From: Mingxun W. <mi...@cs...> - 2013-09-18 01:58:58
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Proteowizard, So we are using pwiz to load mzXML files and it seems that if there is an XML tag for nameValue it doesn't allow it to load. nameValue is part of the standard so it should load these mzXML files. -Ming -- Mingxun Wang UCSD CSE Graduate Student mi...@cs... |
From: Parag M. <pa...@st...> - 2013-09-18 23:48:28
|
Hiya, Could we please get copies of the files to see? Is msConvert/etc choking on the files or are you using the API directly? Best, ~ Parag M ~ On Sep 17, 2013, at 9:58 PM, Mingxun Wang <mi...@cs...> wrote: > Proteowizard, > > So we are using pwiz to load mzXML files and it seems that if there is an XML tag for nameValue it doesn't allow it to load. nameValue is part of the standard so it should load these mzXML files. > > -Ming > > -- > Mingxun Wang > UCSD CSE Graduate Student > mi...@cs... > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
From: Matt C. <mat...@gm...> - 2013-10-03 16:02:26
|
I just checked to make sure that pwiz does allow nameValue in the two places that mzXML allows nameValue elements: the msInstrument element and the scan element. Not sure what the issue is here. -Matt On 9/18/2013 6:40 PM, Parag Mallick wrote: > Hiya, > > Could we please get copies of the files to see? Is msConvert/etc choking on the files or are you using the API directly? > > Best, > ~ Parag M ~ > > > > On Sep 17, 2013, at 9:58 PM, Mingxun Wang <mi...@cs...> wrote: > >> Proteowizard, >> >> So we are using pwiz to load mzXML files and it seems that if there is an XML tag for nameValue it doesn't allow it to load. nameValue is part of the standard so it should load these mzXML files. >> >> -Ming |
From: Mingxun W. <mi...@cs...> - 2013-10-04 05:38:28
|
We are using the API directly. The file we are converting has the line: <nameValue name="recalibrationTime" value="2012-12-12T06:33:31"/> and we get this error: Error loadding file: [Serializer_mzXML::Handler_dataProcessing] Unexpected element name: nameValue -Ming On Thu, Oct 3, 2013 at 9:01 AM, Matt Chambers <mat...@gm...>wrote: > I just checked to make sure that pwiz does allow nameValue in the two > places that mzXML allows nameValue elements: the msInstrument element and > the scan element. Not sure what the issue is here. > > -Matt > > > > On 9/18/2013 6:40 PM, Parag Mallick wrote: > >> Hiya, >> >> Could we please get copies of the files to see? Is msConvert/etc choking >> on the files or are you using the API directly? >> >> Best, >> ~ Parag M ~ >> >> >> >> On Sep 17, 2013, at 9:58 PM, Mingxun Wang <mi...@cs...> wrote: >> >> Proteowizard, >>> >>> So we are using pwiz to load mzXML files and it seems that if there is >>> an XML tag for nameValue it doesn't allow it to load. nameValue is part of >>> the standard so it should load these mzXML files. >>> >>> -Ming >>> >> > -- Mingxun Wang UCSD CSE Graduate Student mi...@cs... |
From: Matt C. <mat...@gm...> - 2013-10-04 15:51:20
|
I don't think that is valid in the schema. Only software, processingOperation, and comment elements are allowed. The processingOperation element derives from namevalueType so it has the same attributes, but not the same name: <xs:element name="dataProcessing" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element ref="cff:software"> </xs:element> <xs:sequence minOccurs="0" maxOccurs="unbounded"> <xs:element name="processingOperation" type="cff:namevalueType"> </xs:element> <xs:element name="comment" type="xs:string" minOccurs="0"> </xs:element> </xs:sequence> </xs:sequence> <xs:attribute name="intensityCutoff" type="xs:float" use="optional"> </xs:attribute> <xs:attribute name="centroided" type="xs:boolean" use="optional"> </xs:attribute> <xs:attribute name="deisotoped" type="xs:boolean" use="optional"> </xs:attribute> <xs:attribute name="chargeDeconvoluted" type="xs:boolean" use="optional"> </xs:attribute> <xs:attribute name="spotIntegration" type="xs:boolean" use="optional"/> </xs:complexType> </xs:element> What software wrote your mzXML file? -Matt On 10/4/2013 12:38 AM, Mingxun Wang wrote: > We are using the API directly. > > The file we are converting has the line: > > <nameValue name="recalibrationTime" value="2012-12-12T06:33:31"/> > > and we get this error: > > Error loadding file: [Serializer_mzXML::Handler_dataProcessing] Unexpected element name: nameValue > > > -Ming > > > On Thu, Oct 3, 2013 at 9:01 AM, Matt Chambers <mat...@gm... > <mailto:mat...@gm...>> wrote: > > I just checked to make sure that pwiz does allow nameValue in the two places that mzXML allows > nameValue elements: the msInstrument element and the scan element. Not sure what the issue is > here. > > -Matt > > > > On 9/18/2013 6:40 PM, Parag Mallick wrote: > > Hiya, > > Could we please get copies of the files to see? Is msConvert/etc choking on the files or > are you using the API directly? > > Best, > ~ Parag M ~ > > > > On Sep 17, 2013, at 9:58 PM, Mingxun Wang <mi...@cs... <mailto:mi...@cs...>> > wrote: > > Proteowizard, > > So we are using pwiz to load mzXML files and it seems that if there is an XML tag for > nameValue it doesn't allow it to load. nameValue is part of the standard so it should > load these mzXML files. > > -Ming > > > > > > -- > Mingxun Wang > UCSD CSE Graduate Student > mi...@cs... <mailto:mi...@cs...> |
From: Mingxun W. <mi...@cs...> - 2013-11-14 23:33:59
|
This data was generated by Bruker software. I'm not sure on the exact version. -Ming On Fri, Oct 4, 2013 at 8:51 AM, Matt Chambers <mat...@gm...>wrote: > I don't think that is valid in the schema. Only software, > processingOperation, and comment elements are allowed. The > processingOperation element derives from namevalueType so it has the same > attributes, but not the same name: > > <xs:element name="dataProcessing" maxOccurs="unbounded"> > <xs:complexType> > <xs:sequence> > <xs:element ref="cff:software"> > </xs:element> > <xs:sequence minOccurs="0" maxOccurs="unbounded"> > <xs:element name="processingOperation" > type="cff:namevalueType"> > </xs:element> > <xs:element name="comment" type="xs:string" minOccurs="0"> > </xs:element> > </xs:sequence> > </xs:sequence> > <xs:attribute name="intensityCutoff" type="xs:float" > use="optional"> > </xs:attribute> > <xs:attribute name="centroided" type="xs:boolean" use="optional"> > </xs:attribute> > <xs:attribute name="deisotoped" type="xs:boolean" use="optional"> > </xs:attribute> > <xs:attribute name="chargeDeconvoluted" type="xs:boolean" > use="optional"> > </xs:attribute> > <xs:attribute name="spotIntegration" type="xs:boolean" > use="optional"/> > </xs:complexType> > </xs:element> > > What software wrote your mzXML file? > > -Matt > > > > On 10/4/2013 12:38 AM, Mingxun Wang wrote: > >> We are using the API directly. >> >> The file we are converting has the line: >> >> <nameValue name="recalibrationTime" value="2012-12-12T06:33:31"/> >> >> and we get this error: >> >> Error loadding file: [Serializer_mzXML::Handler_dataProcessing] >> Unexpected element name: nameValue >> >> >> -Ming >> >> >> On Thu, Oct 3, 2013 at 9:01 AM, Matt Chambers <mat...@gm...<mailto: >> mat...@gm...>> wrote: >> >> I just checked to make sure that pwiz does allow nameValue in the two >> places that mzXML allows >> nameValue elements: the msInstrument element and the scan element. >> Not sure what the issue is >> here. >> >> -Matt >> >> >> >> On 9/18/2013 6:40 PM, Parag Mallick wrote: >> >> Hiya, >> >> Could we please get copies of the files to see? Is msConvert/etc >> choking on the files or >> are you using the API directly? >> >> Best, >> ~ Parag M ~ >> >> >> >> On Sep 17, 2013, at 9:58 PM, Mingxun Wang <mi...@cs...<mailto: >> mi...@cs...>> >> >> wrote: >> >> Proteowizard, >> >> So we are using pwiz to load mzXML files and it seems that if >> there is an XML tag for >> nameValue it doesn't allow it to load. nameValue is part of >> the standard so it should >> load these mzXML files. >> >> -Ming >> >> >> >> >> >> -- >> Mingxun Wang >> UCSD CSE Graduate Student >> mi...@cs... <mailto:mi...@cs...> >> > > -- Mingxun Wang UCSD CSE Graduate Student mi...@cs... |
From: Mingxun W. <mi...@cs...> - 2014-04-20 02:32:42
|
Matt, So should we go yell at Bruker and tell them to fix their mzXML output as it is not in spec? -Ming On Thu, Nov 14, 2013 at 3:33 PM, Mingxun Wang <mi...@cs...> wrote: > This data was generated by Bruker software. I'm not sure on the exact > version. > > -Ming > > > On Fri, Oct 4, 2013 at 8:51 AM, Matt Chambers <mat...@gm...>wrote: > >> I don't think that is valid in the schema. Only software, >> processingOperation, and comment elements are allowed. The >> processingOperation element derives from namevalueType so it has the same >> attributes, but not the same name: >> >> <xs:element name="dataProcessing" maxOccurs="unbounded"> >> <xs:complexType> >> <xs:sequence> >> <xs:element ref="cff:software"> >> </xs:element> >> <xs:sequence minOccurs="0" maxOccurs="unbounded"> >> <xs:element name="processingOperation" >> type="cff:namevalueType"> >> </xs:element> >> <xs:element name="comment" type="xs:string" minOccurs="0"> >> </xs:element> >> </xs:sequence> >> </xs:sequence> >> <xs:attribute name="intensityCutoff" type="xs:float" >> use="optional"> >> </xs:attribute> >> <xs:attribute name="centroided" type="xs:boolean" use="optional"> >> </xs:attribute> >> <xs:attribute name="deisotoped" type="xs:boolean" use="optional"> >> </xs:attribute> >> <xs:attribute name="chargeDeconvoluted" type="xs:boolean" >> use="optional"> >> </xs:attribute> >> <xs:attribute name="spotIntegration" type="xs:boolean" >> use="optional"/> >> </xs:complexType> >> </xs:element> >> >> What software wrote your mzXML file? >> >> -Matt >> >> >> >> On 10/4/2013 12:38 AM, Mingxun Wang wrote: >> >>> We are using the API directly. >>> >>> The file we are converting has the line: >>> >>> <nameValue name="recalibrationTime" value="2012-12-12T06:33:31"/> >>> >>> and we get this error: >>> >>> Error loadding file: [Serializer_mzXML::Handler_dataProcessing] >>> Unexpected element name: nameValue >>> >>> >>> -Ming >>> >>> >>> On Thu, Oct 3, 2013 at 9:01 AM, Matt Chambers <mat...@gm...<mailto: >>> mat...@gm...>> wrote: >>> >>> I just checked to make sure that pwiz does allow nameValue in the >>> two places that mzXML allows >>> nameValue elements: the msInstrument element and the scan element. >>> Not sure what the issue is >>> here. >>> >>> -Matt >>> >>> >>> >>> On 9/18/2013 6:40 PM, Parag Mallick wrote: >>> >>> Hiya, >>> >>> Could we please get copies of the files to see? Is >>> msConvert/etc choking on the files or >>> are you using the API directly? >>> >>> Best, >>> ~ Parag M ~ >>> >>> >>> >>> On Sep 17, 2013, at 9:58 PM, Mingxun Wang <mi...@cs...<mailto: >>> mi...@cs...>> >>> >>> wrote: >>> >>> Proteowizard, >>> >>> So we are using pwiz to load mzXML files and it seems that >>> if there is an XML tag for >>> nameValue it doesn't allow it to load. nameValue is part of >>> the standard so it should >>> load these mzXML files. >>> >>> -Ming >>> >>> >>> >>> >>> >>> -- >>> Mingxun Wang >>> UCSD CSE Graduate Student >>> mi...@cs... <mailto:mi...@cs...> >>> >> >> > > > -- > Mingxun Wang > UCSD CSE Graduate Student > mi...@cs... > -- Mingxun Wang UCSD CSE Graduate Student mi...@cs... |
From: Chambers, M. <mat...@gm...> - 2014-04-21 21:29:41
|
I'm afraid so. -Matt On 4/19/2014 9:32 PM, Mingxun Wang wrote: > Matt, > > So should we go yell at Bruker and tell them to fix their mzXML output > as it is not in spec? > > -Ming > > > On Thu, Nov 14, 2013 at 3:33 PM, Mingxun Wang <mi...@cs... > <mailto:mi...@cs...>> wrote: > > This data was generated by Bruker software. I'm not sure on the > exact version. > > -Ming > |
From: Mingxun W. <mi...@cs...> - 2014-04-21 21:31:11
|
No problem. We'll push as hard as we can to either have them put it in spec or push them to move on to mzML and output that to spec. Thanks! -Ming On Mon, Apr 21, 2014 at 2:29 PM, Chambers, Matthew < mat...@gm...> wrote: > I'm afraid so. > > -Matt > > > > On 4/19/2014 9:32 PM, Mingxun Wang wrote: > > Matt, > > So should we go yell at Bruker and tell them to fix their mzXML output > as it is not in spec? > > -Ming > > > On Thu, Nov 14, 2013 at 3:33 PM, Mingxun Wang <mi...@cs...> wrote: > >> This data was generated by Bruker software. I'm not sure on the exact >> version. >> >> -Ming >> >> -- Mingxun Wang UCSD CSE Graduate Student mi...@cs... |