Re: [Psidev-ms-dev] <precursor msLevel="1" or msLevel="2" for msms data in the mzdata format (LTQ d

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I agree, that doesn't make sense.  It sounds like there's a bug in the module that wrote the data.

- Brian Pratt
www.insilicos.com

> -----Original Message-----
> From: psi...@li... 
> [mailto:psi...@li...] On 
> Behalf Of Alexandre Masselot
> Sent: Thursday, September 28, 2006 6:10 AM
> To: psi...@li...
> Subject: [Psidev-ms-dev] <precursor msLevel="1" or 
> msLevel="2" for msms data in the mzdata format (LTQ data)
> 
> Hello,
> something raised a problem in our code and into my understanding of
> mzdata format for msms peaklist
> 
> We have been writing (and still writing...) some  opensource 
> perl module
> InSilicoSpectro (CPAN & http://insilicospectro.vital-it.ch), 
> which does,
> among plenty of other things MS peaklist conversion from/to 
> various formats
> 
> In demo file, spectrumentInstrument is set to msLevel="2", then the
> precursor info is set msLevel="1", which can seems logical.
> 
> Then I have some LTQ data
> spectrumentInstrument still msLevel="2", then precursor msLevel="2",
> which either follows an other logic, no?
> 
> This happen for all the spectra in each files.
> 
> Anyone could give me some light would be very welcome,
> 
> Thanks in advance
> Alex
> 
> 
>       myo_ms2_1.05
> 
>     <spectrum id="3">
>             <spectrumDesc>
>                 <spectrumSettings>
>                     <acqSpecification spectrumType="discrete"
> methodOfCombination="sum" count="1">
>                         <acquisition acqNumber="3"/>
>                     </acqSpecification>
>                     <spectrumInstrument *msLevel="2"
> *mzRangeStart="100.000000" mzRangeStop="1350.000000">
>                         <cvParam cvLabel="psi" accession="PSI:1000036"
> name="ScanMode" value="MassScan"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000037"
> name="Polarity" value="Positive"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000038"
> name="TimeInMinutes" value="0.045000"/>
>                         <userParam name="ScanType" value="full"/>
>                     </spectrumInstrument>
>                 </spectrumSettings>
>                 <precursorList count="1">
>                     <precursor *msLevel="1" *spectrumRef="1">
>                         <ionSelection>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000040" name="MassToChargeRatio" value="334.82"/>
>                         </ionSelection>
>                         <activation>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000044" name="Method" value="CID"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000045" name="CollisionEnergy" value="28.00"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000046" name="EnergyUnits" value="Percent"/>
>                         </activation>
>                     </precursor>
>                 </precursorList>
>             </spectrumDesc>
>             <mzArrayBinary>
>                 <data precision="32" endian="little"
> length="77">+hMVQ1A1K0NGFjFDmBQ5QzxKPUPc/UpDLhJPQ6jrVkMEol1D/G
> heQygoYUNOHmdD/kloQyjwaEPm8WpDcDx2Q8otd0O6PXhDICJ7QzCjfUPYfH9D
> kAeDQ/CHiEOI8YhDqmSJQ5TeiUOYUIxDmByPQ+iSj0Pa9Y9DYHCQQzAtkUMIe5
> FDGNSRQ0RDkkMkxJJDdDqTQzACl0OQj5dDdOmXQzhzmENs1ZhDzmiZQ7DOmUM4
> RZpDMAGbQ0h1m0MU2ptDSDqcQ0TFnUN8Mp5DSqGeQ9gdn0O+0J9D0HygQwLuoE
PiMKJDctqjQxiwpEOcDaVDgIemQ1D/pkPEfadDpP2nQ4hmq0PA/6xDdOmtQ8gKr0PEM7BDysqwQzg4sUOcZ7ND7Ni4Qyo+uU> PClblD2DzmQ+gH8UM=</data>
>             </mzArrayBinary>
>             <intenArrayBinary>
>                 <data precision="32" endian="little"
> length="77">ALBORQCAC0QAYDNFAOCoRAAABkUAIOJEAADbRABgkkUAMFxFAJ
AnRQCAjkQAgChEAKBoRQAQeUYAAAFEAIA/RADAPEQAoIdEAKDqRABACUUAABFEAADTRAAO2UYAwE1EwHJgSAA8HkYAgGhEAA>
AnRACAeUUAyNtFAPwkRgAW6kYA0F9GAD+tR8B6k0gAHo1GAEAcRADgZUUAIFZF
> AJAKRQDAh0YA4KFFAAh3RgCZBkcAMAdFAHixRQAAakQA6L1FAGC9RQBmpUYAAM
> 5EAMiuRQAAcEQAoLhEAFAmRQAAtkQA4BlFANBVRQBAAkQAALNDAPxnRgDQvUUA
> oKlFAOBNRQBAMUUAsCpFAAC2RADAWkQAEIZFAJDQRQCwCUUAAGpEABB/RQDAlk
> QAwEBEAIDsQwDANUQ=</data>
>             </intenArrayBinary>
>         </spectrum>
> 
> 
>       LTQ exported mzdata
> 
> 
> <spectrum id="2">
>             <spectrumDesc>
>                 <spectrumSettings>
>                     <acqSpecification
> spectrumType="CentroidMassSpectrum" methodOfCombination="sum" 
> count="1">
>                         <acquisition acqNumber="2"/>
>                     </acqSpecification>
>                     <spectrumInstrument *msLevel="2"*
> mzRangeStart="110.000000" mzRangeStop="910.000000">
>                         <cvParam cvLabel="psi" accession="PSI:1000036"
> name="ScanMode" value="MassScan"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000037"
> name="Polarity" value="Positive"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000038"
> name="TimeInMinutes" value="14.002800"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000035"
> name="PeakProcessing" value="ContinuumMassSpectrum"/>
>                     </spectrumInstrument>
>                 </spectrumSettings>
>                 <precursorList count = "1">
>                     <precursor *msLevel="2"* spectrumRef="1">
>                         <ionSelection>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000040" name="MassToChargeRatio" value="449.728607"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000041" name="ChargeState" value="2"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000041" name="ChargeState" value="3"/>
>                         </ionSelection>
>                         <activation>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000044" name="Method" value="CID"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
>                         </activation>
>                     </precursor>
>                 </precursorList>
>             </spectrumDesc>
>             <mzArrayBinary>
>                 <data precision="64" endian="little"
> length="26">AAAAgHL8aEAAAADANSppQAAAAMBNAWxAAAAAANhdbEAAAAAAch
lwQAAAAOBez3FAAAAAwHsSckAAAACAKkJzQAAAAADZEnVAAAAAQDCQdUAAAADg4AR2QAAAAMBrhnZAAAAAAJdNd0AAAABgUp>
B3QAAAAOA1sHdAAAAAQGWReEAAAACAUyx6QAAAAAACanpAAAAAIMSgekAAAABg
> h+F6QAAAAOCg9HpAAAAAoL8Be0AAAADgphN7QAAAAOAUhHtAAAAAILUifEAAAA
> BgRjt9QA==</data>
>             </mzArrayBinary>
>             <intenArrayBinary>
>                 <data precision="64" endian="little"
> length="26">AAAAYA24EkAAAAAASOjmPwAAAEAcNOs/AAAAIHZw4z8AAACAIQ
T7PwAAAEB8qxNAAAAAAPF5D0AAAACg6X3/PwAAAMC/> +BFAAAAA4JNY7z8AAAAgKVznPwAAAMCfQvI/AAAAoDyfFUAAAABghBLpPwAAAM
> AoJgFAAAAAYOGaGkAAAABgf5AYQAAAAMBj6gJAAAAAYHv/6T8AAADgiaUFQAAA
> AAAb2jJAAAAA4D06IEAAAABACm9BQAAAAGBbqRVAAAAAoLdPBUAAAABgNsjpPw
> ==</data>
>             </intenArrayBinary>
>         </spectrum>
>         <spectrum id="3">
>             <spectrumDesc>
>                 <spectrumSettings>
>                     <acqSpecification
> spectrumType="CentroidMassSpectrum" methodOfCombination="sum" 
> count="1">
>                         <acquisition acqNumber="3"/>
>                     </acqSpecification>
>                     <spectrumInstrument *msLevel="2"*
> mzRangeStart="95.000000" mzRangeStop="795.000000">
>                         <cvParam cvLabel="psi" accession="PSI:1000036"
> name="ScanMode" value="MassScan"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000037"
> name="Polarity" value="Positive"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000038"
> name="TimeInMinutes" value="14.015817"/>
>                         <cvParam cvLabel="psi" accession="PSI:1000035"
> name="PeakProcessing" value="ContinuumMassSpectrum"/>
>                     </spectrumInstrument>
>                 </spectrumSettings>
>                 <precursorList count = "1">
>                     <precursor *msLevel="2"* spectrumRef="2">
>                         <ionSelection>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000040" name="MassToChargeRatio" value="391.069244"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000041" name="ChargeState" value="2"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000041" name="ChargeState" value="3"/>
>                         </ionSelection>
>                         <activation>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000044" name="Method" value="CID"/>
>                             <cvParam cvLabel="psi"
> accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
>                         </activation>
>                     </precursor>
>                 </precursorList>
>             </spectrumDesc>
>             <mzArrayBinary>
>                 <data precision="64" endian="little"
> length="85">AAAAQAo8XkAAAABgK8FeQAAAAABoWWBAAAAAoGKlYEAAAAAAzy
NhQAAAAMAHVmFAAAAAoD+eYUAAAADAzONhQAAAACAwnmJAAAAAIHzcYkAAAADAkv5iQAAAACC9j2NAAAAAYBEkZEAAAADAZN>
1kQAAAAGCnnmVAAAAAgJTiZUAAAADA3QJmQAAAAECVOmdAAAAAwGJPZ0AAAABA
> XBhoQAAAAKASnGlAAAAAoMPgaUAAAACAG1tqQAAAAACIKGtAAAAAALOra0AAAA
> CAOdxrQAAAAIAPIWxAAAAAALw2bEAAAADAtppsQAAAACCXvWxAAAAAQOWebUAA
> AADgUeNtQAAAAGBkUG5AAAAAwCBkb0AAAABgmt9vQAAAAACVL3BAAAAAALhAcE
> AAAABg6UtwQAAAAADAVXBAAAAAQH9ucEAAAABA0pBwQAAAACAG83BAAAAAYKYL
> cUAAAAAA1iZxQAAAAABEMXFAAAAA4IlQcUAAAAAAWHBxQAAAAOBfjnFAAAAAgO
> EMckAAAACA5pFyQAAAAECoqXJAAAAA4AjzckAAAACAwDdzQAAAAOA7k3NAAAAA
> wCSmc0AAAAAAW8FzQAAAAIBSDHRAAAAAIIlWdEAAAABAaWB0QAAAAMAqj3RAAA
> AAAH6hdEAAAABAJDx1QAAAAADEk3VAAAAAgPCxdUAAAACAKL51QAAAAAAo8XVA
> AAAAIJ+kdkAAAABgwLp2QAAAAMDAAHdAAAAAQPNBd0AAAACg7k93QAAAAMCPW3
> dAAAAAADBld0AAAACgvuR3QAAAAED5fnhAAAAAwIXkeEAAAABgT4t5QAAAACBv
> jHpAAAAAwBcSfUAAAABgOpN9QAAAACDxpH5AAAAAgBlsgUAAAACAV8GBQAAAAA
> DUFYJAAAAAwJYshEA=</data>
>             </mzArrayBinary>
>             <intenArrayBinary>
>                 <data precision="64" endian="little"
> length="85">AAAAwMPJAUAAAABArr70PwAAAMD/xgBAAAAAoH+3/D8AAACgkT
4LQAAAAICGFhNAAAAAIFnSG0AAAADgCTflPwAAAMAIB29AAAAA4IQHM0AAAAAg3CwDQAAAAOCtROM/AAAAYPO15z8AAADApR>
9IQAAAAICUefg/AAAAQMlXMUAAAAAg8krxPwAAAEDJavk/AAAAIAaR8T8AAABA
> uVEkQAAAAMCItglAAAAAwGV95z8AAACAF9o4QAAAAMCmzQ5AAAAAIPfSAUAAAA
> AAsnwaQAAAAEBm+e0/AAAAgG4sAEAAAAAg0Sw7QAAAAADCngVAAAAAgFatB0AA
> AABA5fTsPwAAAAD2lARAAAAAYFmJEEAAAADAAo4xQAAAAMBx1QJAAAAAQNaQNE
> AAAABgJoNTQAAAAGCvGCRAAAAAwBaGIUAAAABAjE36PwAAAADyNQBAAAAAoKzt
> IkAAAACAlW/tPwAAAIBRJO8/AAAAYNy5CUAAAABAhiBaQAAAAIDzvgpAAAAA4B
> zgA0AAAADg3CbyPwAAAOB7xw5AAAAAAImSI0AAAAAgdOwQQAAAACAeuPo/AAAA
> oGo07D8AAABg4JTzPwAAACBtRhVAAAAA4KLT9D8AAACAIQUhQAAAAODRDARAAA
> AAACjGFkAAAADApNzpPwAAAEBNTvU/AAAAIBY9CEAAAABAfF0PQAAAAGBcPx1A
> AAAAgDyQBEAAAACAMhf6PwAAAADboPI/AAAAgPUCFUAAAAAA4yA6QAAAAEDaqA
> pAAAAAALA0BEAAAABgV+YwQAAAAACdvPY/AAAAIBdaAUAAAADgLFwJQAAAAECs
> DQxAAAAAoDSWB0AAAAAASu0BQAAAAECuaBRAAAAAoN22IkAAAADAYNTxPwAAAG
> D5xwJAAAAAINkzB0A=</data>
>             </intenArrayBinary>
>         </spectrum>
> 
> -- 
> Alexandre Masselot, phD
> Senior bioinformatician
> www.genebio.com
> voice: +41 22 702 99 00
> 
> 
> 
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Re: [Psidev-ms-dev] <precursor msLevel="1" or msLevel="2" for msms data in the mzdata format (LTQ d

Re: [Psidev-ms-dev] <precursor msLevel="1" or msLevel="2" for msms data in the mzdata format (LTQ data)