10.36S" >> >> lowMz="400.07" >> >> highMz="1000" >> >> basePeakMz="534.134" >> >> basePeakIntensity="193.052" >> >> totIonCurrent="26106.7" > >> >> <peaks precision="32" >> >> byteOrder="network" >> >> contentType="m/z-int" >> >> compressionType="none" >> >> compressedLen="0" > ** coded data ** >> >> </scan> >> >> >> >> >> >> >> >> File generated using new MSconvert: >> >> <scan num="1" >> >> scanType="Q1" >> >> centroided="0" >> >> msLevel="2" >> >> peaksCount="8571" >> >> polarity="+" >> >> retentionTime="PT0.342S" >> >> collisionEnergy="0.0" >> >> lowMz="400.070007324219" >> >> highMz="1000.000020071864" >> >> basePeakMz="404.760498046875" >> >> basePeakIntensity="5422.462890625" >> >> totIonCurrent="32997.09765625" >> >> msInstrumentID="1"> >> >> <precursorMz precursorIntensity="0" >> activationMethod="CID"></precursorMz> >> >> <peaks compressionType="none" >> >> compressedLen="0" >> >> precision="32" >> >> byteOrder="network" >> >> contentType="m/z-int"> ** coded data ** >> >> </scan> >> >> >> >> >> >> -- >> >> Mia Pras-Raves, PhD >> >> AMC Medical Research >> >> Dept. of Clinical Epidemiology, Bioinformatics and Biostatistics >> >> Meibergdreef 9, Amsterdam >> >> Room J1B-220 >> >> Tel. +31-(0)20-5666885 >> >> >> >> ------------------------------ >> >> AMC Disclaimer : http://www.amc.nl/disclaimer >> ------------------------------ >> >> >> >> ------------------------------------------------------------------------------ >> October Webinars: Code for Performance >> Free Intel webinars can help you accelerate application performance. >> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most >> from >> the latest Intel processors and coprocessors. See abstracts and register > >> >> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >> _______________________________________________ >> proteowizard-support mailing list >> pro...@li... >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support >> >> > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk > > _______________________________________________ > proteowizard-developer mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-developer > > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk > _______________________________________________ > proteowizard-developer mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-developer > > |