Re: [proteowizard-developer] [proteowizard-support] splitting mzXML files with different scan modes

[Brian P. <bri...@in...>]

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
> ------------------------------
>
>
>
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