psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] mzML for GCxGC/MS

[pierre-alain b. <pie...@is...>]

Hi Steven,

On 27.09.2012 21:58, Robles, Steve wrote:
>
> Hi Nils, Pierre-Alain, Matt and all,
>
> Thanks for the feedback. It seems like everyone agrees that there 
> should be an elution time for each column.
>
> Pierre-Alain's suggestion for MS:100826 definition change to "The time 
> of elution from all used chromatographic columns (one or more) in the 
> chromatographic separation step, relative to the start of the 
> chromatography." sounds good to me. But I'm not sure what the third 
> global term for the function would be. Are you suggesting a term for 
> the run element that indicates if it GCxGC, LCxLC ? Or something about 
> the modulation period?
>
I'm referring to a term describing the function that implements the 
relationship between elution time and modulation time (you have given 
two examples below). This might be useful or not. mzML describes MS 
acquisition parameters, and we could as well describe this as part of 
the run gobal params. If this sounds a useful term, I let you propose 
what is the most appropriate.

Cheers
Pierre-Alain

> Thanks again,
>
> *Steven Robles *| Software design engineer
> ste...@le...
>
> Description: LECOLOGO3.png*
> **Delivering the Right Results* | 3000 Lakeview Ave. | St. Joseph | MI 
> | 49085
>
> Visit us online at www.leco.com <http://www.leco.com/>|Register to 
> receive e-news & updates 
> <http://visitor.r20.constantcontact.com/manage/optin/ea?v=001Ii8Y_QGk40pWa6GMO_HQlr4axErCoyfnebuJojN8G0hnJbPCz9PezRG9EoMLF3XTe8r9jqIrcaw%3D>
>
> *From:*Nils Hoffmann [mailto:nil...@ce...]
> *Sent:* Thursday, September 27, 2012 2:32 PM
> *To:* Robles, Steve
> *Cc:* psi...@li...
> *Subject:* Re: [Psidev-ms-dev] mzML for GCxGC/MS
>
> Hi Steve,
> as one of the original requestors of the modulation_time term, I 
> totally agree with your option nr. 2 to handle more possible 
> use-cases. We simply opted for the simpler option first since we did 
> not have reference data available for other modulation regimes. Fyi, 
> there was a thread started by Steve Reichenbach recently on 2D LC-MS 
> that circled around non-uniform modulation schemes and which might 
> also be of interest here.
>
> Nils Hoffmann
>
> -- 
> Nils Hoffmann                                   phone: +49-521-106-4342
> Bielefeld University room:             U10-144
> Faculty of Technology, Genome Informatics
> P.O. Box 10 01 31
> 33501 Bielefeld, Germany
>
>
> "Robles, Steve" <Ste...@le... 
> <mailto:Ste...@le...>> schrieb:
>
> Hi everyone,
>
> We would like to export our two-dimensional GCxGC-MS data to mzML and 
> include the first and second column elution times.
>
> There was a thread in the psidev-ms-dev email archive that covered 
> this topic and resulted in the modulation time term being added to CV 
> https://sourceforge.net/mailarchive/forum.php?thread_name=assp.7128de5073.1306482337.4700.551.camel%40paddy&forum_name=psidev-ms-dev.
>
> [Term]
>
> id: MS:1002042
>
> name: modulation time
>
> def: "The duration of a complete cycle of modulation in a 
> comprehensive two-dimensional separation system, equals the length of 
> a second dimension chromatogram, i.e., the time between two successive 
> injections into the second column." 
> [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1000857 ! run attribute
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> The modulation time allows the elution time from the first and second 
> column to be calculated. However, our instrument allows the modulation 
> time to vary over the course of a single run so that there can be more 
> than one value for this field. Examples can be found on page 4 of this 
> site 
> http://www.leco.com/products/sep_sci/pegasus_4d/pdf/SEP%20SCI%20PEGASUS%204D%20GCxGC-TOFMS%20209-183.pdf 
> and 
> http://www.labmate-online.com/articles/chromatography/1/leco_corporation/analysis_of_samples_from_the_gulf_of_mexico_oil_spill_by_gcxgc-tofms_-_leco_corporation/815/
>
> To fully describe the data we would not only need a term for each 
> modulation time but also a matching field that describes the scan or 
> elution time that the modulation time is effective. For example 
> consider the following table:
>
> Time from injection (s)                  Modulation Time (s)
>
> 0 0
>
> 50 4
>
> 130 5
>
> 430 `                               6
>
> Here acquisition starts at 50 seconds from injection. Spectra acquired 
> from 50 s to anything less than 130 s will have a modulation time of 4 
> s; spectra acquired from 130 s to anything less than 430 s will have a 
> modulation time of 5 s; and anything acquired at 430 s or after will 
> have a modulation time of 6 s.
>
> The second and first column elution time can be described by:
>
> t2 = (t -- ti) % mi
>
> t1 = t -- t2
>
> Where:
>
> t1 is the first column elution time
>
> t2 is the second column elution time
>
> t is the time from injection
>
> ti is the greatest modulation start time from injection that is less 
> than or equal to t
>
> mi is the modulation time that goes with ti
>
> So for example a spectrum at t = 136 would have a second column 
> elution time of 1 and a first column elution time of 135.
>
> The only way we could represent this data with the current schema and 
> CV would be to break the sample into three different files, each with 
> a different modulation time. However we would prefer to keep the 
> sample in a single file.
>
> We can think of a few ways to handle this problem.
>
> 1)The first would be to include the list of modulation times and have 
> the software that is reading the file calculate the first and second 
> column elution times. This could be implemented in at least a couple 
> of different ways.
>
> a.A new list object added to the run element. Each item in the list 
> would require two cvParams, one for the modulation start time (a new 
> term?) and a modulation time.
>
> b.Instead of a list element, create a specific series of elements for 
> both the modulation time and modulation start time (i.e. modulation 
> time 1, modulation start time 1, modulation time 2, modulation start 
> time 2, ...).
>
> 2)Another approach would be to create two new terms "first column 
> elution time" and "second column elution time", and add these to scan 
> elements. There was a suggestion like this in the original thread that 
> wasn't implemented.
>
> 3)Just create a " second column elution time term" and store the first 
> column term in the elution time MS:1000826.
>
> The first approach will not increase the file size as much as the 
> others but requires more changes to the schema or CV. It also requires 
> the importing application to calculate the elution times. The second 
> approach doesn't require the importing application to know how to 
> determine the elution times. It only requires a couple of new CV terms 
> but will increase the file size the most. The third option has the 
> drawback that the it will usually produce multiple spectra with the 
> same elution time MS:1000826 which may cause trouble for some 
> applications.
>
> We prefer the second option since its straight-forward and it avoids 
> the possibility of misinterpretation by the application reading the 
> file. Does anyone have any other suggestions?
>
> It might also be a good idea to update the definition of MS:1000826 -- 
> elution time from "The time of elution from a chromatographic column, 
> relative to the start of the chromatography."" to "The time of elution 
> from all chromatographic columns, relative to the start of the 
> chromatography."
>
> Sorry we missed the original thread when this topic came up; we've 
> been following Psidev-ms-vocab and not Psidev-ms-dev. We're glad to 
> see an effort is being made to support comprehensive separation 
> techniques with mzML.
>
> Thank you,
>
> *Steven Robles *| Software design engineer
> ste...@le... <mailto:ste...@le...>
>
> Description: LECOLOGO3.png*
> **Delivering the Right Results* | 3000 Lakeview Ave. | St. Joseph | MI 
> | 49085
>
> Visit us online at www.leco.com <http://www.leco.com/>|Register to 
> receive e-news & updates 
> <http://visitor.r20.constantcontact.com/manage/optin/ea?v=001Ii8Y_QGk40pWa6GMO_HQlr4axErCoyfnebuJojN8G0hnJbPCz9PezRG9EoMLF3XTe8r9jqIrcaw%3D>
>
> ------------------------------------------------------------------------
>
>
>           *LECO Corporation Notice:*This communication may contain
>           confidential information intended for the named recipient(s)
>           only. If you received this by mistake, please destroy it and
>           notify us of the error. Thank you.
>
> ------------------------------------------------------------------------
>
>
>           *LECO Corporation Notice:* This communication may contain
>           confidential information intended for the named recipient(s)
>           only. If you received this by mistake, please destroy it and
>           notify us of the error. Thank you.
>
>
>
> ------------------------------------------------------------------------------
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Re: [Psidev-ms-dev] mzML for GCxGC/MS

[Nils H. <nil...@ce...>]

Hi Steve, 
as one of the original requestors of the modulation_time term, I totally agree with your option nr. 2 to handle more possible use-cases. We simply opted for the simpler option first since we did not have reference data available for other modulation regimes. Fyi, there was a thread started by Steve Reichenbach recently on 2D LC-MS that  circled around non-uniform modulation schemes and which might also be of interest here.

Nils Hoffmann

-- 
Nils Hoffmann                                   phone:    +49-521-106-4342
Bielefeld University                            room:             U10-144
Faculty of Technology, Genome Informatics
P.O. Box 10 01 31
33501 Bielefeld, Germany


"Robles, Steve" <Ste...@le...> schrieb:

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Re: [Psidev-ms-dev] mzML for GCxGC/MS

[pierre-alain b. <pie...@is...>]

Hi Steve,
thanks for this input and analysis.
Right... if there is a viable solution that does not require a format 
(schema) change, I'm sure this option would be preferable. According to 
your argumentation, option 2 would be fine, even if it does increase the 
size of the file. Apparently it also provide the most explicit 
description of the required modulation time related info.

I'd suggest the creation of the two terms you mention (first and second 
column modulation time), and maybe even a third global term that might 
describe the function itself (would that make sense to capture this?).

About MS:1000826 -- elution time from "The time of elution from a 
chromatographic column, relative to the start of the chromatography."" 
to "The time of elution from all chromatographic columns, relative to 
the start of the chromatography."
Why not then "The time of elution from all used chromatographic columns 
(one or more) in the chromatographic separation step, relative to the 
start of the chromatography." It's a bit verbous, but may be more explicit.

Open to comments, and if you agree, we can add the terms in the CV.

Best regards
Pierre-Alain


On 27.09.2012 14:41, Robles, Steve wrote:
>
> Hi everyone,
>
> We would like to export our two-dimensional GCxGC-MS data to mzML and 
> include the first and second column elution times.
>
> There was a thread in the psidev-ms-dev email archive that covered 
> this topic and resulted in the modulation time term being added to CV 
> https://sourceforge.net/mailarchive/forum.php?thread_name=assp.7128de5073.1306482337.4700.551.camel%40paddy&forum_name=psidev-ms-dev.
>
> [Term]
>
> id: MS:1002042
>
> name: modulation time
>
> def: "The duration of a complete cycle of modulation in a 
> comprehensive two-dimensional separation system, equals the length of 
> a second dimension chromatogram, i.e., the time between two successive 
> injections into the second column." 
> [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1000857 ! run attribute
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> The modulation time allows the elution time from the first and second 
> column to be calculated. However, our instrument allows the modulation 
> time to vary over the course of a single run so that there can be more 
> than one value for this field. Examples can be found on page 4 of this 
> site 
> http://www.leco.com/products/sep_sci/pegasus_4d/pdf/SEP%20SCI%20PEGASUS%204D%20GCxGC-TOFMS%20209-183.pdf 
> and 
> http://www.labmate-online.com/articles/chromatography/1/leco_corporation/analysis_of_samples_from_the_gulf_of_mexico_oil_spill_by_gcxgc-tofms_-_leco_corporation/815/
>
> To fully describe the data we would not only need a term for each 
> modulation time but also a matching field that describes the scan or 
> elution time that the modulation time is effective. For example 
> consider the following table:
>
> Time from injection (s) Modulation Time (s)
>
> 0 0
>
> 50 4
>
> 130 5
>
> 430 `                               6
>
> Here acquisition starts at 50 seconds from injection. Spectra acquired 
> from 50 s to anything less than 130 s will have a modulation time of 4 
> s; spectra acquired from 130 s to anything less than 430 s will have a 
> modulation time of 5 s; and anything acquired at 430 s or after will 
> have a modulation time of 6 s.
>
> The second and first column elution time can be described by:
>
> t2 = (t -- ti) % mi
>
> t1 = t -- t2
>
> Where:
>
> t1 is the first column elution time
>
> t2 is the second column elution time
>
> t is the time from injection
>
> ti is the greatest modulation start time from injection that is less 
> than or equal to t
>
> mi is the modulation time that goes with ti
>
> So for example a spectrum at t = 136 would have a second column 
> elution time of 1 and a first column elution time of 135.
>
> The only way we could represent this data with the current schema and 
> CV would be to break the sample into three different files, each with 
> a different modulation time. However we would prefer to keep the 
> sample in a single file.
>
> We can think of a few ways to handle this problem.
>
> 1)The first would be to include the list of modulation times and have 
> the software that is reading the file calculate the first and second 
> column elution times. This could be implemented in at least a couple 
> of different ways.
>
> a.A new list object added to the run element. Each item in the list 
> would require two cvParams, one for the modulation start time (a new 
> term?) and a modulation time.
>
> b.Instead of a list element, create a specific series of elements for 
> both the modulation time and modulation start time (i.e. modulation 
> time 1, modulation start time 1, modulation time 2, modulation start 
> time 2, ...).
>
> 2)Another approach would be to create two new terms "first column 
> elution time" and "second column elution time", and add these to scan 
> elements. There was a suggestion like this in the original thread that 
> wasn't implemented.
>
> 3)Just create a " second column elution time term" and store the first 
> column term in the elution time MS:1000826.
>
> The first approach will not increase the file size as much as the 
> others but requires more changes to the schema or CV. It also requires 
> the importing application to calculate the elution times. The second 
> approach doesn't require the importing application to know how to 
> determine the elution times. It only requires a couple of new CV terms 
> but will increase the file size the most. The third option has the 
> drawback that the it will usually produce multiple spectra with the 
> same elution time MS:1000826 which may cause trouble for some 
> applications.
>
> We prefer the second option since its straight-forward and it avoids 
> the possibility of misinterpretation by the application reading the 
> file. Does anyone have any other suggestions?
>
> It might also be a good idea to update the definition of MS:1000826 -- 
> elution time from "The time of elution from a chromatographic column, 
> relative to the start of the chromatography."" to "The time of elution 
> from all chromatographic columns, relative to the start of the 
> chromatography."
>
> Sorry we missed the original thread when this topic came up; we've 
> been following Psidev-ms-vocab and not Psidev-ms-dev. We're glad to 
> see an effort is being made to support comprehensive separation 
> techniques with mzML.
>
> Thank you,
>
> *Steven Robles *| Software design engineer
> ste...@le...
>
> Description: LECOLOGO3.png*
> **Delivering the Right Results* | 3000 Lakeview Ave. | St. Joseph | MI 
> | 49085
>
> Visit us online at www.leco.com <http://www.leco.com/>|Register to 
> receive e-news & updates 
> <http://visitor.r20.constantcontact.com/manage/optin/ea?v=001Ii8Y_QGk40pWa6GMO_HQlr4axErCoyfnebuJojN8G0hnJbPCz9PezRG9EoMLF3XTe8r9jqIrcaw%3D>
>
> ------------------------------------------------------------------------
>
>
>           *LECO Corporation Notice:* This communication may contain
>           confidential information intended for the named recipient(s)
>           only. If you received this by mistake, please destroy it and
>           notify us of the error. Thank you.
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://ad.doubleclick.net/clk;258768047;13503038;j?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>
>
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] mzML for GCxGC/MS

[Matthew C. <mat...@gm...>]

Hi Steve,

Since there can be more than two columns and the timing can get non-linear (potentially even more 
complicated than your table allows, i.e. it could be adjusted on the fly based on current elution 
rate), I think it makes the most sense to add the first/second/third elution time terms. These will 
be distinct from the scan start time term (which will remain the time since the start of 
acquisition). It might make sense to refactor the elution time term to be "first column elution 
time" but that will need to be ok with TraML as well (it's really the only format that uses "elution 
time" right now AFAIK).

-Matt


On 9/27/2012 7:41 AM, Robles, Steve wrote:
> Hi everyone,
>
> We would like to export our two-dimensional GCxGC-MS data to mzML and include the first and second
> column elution times.
>
> There was a thread in the psidev-ms-dev email archive that covered this topic and resulted in the
> modulation time term being added to CV
> https://sourceforge.net/mailarchive/forum.php?thread_name=assp.7128de5073.1306482337.4700.551.camel%40paddy&forum_name=psidev-ms-dev.
>
> [Term]
>
> id: MS:1002042
>
> name: modulation time
>
> def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation
> system, equals the length of a second dimension chromatogram, i.e., the time between two successive
> injections into the second column."
> [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
>
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>
> is_a: MS:1000857 ! run attribute
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> The modulation time allows the elution time from the first and second column to be calculated.
> However, our instrument allows the modulation time to vary over the course of a single run so that
> there can be more than one value for this field. Examples can be found on page 4 of this site
> http://www.leco.com/products/sep_sci/pegasus_4d/pdf/SEP%20SCI%20PEGASUS%204D%20GCxGC-TOFMS%20209-183.pdf
> and
> http://www.labmate-online.com/articles/chromatography/1/leco_corporation/analysis_of_samples_from_the_gulf_of_mexico_oil_spill_by_gcxgc-tofms_-_leco_corporation/815/
>
> To fully describe the data we would not only need a term for each modulation time but also a
> matching field that describes the scan or elution time that the modulation time is effective. For
> example consider the following table:
>
> Time from injection (s)                  Modulation Time (s)
>
> 0                                                                      0
>
> 50                                                                   4
>
> 130                                                                 5
>
> 430                                 `                               6
>
> Here acquisition starts at 50 seconds from injection. Spectra acquired from 50 s to anything less
> than 130 s will have a modulation time of 4 s; spectra acquired from 130 s to anything less than 430
> s will have a modulation time of 5 s; and anything acquired at 430 s or after will have a modulation
> time of 6 s.
>
> The second and first column elution time can be described by:
>
> t2 = (t – ti) % mi
>
> t1 = t – t2
>
> Where:
>
> t1 is the first column elution time
>
> t2 is the second column elution time
>
> t is the time from injection
>
> ti is the greatest modulation start time from injection that is less than or equal to t
>
> mi is the modulation time that goes with ti
>
> So for example a spectrum at t = 136 would have a second column elution time of 1 and a first column
> elution time of 135.
>
> The only way we could represent this data with the current schema and CV would be to break the
> sample into three different files, each with a different modulation time. However we would prefer to
> keep the sample in a single file.
>
> We can think of a few ways to handle this problem.
>
> 1)The first would be to include the list of modulation times and have the software that is reading
> the file calculate the first and second column elution times. This could be implemented in at least
> a couple of different ways.
>
> a.A new list object added to the run element. Each item in the list would require two cvParams, one
> for the modulation start time (a new term?) and a modulation time.
>
> b.Instead of a list element, create a specific series of elements for both the modulation time and
> modulation start time (i.e. modulation time 1, modulation start time 1, modulation time 2,
> modulation start time 2, …).
>
> 2)Another approach would be to create two new terms “first column elution time” and “second column
> elution time”, and add these to scan elements. There was a suggestion like this in the original
> thread that wasn’t implemented.
>
> 3)Just create a “ second column elution time term” and store the first column term in the elution
> time MS:1000826.
>
> The first approach will not increase the file size as much as the others but requires more changes
> to the schema or CV. It also requires the importing application to calculate the elution times. The
> second approach doesn’t require the importing application to know how to determine the elution
> times. It only requires a couple of new CV terms but will increase the file size the most. The third
> option has the drawback that the it will usually produce multiple spectra with the same elution time
> MS:1000826 which may cause trouble for some applications.
>
> We prefer the second option since its straight-forward and it avoids the possibility of
> misinterpretation by the application reading the file. Does anyone have any other suggestions?
>
> It might also be a good idea to update the definition of MS:1000826 – elution time from “The time of
> elution from a chromatographic column, relative to the start of the chromatography."” to “The time
> of elution from all chromatographic columns, relative to the start of the chromatography.”
>
> Sorry we missed the original thread when this topic came up; we’ve been following Psidev-ms-vocab
> and not Psidev-ms-dev. We’re glad to see an effort is being made to support comprehensive separation
> techniques with mzML.
>
> Thank you,
>
> *Steven Robles *| Software design engineer

[Psidev-ms-dev] New version 3.34.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.34.0 of the psi-ms.obo.
It contains a new term for the Bruker maXis impact
and 4 new terms for ProteomeDiscoverer input parameters.


Changed CV terms in version 3.34.0 of psi-ms.obo:
=================================================
************ Added the missing def item to the following CV terms
[Term]
id: MS:1001533
name: Bruker Daltonics esquire series
def: "Bruker Daltonics esquire series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001534
name: Bruker Daltonics flex series
def: "Bruker Daltonics flex series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001535
name: Bruker Daltonics BioTOF series
def: "Bruker Daltonics BioTOF series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001536
name: Bruker Daltonics micrOTOF series
def: "Bruker Daltonics micrOTOF series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001545
name: Bruker Daltonics amaZon series
def: "Bruker Daltonics amaZon series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001547
name: Bruker Daltonics maXis series
def: "Bruker Daltonics maXis series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001556
name: Bruker Daltonics apex series
def: "Bruker Daltonics apex series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001557
name: Shimadzu Biotech software
def: "Shimadzu Biotech software." [PSI:PI]
is_a: MS:1000531 ! software



New CV terms in version 3.34.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002077
name: maXis impact
def: "maXis impact." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1002078
name: ProteomeDiscoverer:1. Static Modification
def: "Determine 1st static post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002079
name: ProteomeDiscoverer:2. Static Modification
def: "Determine 2nd static post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002080
name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
def: "Precursor clipping range before." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1002081
name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
def: "Precursor clipping range after." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
relationship: has_units UO:0000221 ! dalton

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.34.0_rc2 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate version 3.34.0_rc2 of the psi-ms.obo.
It contains a new term for the Bruker maXis impact
and 4 new terms for ProteomeDiscoverer input parameters.


Changed CV terms in version 3.34.0_rc2 of psi-ms.obo:
=====================================================
************ Added the missing def item to the following CV terms
[Term]
id: MS:1001533
name: Bruker Daltonics esquire series
def: "Bruker Daltonics esquire series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001534
name: Bruker Daltonics flex series
def: "Bruker Daltonics flex series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001535
name: Bruker Daltonics BioTOF series
def: "Bruker Daltonics BioTOF series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001536
name: Bruker Daltonics micrOTOF series
def: "Bruker Daltonics micrOTOF series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001545
name: Bruker Daltonics amaZon series
def: "Bruker Daltonics amaZon series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001547
name: Bruker Daltonics maXis series
def: "Bruker Daltonics maXis series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001556
name: Bruker Daltonics apex series
def: "Bruker Daltonics apex series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1001557
name: Shimadzu Biotech software
def: "Shimadzu Biotech software." [PSI:PI]
is_a: MS:1000531 ! software



New CV terms in version 3.34.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002077
name: maXis impact
def: "maXis impact." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1002078
name: ProteomeDiscoverer:1. Static Modification
def: "Determine 1st static post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002079
name: ProteomeDiscoverer:2. Static Modification
def: "Determine 2nd static post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002080
name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
def: "Precursor clipping range before." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1002081
name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
def: "Precursor clipping range after." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
relationship: has_units UO:0000221 ! dalton

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] REVISED VERSION: minimal information document (MIAPE-Quant)

[Martin E. <mar...@ru...>]

Dear colleague,
dear member of the Proteomics community,

after comments of invited external reviewers and the public it was
decided, that major revisions have to be done on MIAPE-Quant.

You find a revised version 0.9.2 of MIAPE-Quant plus examples and
answers to reviewers on 
http://www.psidev.info/miape-quant-in-docproc 

According to the PSI document process these changes go through another 
shortened public review phase (and I've sent them back to the reviewers).

Please review the changes AND ESPECIALLY the examples of this version
and send any further comments to me. They will be editored after 
October 8th, 2012.

  Many thanks,
    Martin Eisenacher (PSI Editor)


--
Dr. Martin Eisenacher
Leiter AG Bioinformatik / Biostatistik
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

Tel.: +49 / 234 / 32 - 29288
Fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/


>  Dear colleague,
>  dear member of the Proteomics community,
> 
>  please forward this message to potentially interested colleagues!
> 
> 
>  The HUPO Proteomics Standards Initiative (PSI) develops standards
>  for documentation and storage of Proteomics data
>  (see http://www.psidev.info for an overview of activities).
> 
>  The "MIAPE - Quant" document is a module of the MIAPE document
>  suite (http://www.psidev.info/groups/miape). It defines
>  which minimal information has to be given to completely
>  describe a mass spectrometry quantification experiment and analysis.
> 
>  This minimal information document has been submitted into the PSI
>  document process: http://www.psidev.info/miape-quant-in-docproc
> 
>  Please feel free to review the proposed document in conjunction with
>  the accompanying examples. Send any suggestions and comments to me or
>  use the comment functionality of the web page (not tested yet).
> 
>  The official public comment phase ended some time ago, but due to web
>  page problems the public review phase is prolonged until
>  Tuesday, 31st July 2012.
> 
>    Best regards
>      Martin Eisenacher (PSI Editor)
> 
> 
>  --
>  Dr. Martin Eisenacher
>  Group Leader Bioinformatics / Biostatistics
>  Medizinisches Proteom-Center (MPC)
>  Ruhr-Universität Bochum
> 
>  phone: +49 / 234 / 32 - 29288
>  fax: +49 / 234 / 32 - 14554
>  http://www.medizinisches-proteom-center.de/
> 
> 
> 
> 
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Version 3.33.0 of psi-ms.obo releases

[Eric D. <ede...@sy...>]

Thank you, Gerhard!


> -----Original Message-----
> From: Gerhard Mayer [mailto:may...@ru...]
> Sent: Tuesday, September 11, 2012 11:52 PM
> To: psi...@li...; psidev-pi-
> de...@li...; psi...@li...
> Subject: [Psidev-ms-dev] Version 3.33.0 of psi-ms.obo releases
>
> Dear proteomics community,
>
> attached you find the new version 3.33.0 of psi-ms.obo.
>
> It contains some changed and new CV's for use in mzQuantML proposed by
> Martin Eisenacher
> and a new term for the PAnalyzer software.
>
> Comments and hints are as always welcome.
>
>
> Changed CV terms in version 3.33.0 of psi-ms.obo:
> =================================================
> ************ Deleted matchedfeature form the definition as this concept
> was dropped
> [Term]
> id: MS:1001805
> name: quantification datatype
> def: "The data type of the value reported in a QuantLayer for a
> feature,
> peptide, protein, protein group." [PSI:MS]
> is_a: MS:1001129 ! quantification information
>
> ************ Made the following term obsolete
> [Term]
> id: MS:1001849
> name: sum of MatchedFeature values
> def: "OBSOLETE Peptide quantification value calculated as sum of
> MatchedFeature quantification values." [PSI:PI]
> comment: This term was made obsolete because the concept MatchedFeature
> was dropped.
> is_a: MS:1001805 ! quantification datatype
> is_obsolete: true
>
>
> New CV terms in version 3.33.0 of psi-ms.obo:
> =============================================
> [Term]
> id: MS:1002067
> name: protein value: median of peptide ratios
> def: "Protein quantification value calculated as median of peptide
> ratios." [PSI:PI]
> is_a: MS:1001805 ! quantification datatype
>
> [Term]
> id: MS:1002068
> name: metabolic labelling: heavy N (mainly 15N)
> def: "Metabolic labelling: heavy N (mainly 15N)." [PSI:PI]
> is_a: MS:1001055 ! modification parameters
>
> [Term]
> id: MS:1002069
> name: metabolic labelling: labelling purity
> def: "Metabolic labelling: Description of labelling purity. Usually the
> purity of feeding material (e.g. 95%), or the inclusion rate derived
> from isotopic peak pattern shape." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001055 ! modification parameters
>
> [Term]
> id: MS:1002070
> name: t-test
> def: "Perform a t-test (two groups). Specify in string value, whether
> paired / unpaired, variance equal / different, one- / two-sided version
> is performed." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001861 ! quantification data processing
>
> [Term]
> id: MS:1002071
> name: ANOVA-test
> def: "Perform an ANOVA-test (more than two groups). Specify in string
> value, which version is performed." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001861 ! quantification data processing
>
> [Term]
> id: MS:1002072
> name: p-value
> def: "P-value as result of one of the processing steps described.
> Specify in the description, which processing step it was." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001805 ! quantification datatype
>
> [Term]
> id: MS:1002073
> name: mzIdentML
> def: "Proteomics Standards Inititative mzIdentML file format. File
> extension '.mzid'." [PSI:MS]
> is_a: MS:1001040 ! intermediate analysis format
>
> [Term]
> id: MS:1002074
> name: quantification file format
> def: "File format containing quantification results." [PSI:PI]
> is_a: MS:1001459 ! file format
>
> [Term]
> id: MS:1002075
> name: mzQuantML
> def: "Proteomics Standards Inititative mzQuantML file format. File
> extension '.mzq'." [PSI:MS]
> is_a: MS:1002074 ! quantification file format
>
> [Term]
> id: MS:1002076
> name: PAnalyzer
> def: "PAnalyzer software for getting protein evidence categories."
> [http://code.google.com/p/ehu-bio/wiki/PAnalyzer]
> is_a: MS:1001456 ! analysis software
>
>
> Best Regards,
> Gerhard
>
> --
> ------------
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Kairos GmbH
> Universitätsstraße 136 44799 Bochum
> Email: ger...@ka...
>
>
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] Version 3.33.0 of psi-ms.obo releases

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the new version 3.33.0 of psi-ms.obo.

It contains some changed and new CV's for use in mzQuantML proposed by 
Martin Eisenacher
and a new term for the PAnalyzer software.

Comments and hints are as always welcome.


Changed CV terms in version 3.33.0 of psi-ms.obo:
=================================================
************ Deleted matchedfeature form the definition as this concept 
was dropped
[Term]
id: MS:1001805
name: quantification datatype
def: "The data type of the value reported in a QuantLayer for a feature, 
peptide, protein, protein group." [PSI:MS]
is_a: MS:1001129 ! quantification information

************ Made the following term obsolete
[Term]
id: MS:1001849
name: sum of MatchedFeature values
def: "OBSOLETE Peptide quantification value calculated as sum of 
MatchedFeature quantification values." [PSI:PI]
comment: This term was made obsolete because the concept MatchedFeature 
was dropped.
is_a: MS:1001805 ! quantification datatype
is_obsolete: true


New CV terms in version 3.33.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002067
name: protein value: median of peptide ratios
def: "Protein quantification value calculated as median of peptide 
ratios." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002068
name: metabolic labelling: heavy N (mainly 15N)
def: "Metabolic labelling: heavy N (mainly 15N)." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002069
name: metabolic labelling: labelling purity
def: "Metabolic labelling: Description of labelling purity. Usually the 
purity of feeding material (e.g. 95%), or the inclusion rate derived 
from isotopic peak pattern shape." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002070
name: t-test
def: "Perform a t-test (two groups). Specify in string value, whether 
paired / unpaired, variance equal / different, one- / two-sided version 
is performed." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001861 ! quantification data processing

[Term]
id: MS:1002071
name: ANOVA-test
def: "Perform an ANOVA-test (more than two groups). Specify in string 
value, which version is performed." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001861 ! quantification data processing

[Term]
id: MS:1002072
name: p-value
def: "P-value as result of one of the processing steps described. 
Specify in the description, which processing step it was." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002073
name: mzIdentML
def: "Proteomics Standards Inititative mzIdentML file format. File 
extension '.mzid'." [PSI:MS]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002074
name: quantification file format
def: "File format containing quantification results." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002075
name: mzQuantML
def: "Proteomics Standards Inititative mzQuantML file format. File 
extension '.mzq'." [PSI:MS]
is_a: MS:1002074 ! quantification file format

[Term]
id: MS:1002076
name: PAnalyzer
def: "PAnalyzer software for getting protein evidence categories." 
[http://code.google.com/p/ehu-bio/wiki/PAnalyzer]
is_a: MS:1001456 ! analysis software


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

[Psidev-ms-dev] Release candidate v.3.33.0_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find a proposal for the release candidate version 
3.33.0_rc1 of psi-ms.obo.

It contains some changed and new CV's for use in mzQuantML proposed by 
Martin Eisenacher.
Comments and hints are as always welcome.


Changed CV terms in version 3.33.0_rc1 of psi-ms.obo:
=====================================================
************ Deleted matchedfeature form the definition as this concept 
was dropped
[Term]
id: MS:1001805
name: quantification datatype
def: "The data type of the value reported in a QuantLayer for a feature, 
peptide, protein, protein group." [PSI:MS]
is_a: MS:1001129 ! quantification information

************ Made the following term obsolete
[Term]
id: MS:1001849
name: sum of MatchedFeature values
def: "OBSOLETE Peptide quantification value calculated as sum of 
MatchedFeature quantification values." [PSI:PI]
comment: This term was made obsolete because the concept MatchedFeature 
was dropped.
is_a: MS:1001805 ! quantification datatype
is_obsolete: true


New CV terms in version 3.33.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002067
name: protein value: median of peptide ratios
def: "Protein quantification value calculated as median of peptide 
ratios." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002068
name: metabolic labelling: heavy N (mainly 15N)
def: "Metabolic labelling: heavy N (mainly 15N)." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002069
name: metabolic labelling: labelling purity
def: "Metabolic labelling: Description of labelling purity. Usually the 
purity of feeding material (e.g. 95%), or the inclusion rate derived 
from isotopic peak pattern shape." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002070
name: t-test
def: "Perform a t-test (two groups). Specify in string value, whether 
paired / unpaired, variance equal / different, one- / two-sided version 
is performed." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001861 ! quantification data processing

[Term]
id: MS:1002071
name: ANOVA-test
def: "Perform an ANOVA-test (more than two groups). Specify in string 
value, which version is performed." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001861 ! quantification data processing

[Term]
id: MS:1002072
name: p-value
def: "P-value as result of one of the processing steps described. 
Specify in the description, which processing step it was." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002073
name: mzIdentML
def: "Proteomics Standards Inititative mzIdentML file format. File 
extension '.mzid'." [PSI:MS]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002074
name: quantification file format
def: "File format containing quantification results." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002075
name: mzQuantML
def: "Proteomics Standards Inititative mzQuantML file format. File 
extension '.mzq'." [PSI:MS]
is_a: MS:1002074 ! quantification file format


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

[Psidev-ms-dev] Version 3.32.0 of psi-ms.obo released

[Gerhard M. <may...@ru...>]

Dear proteomics community,

the new version 3.32.0 of psi-ms.obo was released today, see
http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo

It contains changes and CV's proposed by Martin Eisenacher 
(http://code.google.com/p/mzquantml/issues/detail?id=22).
Comments and hints are as always welcome.


Changed CV terms in version 3.32.0 of psi-ms.obo:
=================================================
************ Added the URL 
https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default 
to the dbxref part
[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well 
as analyze the results of selected reaction monitoring runs developed 
and distributed by the MacCoss lab at the University of Washington." 
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default]
is_a: MS:1000871 ! SRM software

************ changed name from "database SwissProt" to "database 
UniProtKB/Swiss-Prot"
[Term]
id: MS:1001104
name: database UniProtKB/Swiss-Prot
is_a: MS:1001013 ! UniProtKB/database name

************ changed name from "decoy DB from SwissProt" to "decoy DB 
from UniProtKB/Swiss-Prot"
[Term]
id: MS:1001297
name: decoy DB from UniProtKB/Swiss-Prot
is_a: MS:1001284 ! decoy DB derived from

************ Added the URL http://greylag.org/ to the dbxref part
[Term]
id: MS:1001461
name: greylag
def: "Greylag identification software." [http://greylag.org/ ""]
is_a: MS:1001456 ! analysis software

************ Added the URL http://www.proteomesoftware.com to the dbxref 
part
[Term]
id: MS:1001561
name: Scaffold
def: "Scaffold analysis software." [http://www.proteomesoftware.com ""]
is_a: MS:1001456 ! analysis software

************ Added value-type xsd\:string
[Term]
id: MS:1001832
name: quantitation software comment / customizations
def: "Quantitation software comment or any customizations to the default 
setup of the software." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

************ Changed typo (added 's') and is now a child of MS:1002066 ! 
ratio calculation method
[Term]
id: MS:1001848
name: simple ratio of two values
def: "Simple ratio of two values (enumerator and denominator)." [PSI:PI]
is_a: MS:1002066 ! ratio calculation method


New CV terms in version 3.32.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002059
name: Microsoft Excel
def: "Microsoft Excel (can be used for spectral counting)." [PSI:PI]
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002060
name: database UniProtKB/TrEMBL
is_a: MS:1001013 ! UniProtKB/database name

[Term]
id: MS:1002061
name: decoy DB from UniProtKB/TrEMBL
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1002062
name: metabolic labelling: natural N (mainly 14N)
def: "Metabolic labelling: natural N (mainly 14N)." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002063
name: FindPairs
def: "Software e.g. for SILAC and 14N/15N workflow, part of the 
PeakQuant suite." [http://www.medizinisches-proteom-center.de/software ""]
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002064
name: peptide consensus RT
def: "Peptide consensus retention time." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002065
name: peptide consensus m/z
def: "Peptide consensus mass/charge ratio." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002066
name: ratio calculation method
def: "Method used to calculate the ratio." [PSI:PI]
is_a: MS:1001805 ! quantification datatype


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

[Psidev-ms-dev] Release candidate v3.32.0_rc2 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.32.0_rc2 of psi-ms.obo.
It contains changes and CV's proposed by Martin Eisenacher 
(http://code.google.com/p/mzquantml/issues/detail?id=22).
Comments and hints are as always welcome.


Changed CV terms in version 3.32.0_rc2 of psi-ms.obo:
=====================================================
************ Added the URL 
https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default 
to the dbxref part
[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well 
as analyze the results of selected reaction monitoring runs developed 
and distributed by the MacCoss lab at the University of Washington." 
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default]
is_a: MS:1000871 ! SRM software

************ changed name from "database SwissProt" to "database 
UniProtKB/Swiss-Prot"
[Term]
id: MS:1001104
name: database UniProtKB/Swiss-Prot
is_a: MS:1001013 ! UniProtKB/database name

************ changed name from "decoy DB from SwissProt" to "decoy DB 
from UniProtKB/Swiss-Prot"
[Term]
id: MS:1001297
name: decoy DB from UniProtKB/Swiss-Prot
is_a: MS:1001284 ! decoy DB derived from

************ Added the URL http://greylag.org/ to the dbxref part
[Term]
id: MS:1001461
name: greylag
def: "Greylag identification software." [http://greylag.org/ ""]
is_a: MS:1001456 ! analysis software

************ Added the URL http://www.proteomesoftware.com to the dbxref 
part
[Term]
id: MS:1001561
name: Scaffold
def: "Scaffold analysis software." [http://www.proteomesoftware.com ""]
is_a: MS:1001456 ! analysis software

************ Added value-type xsd\:string
[Term]
id: MS:1001832
name: quantitation software comment / customizations
def: "Quantitation software comment or any customizations to the default 
setup of the software." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

************ Changed typo (added 's') and is now a child of MS:1002066 ! 
ratio calculation method
[Term]
id: MS:1001848
name: simple ratio of two values
def: "Simple ratio of two values (enumerator and denominator)." [PSI:PI]
is_a: MS:1002066 ! ratio calculation method


New CV terms in version 3.32.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002059
name: Microsoft Excel
def: "Microsoft Excel (can be used for spectral counting)." [PSI:PI]
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002060
name: database UniProtKB/TrEMBL
is_a: MS:1001013 ! UniProtKB/database name

[Term]
id: MS:1002061
name: decoy DB from UniProtKB/TrEMBL
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1002062
name: metabolic labelling: natural N (mainly 14N)
def: "Metabolic labelling: natural N (mainly 14N)." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002063
name: FindPairs
def: "Software e.g. for SILAC and 14N/15N workflow, part of the 
PeakQuant suite." [http://www.medizinisches-proteom-center.de/software ""]
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002064
name: peptide consensus RT
def: "Peptide consensus retention time." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002065
name: peptide consensus m/z
def: "Peptide consensus mass/charge ratio." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002066
name: ratio calculation method
def: "Method used to calculate the ratio." [PSI:PI]
is_a: MS:1001805 ! quantification datatype


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Version 3.31.0 of psi-ms.obo released

[Qi, D. <D....@li...>]

Gerhard,

Thanks for updating.
When I tried to open it using OBO-Edit 2.2, it gave the following error messages:

***********************************************************************************
Load Error, line 547 48 unrecognized parent terms:      
line 83: PATO:0000146 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 568: PATO:0001718 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2665: PATO:0001747 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 49: PATO:0000128 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2079: PATO:0001674 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2783: PATO:0001574 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1880: PATO:0001019 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2655: PATO:0001521 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1114: PATO:0000044 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1332: PATO:0001740 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2684: PATO:0001757 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2623: PATO:0000992 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 2314: PATO:0001682 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 61: PATO:0000165 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1255: PATO:0001414 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1633: PATO:0001717 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1655: PATO:0001299 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 507: PATO:0001709 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 1362: PATO:0001744 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo      
line 547: PATO:0000033 of http://unit-ontology.googlecode.com/svn/trunk/unit.obo  
org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614)
org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74)
org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270)
org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43)
org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60)
org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137)
org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79)

*************************************************************************************************

Although there is no problem using text editor.

Thanks,
Da

-----Original Message-----
From: Gerhard Mayer [mailto:may...@ru...] 
Sent: 30 August 2012 09:56
To: psi...@li...; psi...@li...; psi...@li...
Subject: [Psidev-ms-vocab] Version 3.31.0 of psi-ms.obo released

Dear proteomics community,

attached you find the version 3.31.0 of psi-ms.obo.

It now distinguishes the C-term resp. N-term modification terms to be peptide-specific or protein-specific.


Changed CV terms in version 3.31.0 of psi-ms.obo:
=================================================
************ Changed the term to be peptide-centric
[Term]
id: MS:1001189
name: modification specificity peptide N-term
def: "As parameter for search engine: apply the modification only at the 
N-terminus of a peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

************ Changed the term to be peptide-centric
[Term]
id: MS:1001190
name: modification specificity peptide C-term
def: "As parameter for search engine: apply the modification only at the 
C-terminus of a peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

************ Corrected the Pubmed reference to point to PMID:20829449
[Term]
id: MS:1002047
name: MS-GF
def: "MS-GF software used to re-score the peptide-spectrum matches." 
[DOI:10.1074/mcp.M110.003731, PMID:20829449]
is_a: MS:1001456 ! analysis software

************ MS-GFDB is now an exact synonym of MS-GF+
[Term]
id: MS:1002048
name: MS-GF+
synonym: "MS-GFDB" EXACT []
def: "MS-GF+ software used to analyze the spectra." [PSI:PI]
is_a: MS:1001456 ! analysis software


New CV terms in version 3.31.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002057
name: modification specificity protein N-term
def: "As parameter for search engine: apply the modification only at the 
N-terminus of a protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:1002058
name: modification specificity protein C-term
def: "As parameter for search engine: apply the modification only at the 
C-terminus of a protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

[Psidev-ms-dev] Version 3.31.0 of psi-ms.obo released

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the version 3.31.0 of psi-ms.obo.

It now distinguishes the C-term resp. N-term modification terms to be 
peptide-specific or protein-specific.


Changed CV terms in version 3.31.0 of psi-ms.obo:
=================================================
************ Changed the term to be peptide-centric
[Term]
id: MS:1001189
name: modification specificity peptide N-term
def: "As parameter for search engine: apply the modification only at the 
N-terminus of a peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

************ Changed the term to be peptide-centric
[Term]
id: MS:1001190
name: modification specificity peptide C-term
def: "As parameter for search engine: apply the modification only at the 
C-terminus of a peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

************ Corrected the Pubmed reference to point to PMID:20829449
[Term]
id: MS:1002047
name: MS-GF
def: "MS-GF software used to re-score the peptide-spectrum matches." 
[DOI:10.1074/mcp.M110.003731, PMID:20829449]
is_a: MS:1001456 ! analysis software

************ MS-GFDB is now an exact synonym of MS-GF+
[Term]
id: MS:1002048
name: MS-GF+
synonym: "MS-GFDB" EXACT []
def: "MS-GF+ software used to analyze the spectra." [PSI:PI]
is_a: MS:1001456 ! analysis software


New CV terms in version 3.31.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002057
name: modification specificity protein N-term
def: "As parameter for search engine: apply the modification only at the 
N-terminus of a protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:1002058
name: modification specificity protein C-term
def: "As parameter for search engine: apply the modification only at the 
C-terminus of a protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

[Psidev-ms-dev] Release candidate 3.31.0_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.31.0_rc1 of psi-ms.obo.

Following the proposal of Matt it now distinguishes the C-term resp. 
N-term modification terms
to be peptide-specific or protein-specific.

Changed CV terms in version 3.31.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the term to be peptide-centric
[Term]
id: MS:1001189
name: modification specificity peptide N-term
def: "As parameter for search engine: apply the modification only at the 
N-terminus of a peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

************ Changed the term to be peptide-centric
[Term]
id: MS:1001190
name: modification specificity peptide C-term
def: "As parameter for search engine: apply the modification only at the 
C-terminus of a peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

************ Corrected the Pubmed reference to point to PMID:20829449
[Term]
id: MS:1002047
name: MS-GF
def: "MS-GF software used to re-score the peptide-spectrum matches." 
[DOI:10.1074/mcp.M110.003731, PMID:20829449]
is_a: MS:1001456 ! analysis software

************ MS-GFDB is now an exact synonym of MS-GF+
[Term]
id: MS:1002048
name: MS-GF+
synonym: "MS-GFDB" EXACT []
def: "MS-GF+ software used to analyze the spectra." [PSI:PI]
is_a: MS:1001456 ! analysis software


New CV terms in version 3.31.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002057
name: modification specificity protein N-term
def: "As parameter for search engine: apply the modification only at the 
N-terminus of a protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:1002058
name: modification specificity protein C-term
def: "As parameter for search engine: apply the modification only at the 
C-terminus of a protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule


Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...

[Psidev-ms-dev] submission of PSI recommendation document (mzTab): now open for Public Comment

[Martin E. <mar...@ru...>]

Dear colleague,
dear member of the Proteomics community,
 
please forward this message to potentially interested colleagues!

The HUPO Proteomics Standards Initiative (PSI) develops standards
for documentation and storage of Proteomics data
(see http://www.psidev.info for an overview of activities).
 

A recommendation document specifying the mzTab file format has been 
submitted to the PSI document process.
The submission can be found here: http://www.psidev.info/node/83

After having passed a 30-day review of the PSI steering commitee with 
minor formal changes, the proposed document version 1.0 release candidate 
now goes through 60-days public comments and external review phase 
(end: 12th October 2012).

"mzTab is intended as a lightweight supplement to the already existing 
standard file formats mzIdentML and mzQuantML, providing a summary 
of the final results of a MS-based proteomics experiment. mzTab 
files can contain protein, peptide, and small molecule identifications 
together with basic quantitative information and supports different levels 
of metadata reporting." (see also Cover Letter submitted)

It is important to highlight again that mzTab is not intended to store 
an experiment’s complete data / evidence but only its final reported
results.

The public comment period enables the wider community to provide feedback 
on a proposed standard before it is formally accepted, and thus is an
important 
step in the standardisation process.


PLEASE ADD COMMENTS to the submission page (http://www.psidev.info/node/83)
(or send them directly to martin.eisenacher: at : rub.de) for example 
regarding the following criteria:

- That it is well formed – that is, it is presented in accordance with the
  templates and is clearly written.
- That it is sufficiently detailed and clearly contains and comprehensively
  describes the necessary and sufficient explanation of the format.
- That the examples are in accordance with the specification.

This message is to encourage you to contribute to the standards development 
activity by commenting on the material that is available online. We invite 
both positive and negative comments. If negative comments are being made,
these 
could be on the relevance, clarity, correctness, appropriateness, etc, of 
the proposal as a whole or of specific parts of the proposal.

   Many thanks for your valuable time and participation
     Martin Eisenacher (PSI Editor)
 
 
--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/

[Psidev-ms-dev] Version 3.30.0 of psi-ms.obo released

[Gerhard M. <may...@ru...>]

Dear proteomics community,

the new version 3.30.0 of psi-ms.obo has been released.
It contains the new terms proposed by Matt concerning scoring with the 
MS-GF software.

New CV terms in version 3.30.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002047
name: MS-GF
def: "MS-GF software used to re-score the peptide-spectrum matches." 
[DOI:10.1021/pr8001244, PMID:18597511]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002048
name: MS-GF+
def: "MS-GF+ software used to analyze the spectra." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002049
name: MS-GF:RawScore
def: "MS-GF raw score." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002050
name: MS-GF:DeNovoScore
def: "MS-GF de novo score." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002051
name: MS-GF:Energy
def: "MS-GF energy score." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002052
name: MS-GF:SpecEValue
def: "MS-GF spectral E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001872 ! E-value for peptides

[Term]
id: MS:1002053
name: MS-GF:EValue
def: "MS-GF E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001872 ! E-value for peptides

[Term]
id: MS:1002054
name: MS-GF:QValue
def: "MS-GF Q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001868 ! q-value for peptides

[Term]
id: MS:1002055
name: MS-GF:PepQValue
def: "MS-GF peptide-level Q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001868 ! q-value for peptides

[Term]
id: MS:1002056
name: MS-GF:PEP
def: "MS-GF posterior error probability." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

Best Regards,
Gerhard

-- 
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
MPC University of Bochum, ZKF
Universitätsstrasse 150 44801 Bochum
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...
        gma...@ru...

[Psidev-ms-dev] minimal information document (MIAPE-Quant): prolonged Public Comment phase

[Martin E. <mar...@ru...>]

 Dear colleague,
 dear member of the Proteomics community,
 
 please forward this message to potentially interested colleagues!
 
 
 The HUPO Proteomics Standards Initiative (PSI) develops standards
 for documentation and storage of Proteomics data
 (see http://www.psidev.info for an overview of activities).
 
 The "MIAPE - Quant" document is a module of the MIAPE document
 suite (http://www.psidev.info/groups/miape). It defines
 which minimal information has to be given to completely
 describe a mass spectrometry quantification experiment and analysis.
  
 This minimal information document has been submitted into the PSI
 document process: http://www.psidev.info/node/84
 
 Please feel free to review the proposed document in conjunction with
 the accompanying examples. Send any suggestions and comments to me or
 use the comment functionality of the web page (not tested yet).
 
 The official public comment phase ended some time ago, but due to web
 page problems the public review phase is prolonged until
 Tuesday, 31st July 2012.

   Best regards
     Martin Eisenacher (PSI Editor)
 
 
 --
 Dr. Martin Eisenacher
 Group Leader Bioinformatics / Biostatistics
 Medizinisches Proteom-Center (MPC)
 Ruhr-Universität Bochum
 
 phone: +49 / 234 / 32 - 29288
 fax: +49 / 234 / 32 - 14554
 http://www.medizinisches-proteom-center.de/
 

Re: [Psidev-ms-dev] update of minimal information document (MIAPE-MS): now open for Public Comment

[Martin E. <mar...@ru...>]

Dear colleague,
dear member of the Proteomics community,

the public and external review phase of the "MIAPE - MS" document update has
ended.

Minor comments and feedback went back to the submitting work group to
integrate
or answer them.

  Best regards
   Martin



> -----Ursprüngliche Nachricht-----
> Von: Martin Eisenacher [mailto:mar...@ru...]
> Gesendet: Montag, 4. Juni 2012 22:46
> An: psi...@li...; 'psi...@eb...';
> 'psi...@li...'
> Cc: 'Andy Jones'
> Betreff: update of minimal information document (MIAPE-MS): now open
> for Public Comment
> 
> Dear colleague,
> dear member of the Proteomics community,
> 
> please forward this message to potentially interested colleagues!
> 
> 
> The HUPO Proteomics Standards Initiative (PSI) develops standards
> for documentation and storage of Proteomics data
> (see http://www.psidev.info for an overview of activities).
> 
> The "MIAPE - MS" document is a module of the MIAPE document
> suite (http://www.psidev.info/groups/miape). It defines
> which minimal information has to be given to completely
> describe a mass spectrometry experiment.
> 
> 
> An UPDATED VERSION of this minimal information document has been
> submitted into the PSI document process:
> http://www.psidev.info/node/82.
> 
> Please feel free to review the proposed document in conjunction with
> the accompanying examples. Send any suggestions and comments to me or
> use
> the comment functionality of the web page (not tested yet).
> 
> As this is an update with significant adjustments the review period
> ends
> after 30 days on 4th of July, 2012.
> 
>   Best regards
>     Martin Eisenacher (PSI Editor)
> 
> 
> --
> Dr. Martin Eisenacher
> Group Leader Bioinformatics / Biostatistics
> Medizinisches Proteom-Center (MPC)
> Ruhr-Universität Bochum
> 
> phone: +49 / 234 / 32 - 29288
> fax: +49 / 234 / 32 - 14554
> http://www.medizinisches-proteom-center.de/
> 

[Psidev-ms-dev] PSI meeting 2013 - dates for your diaries

[Eric D. <ede...@sy...>]

-----Original Message-----
From: Sandra Orchard
Sent: Monday, July 09, 2012 7:28 AM
To: psi...@eb...
Subject: [Psi-announce] PSI meeting 2013 - dates for your diaries

Dear All

This is preliminary announcement that the 2013  meeting of the HUPO-PSI
will be held at the Foresight Centre, University of Liverpool, UK on
15-17th April. The PSIMEx/ProteomeXchange meetings will then follow on
the 18-19th. We will obviously not be opening registration until much
closer to the time, but please mark off these dates and leave yourselves
free. We will also put the preliminary announcement on the PSI website,
and of course will announce registration nearer the time.

Please can someone on the MS, PI and Gel lists forward this message to
these as I do not think I have permission to write to those lists.

Best wishes
Sandra

[Psidev-ms-dev] MIAPE-MS

[Juan J. C. <jca...@ib...>]

Dear MIAPE developing colleagues,

I have now read the MIAPE-MS updated document and 
may say that found it quite comprehensive and 
easy to implement in the Instructions for Authors 
of J. Proteomics.  However, my impression is that 
as drafted the MIAPE-MS recommendations are 
primarily concerned with the description of 
experiments dealing with the automatic 
identification of proteins from organisms whose 
genome has been sequenced. Perhaps it would make 
sense to split section 4. "Spectrum and peak list 
generation and annotation" into two subsections 
to include how to report de novo mass 
spectrometry-gathered peptide ion sequencing and 
subsequent protein identification (BLAST). 
Current repository do not accept this kind of 
data...
Thanks for your input in this important matter!
Best wishes
Juan
-- 

--------------------------------------------
Prof. Juan J. Calvete
Laboratorio de Venómica y Proteinómica Estructural
Instituto de Biomedicina de Valencia, CSIC
Jaime Roig 11
46010 Valencia
Spain

Phone: +34 96 339 1775 (1778)
Fax: +34 96 369 0800

Journal of Proteomics (IF 2011: 4.878)
The official journal of the European Proteomics 
Association (EuPa, www.eupa.org)
Editor-in-Chief
www.elsevier.com/locate/jprot

SEProt, Sociedad Española de Proteómica (www.cbm.uam.es/seprot)

[Psidev-ms-dev] REMINDER: update of minimal information document (MIAPE-MS): now open for Public Comment

[Martin E. <mar...@ru...>]

Dear colleague,
dear member of the Proteomics community,

this is just a short reminder that the public and external review phase
of the MIAPE-MS update (see http://www.psidev.info/node/82) formally ends
TOMORROW (July 4th).

Each kind of feedback is welcome and will be helpful!

  Best regards
    Martin Eisenacher (PSI editor)


--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/





-----Ursprüngliche Nachricht-----
Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Montag, 4. Juni 2012 22:46
An: psi...@li...; 'psi...@eb...';
'psi...@li...'
Cc: 'Andy Jones'
Betreff: update of minimal information document (MIAPE-MS): now open for
Public Comment

Dear colleague,
dear member of the Proteomics community,

please forward this message to potentially interested colleagues!


The HUPO Proteomics Standards Initiative (PSI) develops standards
for documentation and storage of Proteomics data 
(see http://www.psidev.info for an overview of activities).

The "MIAPE - MS" document is a module of the MIAPE document 
suite (http://www.psidev.info/groups/miape). It defines 
which minimal information has to be given to completely
describe a mass spectrometry experiment.


An UPDATED VERSION of this minimal information document has been
submitted into the PSI document process: 
http://www.psidev.info/node/82.

Please feel free to review the proposed document in conjunction with
the accompanying examples. Send any suggestions and comments to me or use
the comment functionality of the web page (not tested yet).

As this is an update with significant adjustments the review period ends
after 30 days on 4th of July, 2012.

  Best regards
    Martin Eisenacher (PSI Editor)


--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/

[Psidev-ms-dev] psi-ms.obo v.3.29.0 released

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.29.0 of the psi-ms.obo.
It contains two changes proposed by Salvador and a corrected is_a 
relation for the 'unlabeled sample' term
as well as some new terms for the ProteinProspector software.


Changed CV terms in version 3.29.0 of psi-ms.obo:
=================================================
************ renamed from confident peptide --> confident peptide 
sequence number
[Term]
id: MS:1001100
name: confident peptide sequence number
def: "This counts the number of peptide sequences without regard to 
whether they are distinct. Multiple charges states and multiple 
modification states DO count as multiple peptides. The definition of 
'confident' must be qualified elsewhere." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001116 ! single protein result details

************ added the relation is_a: MS:1001153 ! search engine 
specific score
[Term]
id: MS:1001579
name: Scaffold:Protein Probability
def: "Scaffold protein probability score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

************ changed the relation is_a: MS:1002018 ! MS1 label-based 
analysis --> is_a: MS:1000548 ! sample attribute
[Term]
id: MS:1002038
name: unlabeled sample
def: "A sample that has not been labelled or modified. This is often 
referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
synonym: "light labeled sample" EXACT []
is_a: MS:1000548 ! sample attribute


New CV terms in version 3.29.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002043
name: ProteinProspector
def: "ProteinProspector software for data acquisition and analysis." 
[PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002044
name: ProteinProspector:score
def: "The ProteinProspector result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002045
name: ProteinProspector:expectation value
def: "The ProteinProspector result 'Expectation value'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002046
name: native source path
def: "The original source path used for directory-based sources." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] update of minimal information document (MIAPE-MS): now open for Public Comment

[Martin E. <mar...@ru...>]

Due to an Address book error the following announcement
was originally not send to this important list!
Sorry for that!

(Thanks to Pierre-Alain for the hint...)



> Dear colleague,
> dear member of the Proteomics community,
> 
> please forward this message to potentially interested colleagues!
> 
> 
> The HUPO Proteomics Standards Initiative (PSI) develops standards
> for documentation and storage of Proteomics data
> (see http://www.psidev.info for an overview of activities).
> 
> The "MIAPE - MS" document is a module of the MIAPE document
> suite (http://www.psidev.info/groups/miape). It defines
> which minimal information has to be given to completely
> describe a mass spectrometry experiment.
> 
> 
> An UPDATED VERSION of this minimal information document has been
> submitted into the PSI document process:
> http://www.psidev.info/node/82.
> 
> Please feel free to review the proposed document in conjunction with
> the accompanying examples. Send any suggestions and comments to me or
> use the comment functionality of the web page (not tested yet).
> 
> As this is an update with significant adjustments the review period
> ends after 30 days on 4th of July, 2012.
> 
>   Best regards
>     Martin Eisenacher (PSI Editor)
> 
> 
> --
> Dr. Martin Eisenacher
> Group Leader Bioinformatics / Biostatistics
> Medizinisches Proteom-Center (MPC)
> Ruhr-Universität Bochum
> 
> phone: +49 / 234 / 32 - 29288
> fax: +49 / 234 / 32 - 14554
> http://www.medizinisches-proteom-center.de/
> 

[Psidev-ms-dev] Release candidate 3.29.0_rc2 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.29.0_rc2 of the psi-ms.obo.
It contains two changes proposed by Salvador and a corrected is_a 
relation for the 'unlabeled sample' term
as well as some new terms for the ProteinProspector software.

Changed CV terms in version 3.29.0_rc2 of psi-ms.obo:
=====================================================
************ renamed from confident peptide --> confident peptide 
sequence number
[Term]
id: MS:1001100
name: confident peptide sequence number
def: "This counts the number of peptide sequences without regard to 
whether they are distinct. Multiple charges states and multiple 
modification states DO count as multiple peptides. The definition of 
'confident' must be qualified elsewhere." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001116 ! single protein result details

************ added the relation is_a: MS:1001153 ! search engine 
specific score
[Term]
id: MS:1001579
name: Scaffold:Protein Probability
def: "Scaffold protein probability score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

************ changed the relation is_a: MS:1002018 ! MS1 label-based 
analysis --> is_a: MS:1000548 ! sample attribute
[Term]
id: MS:1002038
name: unlabeled sample
def: "A sample that has not been labelled or modified. This is often 
referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
synonym: "light labeled sample" EXACT []
is_a: MS:1000548 ! sample attribute


New CV terms in version 3.29.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002043
name: ProteinProspector
def: "ProteinProspector software for data acquisition and analysis." 
[PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002044
name: ProteinProspector:score
def: "The ProteinProspector result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002045
name: ProteinProspector:expectation value
def: "The ProteinProspector result 'Expectation value'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002046
name: native source path
def: "The original source path used for directory-based sources." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de