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

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Hi all, I'm sure Jim will answer to this as soon as he is back from 
Washington (PSI meeting). Is that the person you were thinking of David?

For your info, the merging work between mzData and mzXML has formely 
started in Washington during the PSI workshop earlier this week. This 
will be most probably drive the next version of mzData (which will 
change its name most probably due to the merge)

Cheers
Pierre-Alain

David Creasy wrote:

>Hi Alex,
>Yes, it's definitely incorrect. I'll pass on the message to the 
>appropriate person and I'm confident they will fix it in a future 
>release. I'm not aware of any other mzData producers doing it this way.
>
>David Creasy.
>
>Brian Pratt wrote:
>  
>
>>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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>>>&CID=DEVDEV
>>>_______________________________________________
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>>>Psi...@li...
>>>https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>>      
>>>
>>-------------------------------------------------------------------------
>>Take Surveys. Earn Cash. Influence the Future of IT
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>>    
>>
>
>  
>

-- 
--
 Dr. Pierre-Alain Binz
 Swiss Institute of Bioinformatics
 Proteome Informatics Group
 1, Rue Michel Servet
 CH-1211 Geneve 4
 Switzerland
 - - - - - - - - - - - - - - - - -
 Tel: +41-22-379 50 50
 Fax: +41-22-379 58 58
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

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)