Menu
▾
▴
psidev-ms-dev
|
From: Eric D. <ede...@sy...> - 2010-09-28 16:09:39
|
Present: Matt, Richard, Steffen, Jim, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been accepted to MCP: http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.full.pdf+html - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink - How do we handle lock mass corrections? - Eric should test FAIMS support in mzML - Eric should test a recent file with multiple fragmentation types to see if they are properly labeled - Other items? + Work on these action items + No other items ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out + Ask Pierre-Alain to send Juan Antonio the latest documents ---- 3) TraML development - TraML version 0.9.4 is available at http://www.psidev.info/index.php?q=node/405 - TraML was submitted to PSI document process - Reviews are back, see attached. Discuss how to address these concerns + Comments from reviewers 1 and 2 were discussed, and response/action outlined. + Eric will start officially addressing these and send around result and open questions + Ran out of time. + Comments from reviewers 3 and 4 next time - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt has finished the C# bindings which will enable Skyline support - Matt will sent out a sample file - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Eric will also contact Amol to discuss TraML implementations - Dave Cox at Sciex will test implement? - Need to add two new terms - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI session at World HUPO in Sydney - Eric presented on the work of the group: mzML 1.1, TraML 0.9.4, MIAPE-MS ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it 6) SRM analysis guidelines and format - At a “Data Quality Metrics” workshop in Sydney before World HUPO (hosted by NCI), there was strong support to try to develop a set of guidelines for reporting of SRM experiments as there currently are none. A working group was identified at the meeting. Eric will organize some discussions on this. - It was also proposed that PSI work on a standard format for the reporting of SRM experiment analysis. There was some support for this. This is distinct from mzML, which holds the chromatograms. It is distinct from TraML which holds the input transitions. It might have some overlap with mzQuantML. This should be discussed and a subgroup identified. Next meeting: - In 2 weeks? Oct 12? + Yes |
|
From: Eric D. <ede...@sy...> - 2010-10-12 22:28:47
|
Present: Florian, Steffen, Pierre-Alain, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been accepted to MCP: http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.full.pdf+html - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink - How do we handle lock mass corrections? - Eric should test FAIMS support in mzML - Eric should test a recent file with multiple fragmentation types to see if they are properly labeled - Other items? + Work on these action items + No other items ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out + Ask Pierre-Alain to send Juan Antonio the latest documents ---- 3) TraML development - TraML version 0.9.4 is available at http://www.psidev.info/index.php?q=node/405 - TraML was submitted to PSI document process - Reviews are back, see attached. Discuss how to address these concerns + Comments from reviewers 3 and 4 were discussed, and response/action outlined. + Eric will start officially addressing these and send around result and open questions + Ran out of time. - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt has finished the C# bindings which will enable Skyline support - Matt will sent out a sample file - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Eric will also contact Amol to discuss TraML implementations - Dave Cox at Sciex will test implement? - Need to add two new terms - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI session at World HUPO in Sydney - Eric presented on the work of the group: mzML 1.1, TraML 0.9.4, MIAPE-MS ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it 6) SRM analysis guidelines and format - At a “Data Quality Metrics” workshop in Sydney before World HUPO (hosted by NCI), there was strong support to try to develop a set of guidelines for reporting of SRM experiments as there currently are none. A working group was identified at the meeting. Eric will organize some discussions on this. - It was also proposed that PSI work on a standard format for the reporting of SRM experiment analysis. There was some support for this. This is distinct from mzML, which holds the chromatograms. It is distinct from TraML which holds the input transitions. It might have some overlap with mzQuantML. This should be discussed and a subgroup identified. Next meeting: - In 2 weeks? Oct 26? + Unclear on what best date is. Create doodle poll. |
|
From: Eric D. <ede...@sy...> - 2010-10-19 17:42:27
|
Present: Matt, Steffen, Florian, Jim, Eric The current response to the review comments was gone through and discussed. Action items: - Do we want to show a little figure showing an out-of-sync transition? - <VerficationStatus> [This is not settled. Eric will grok the situation and email out a question to the list for further discussion]. - The question is do we rely order alone, or do we add a “n” attribute or “order” attribute. OR better yet use MS Level CV term? Come up with an example and email the list. - Add isolation width to mapping file - Talk to Brendan again about Skyline and TraML - add the protein terms - add link to spML file and msrun data URL probably as new CV terms - Matt suggests for last point to just use transitions relative intensity - Steffen asks about adducts? Next meeting: Next in 3 weeks. Nov 9 |
|
From: Eric D. <ede...@sy...> - 2010-11-09 08:19:44
|
Hi everyone, we had tentatively agreed to meet again November 9, but due to vacation and other conflicts, it probably doesn't make sense to have a call today. Instead, I'll follow up with emails. Thanks, Eric _____ From: Eric Deutsch [mailto:ede...@sy...] Sent: Tuesday, October 19, 2010 10:42 AM To: Mass spectrometry standard development Cc: Eric Deutsch Subject: PSI MSS WG call notes Present: Matt, Steffen, Florian, Jim, Eric The current response to the review comments was gone through and discussed. Action items: - Do we want to show a little figure showing an out-of-sync transition? - <VerficationStatus> [This is not settled. Eric will grok the situation and email out a question to the list for further discussion]. - The question is do we rely order alone, or do we add a "n" attribute or "order" attribute. OR better yet use MS Level CV term? Come up with an example and email the list. - Add isolation width to mapping file - Talk to Brendan again about Skyline and TraML - add the protein terms - add link to spML file and msrun data URL probably as new CV terms - Matt suggests for last point to just use transitions relative intensity - Steffen asks about adducts? Next meeting: Next in 3 weeks. Nov 9 |
|
From: Eric D. <ede...@sy...> - 2011-03-15 18:34:05
|
Notes from the PIS MSS WG phone conference Present: Richard, Matt, Jim, Steffen, Eric, Gerhard, Julian, Agenda: 1) PSI Spring Workshop April 11-13 - Collaborative efforts with the PI WG on mzIdentML, mzQuantML, CV - Finishing TraML - Drafting SRM experiment guidelines - Drafting a format for SRM experimental results - MIAPE-MS finalization - MIAPE-Quant work? - Adjacent to the ProteomeXchange workshop - Please attend and encourage attendance ---- 2) mzML 1.1.0 - We have been contacted by Vladimir Likic, who has said that he is representing some portions of the metabolomics community and they are interested in seeing if mzML would be a good fit for them as a next-generation format. See: http://bioinformatics.bio21.unimelb.edu.au/mzml.html + Steffen feels there probably only minor changes required for GC-MS. Probably only mostly just some terms like “travel time” and the like. + Currently the ANDI format is most often used for GC-MS, but it seems out of date and is the format that would be replaced. + Steffen will be at a metabolomics conf next week at EBI and will report - Other outstanding todo items: - Eric should test FAIMS support in mzML - Eric should test a recent file with multiple fragmentation types to see if they are properly labeled - Other items? ---- 3) TraML development - TraML version 0.9.4 is available at http://www.psidev.info/index.php?q=node/405 - TraML was submitted to PSI document process - Reviews are back and partially addressed.Still outstanding todo items - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt has finished the C# bindings which will enable Skyline support + Brendan’s comments were apparently not received so we should ask him - Matt will sent out a sample file generated from ProteoWizard - Eric will try validating with his tools - ISB implementation in ATAQS is done - Jim has an implementation but just will need to update to 0.9.4 - Eric will also contact Amol to discuss TraML implementations - Dave Cox at Sciex will test implement? - Need to add two new terms + Change <Validation> to <ValidationStatus> + Fix <Configuration> to (1..N) + What about MS3 support? + Steffen points out that just adding another <Product> tag isn’t enough. What if there are different collision energies for MS2 and MS3? + Seems like there was agreement to move <Interpretation>, <Prediction>, <ConfigurationList> into <Product>, thereby allowing (requiring!) separate entries for each <Product> entry. For 99% of cases, this is just a trivial move of elements. + Discussion ensued about <Product> should have “isolation window target m/z” or “selection window target m/z”. Are we isolating (pure filter) or selecting (scanning in a range)? Ran out of time. Continue on email or next time. - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out + Progress will continue at the workshop ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it - Some folks from PRIDE have expressed the desired to clean up the CV. Work with them. + Richard will ask David Ovelleiro to send a note to the list on his efforts + There is a list of action items from a previous call ---- 6) SRM analysis guidelines and format - At a “Data Quality Metrics” workshop in Sydney before World HUPO (hosted by NCI), there was strong support to try to develop a set of guidelines for reporting of SRM experiments as there currently are none. A working group was identified at the meeting. Eric will organize some discussions on this. - It was also proposed that PSI work on a standard format for the reporting of SRM experiment analysis. There was some support for this. This is distinct from mzML, which holds the chromatograms. It is distinct from TraML which holds the input transitions. It might have some overlap with mzQuantML. This should be discussed and a subgroup identified. Next meeting: - In 2 weeks Mar 29? + YES |
|
From: Eric D. <ede...@sy...> - 2011-04-05 16:50:44
|
Notes from teleconference on Apr 5, 2011 Present: Florian, Eric, Matt, Pierre-Alain, Jim, Agenda: 1) PSI Spring Workshop April 11-13 - Collaborative efforts with the PI WG on mzIdentML, mzQuantML, CV - Finishing TraML - Drafting SRM experiment guidelines - Drafting a format for SRM experimental results - MIAPE-MS finalization - MIAPE-Quant work? - Adjacent to the ProteomeXchange workshop - Please attend and encourage attendance ---- 2) mzML 1.1.0 - We have been contacted by Vladimir Likic, who has said that he is representing some portions of the metabolomics community and they are interested in seeing if mzML would be a good fit for them as a next-generation format. See: http://bioinformatics.bio21.unimelb.edu.au/mzml.html - Steffen feels there probably only minor changes required for GC-MS. Probably only mostly just some terms like “travel time” and the like. - Currently the ANDI format is most often used for GC-MS, but it seems out of date and is the format that would be replaced. - Steffen attended a metabolomics conf at EBI and will report - Other outstanding todo items: - Eric should test FAIMS support in mzML - Eric should test a recent file with multiple fragmentation types to see if they are properly labeled + Need a term for LTQ Orbitrap Velos. Matt will add. + Jim will send along additional missing instruments + Eric has problems with SF CVS + Need definition for Steffen’s proposed “second column modulation time” - Other items? ---- 3) TraML development - TraML version 0.9.4 is available at http://www.psidev.info/index.php?q=node/405 - TraML was submitted to PSI document process - Reviews are back and partially addressed.Still outstanding todo items - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt has finished the C# bindings which will enable Skyline support - Matt will sent out a sample file generated from ProteoWizard - Eric will try validating with his tools - ISB implementation in ATAQS is done - Jim has an implementation but just will need to update to 0.9.4 - Eric will also contact Amol to discuss TraML implementations - Dave Cox at Sciex will test implement? - Brendan’s comments were found and sent to the list - Need to add two new terms - Change <Validation> to <ValidationStatus> - Fix <Configuration> to (1..N) - What about MS3 support? - Steffen points out that just adding another <Product> tag isn’t enough. What if there are different collision energies for MS2 and MS3? - Seems like there was agreement to move <Interpretation>, <Prediction>, <ConfigurationList> into <Product>, thereby allowing (requiring!) separate entries for each <Product> entry. For 99% of cases, this is just a trivial move of elements. - Discussion ensued about <Product> should have “isolation window target m/z” or “selection window target m/z”. Are we isolating (pure filter) or selecting (scanning in a range)? Ran out of time. Continue on email or next time. + Agreed that <Precursor> is “isolation window” and <Product> is a “selection window”? + To support MS3, Add an <intermediateProduct> element + Eric will put together an example of that and email it out + Discussed Brendan’s Review + Matt will email out how mzIdentML can support non Unimod modifications - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out - Progress will continue at the workshop + Trying to get MIAPE-compliant mzML file + One example from PRIDE + One example article from Proteomics + Ask Juan Pablo for MIAPE example ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it - Some folks from PRIDE have expressed the desired to clean up the CV. Work with them. - Richard will ask David Ovelleiro to send a note to the list on his efforts - There is a list of action items from a previous call - Email from David Ovelleiro this morning + David will present at the meeting next week ---- 6) SRM analysis guidelines and format - At a “Data Quality Metrics” workshop in Sydney before World HUPO (hosted by NCI), there was strong support to try to develop a set of guidelines for reporting of SRM experiments as there currently are none. A working group was identified at the meeting. Eric will organize some discussions on this. - It was also proposed that PSI work on a standard format for the reporting of SRM experiment analysis. There was some support for this. This is distinct from mzML, which holds the chromatograms. It is distinct from TraML which holds the input transitions. It might have some overlap with mzQuantML. This should be discussed and a subgroup identified. Next meeting: - In person next week in Heidelberg |
|
From: Eric D. <ede...@sy...> - 2011-09-13 15:47:57
|
Notes from today’s teleconference. Present: Steffen, Florian, Eric, Agenda: 1) Meetings and workshops - Review of PSI sessions at World HUPO in Geneva - PSI Spring Workshop San Diego March 12-14, 2012 (+ProteomeXchange 15-16) + Start advertizing with vendors - Note nearby US HUPO San Francisco March 4-7, 2012 and ABRF Orlando March 17-20, 2012 - ---- 2) mzML 1.1.0 - mzML for metabolomics + Oliver Kolbacher also may be good to get involved in this. + We need some CV terms for GC-GC coupling: + “modulation time” ? + There was a discussion a few months ago. Try to revive this. + Bioconductor has now officially accepted mzR package, an mzML reader. This is a wrapper around pwiz + Available now, and will be officially distributed with next release of Bioconductor + The next release of xcms will have an improved mzML reader - imzML - mz5 and mzDB - digital signatures - ---- 3) TraML development - TraML version 0.9.5 is available at http://www.psidev.info/index.php?q=node/405 - TraML was resubmitted to PSI document process - Currently in community review period + Clarify with Christian when this is officially over - Discuss response to 5th reviewer + Table this for now until we can get some additional participation + Steffen has an R package for writing inclusion lists + Steffen will find a hyperlink to it and we will post on the TraML dev page ---- 4) MIAPE-MS revision - ---- 5) Improving the controlled vocabulary - Proposed “command line parameters” CV term and implications + This sounds quite sensible to us. Follow up with an email to list + Would this include the executable/path or just everything after that. Probably after. ---- 6) SRM analysis guidelines and format - Review MIAPE-Quant for SRM - Review mzQuantML for SRM + We need to create a sample mzQuantML document for an SRM experiment. Who will try? Next meeting: - Tue Sep 27 8am PDT? + Yes + Try to get greater participation at next call. + Put in hyperlink to dial-in numbers from other countries. Steffen will be in Finland. |
|
From: Oliver K. <oli...@un...> - 2011-09-14 10:39:56
|
On 13.09.2011, at 17:47, Eric Deutsch wrote: > 2) mzML 1.1.0 > - mzML for metabolomics > + Oliver Kolbacher also may be good to get involved in this. Can do. Just couldn't make the phone conference (and will be traveling a lot over the next two months, so I am not sure how often I will be able to make it). So it's best if you let me know what sort of input you need from me and I'll see to it. Cheers, Oliver |
|
From: Eric D. <ede...@sy...> - 2011-09-14 13:55:52
|
Hi Oliver, thank you for your offer and involvement. In the nearest term, we hope to define a few terms to help properly annotate information about GC-GC coupling and maybe you can lend some insight there by reviewing the proposed terms and definitions. Also any experience that can be applied to converting GCMS data into mzML would be welcome. Thank you! Eric > -----Original Message----- > From: Oliver Kohlbacher [mailto:oli...@un...] > Sent: Wednesday, September 14, 2011 3:40 AM > To: Mass spectrometry standard development > Cc: Eric Deutsch > Subject: Re: [Psidev-ms-dev] PSI MSS WG call notes > > > On 13.09.2011, at 17:47, Eric Deutsch wrote: > > 2) mzML 1.1.0 > > - mzML for metabolomics > > + Oliver Kolbacher also may be good to get involved in this. > Can do. Just couldn't make the phone conference (and will be traveling > a lot over the next two months, so I am not sure how often I will be > able > to make it). So it's best if you let me know what sort of input you > need > from me and I'll see to it. > > Cheers, > Oliver > |
|
From: Eric D. <ede...@sy...> - 2011-09-27 16:31:55
|
Notes from today’s teleconference. Present: Matt, Jim, Richard, Eric, Pierre-Alain, Alexey, Agenda: 1) Meetings and workshops - PSI Spring Workshop San Diego March 12-14 (+ProteomeXchange 15-16) - Note nearby US HUPO March 4-7 and ABRF March 17-20 - ---- 2) mzML 1.1.0 - mzML for metabolics + We need some CV terms for GC-GC coupling: + “modulation time” ? + There was a discussion a few months ago. Try to revive this. - mz5 and mzDB + mz5 is exact schema for mzML but with HDF5 + Matt is using it and performance is good + Developed by Steen Lab and contributed to ProteoWizard + mzDB uses SQLite as back end and uses mzML snippets for metadata - digital signatures - ---- 3) TraML development - TraML version 0.9.5 is available at http://www.psidev.info/index.php?q=node/405 - TraML was resubmitted to PSI document process - Currently in community review period + Clarify with Christian when this is officially over - Discuss response to 5th reviewer + Clarify the scope of TraML at the beginning of the response as the list of transitions between vendor software, repositories, + Amplify the response to “no one wants to parse .sky files” + Clarify that “neutral loss scans” and “precursor ion scans” are not supported in section 1.3.5 - Discuss Alexey’s use case and needed terms + Signal to noise probably better than intensity even + Alexey’s proposal seems quite reasonable to try + Eric will send an email with the terms proposed + Steffen has an R package for writing inclusion lists + Steffen will find a hyperlink to it and we will post on the TraML dev page ---- 4) MIAPE-MS revision - Special call on Thursday for MIAPE - * ---- 5) Improving the controlled vocabulary - Proposed “command line parameters” CV term and implications + This sounds quite sensible to us. Follow up with an email to list + Would this include the executable/path or just everything after that. Probably after. + Matt points out that pretty much all options are encoded in the file. But gathering them is difficult to recreate the step + Everyone agreed that it was useful to add - CV term requests from Sean ---- 6) SRM analysis guidelines and format - Review MIAPE-Quant for SRM - Review mzQuantML for SRM + We need to create a sample mzQuantML document for an SRM experiment. Who will try? + Steffen may try Next meeting: - Tue Oct 11 8am PDT? + Yes |
|
From: Eric D. <Eri...@sy...> - 2011-11-01 17:03:39
|
Present: Steffen, Juanan, Andy, Matt, Eric, David
Discussion of CV terms is captured below. Please let me know if there are
further comments or errors. David will follow up with a slightly more
official CV amendment proposal.
modulation time
[Term]
id: MS:1000XXX
name: modulation time
def: "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." [PSI:MS]
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
inlet temperature
[Term]
id: MS:1000XXX
name: inlet temperature
def: "Temperature of the instrument inlet." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000XXX ! inlet attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius
source temperature
[Term]
id: MS:1000XXX
name: source temperature
def: "Temperature of the instrument source." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius
[Term]
id: MS:100????
name: inlet attribute
def: "Property of an instrument inlet that needs a value." [PSI:MS]
relationship: part_of MS:1000458 ! source
+ Need to add to mzML mapping file the addition of inlet attributes,
modulation time.
SQID:
+ David will create a formal proposal of the SQID terms as suggested and
send it out for discussion/approval
Peak intensity discussion:
1) Add a “spectrum” prefix to the current “peak” terms as listed here:
MS:1000442 spectrum
+ MS:1000231 spectrum peak
+ MS:1000042 spectrum peak intensity (has units and value) defined
for mass spectrum
+ MS:100???? spectrum peak height (has units and value)
+ MS:100???? spectrum peak area (has units and value)
[Term]
id: MS:1000231
name: spectrum peak
def: "A localized region of relatively large ion signal in a mass spectrum.
Although peaks are often associated with particular ions, the terms peak
and ion should not be used interchangeably." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum
[Term]
id: MS:1000042
name: spectrum peak intensity
def: "Intensity of ions as measured by the height or area of a peak in a
mass spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
relationship: part_of MS:1000231 ! spectrum peak
[Term]
id: MS:100????
name: spectrum peak height
def: "Intensity of ions as measured by the height of a peak in a mass
spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000042 ! spectrum peak intensity
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
[Term]
id: MS:100????
name: spectrum peak area
def: "Intensity of ions as measured by the area of a peak in a mass
spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000042 ! spectrum peak intensity
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
MS:1000625 chromatogram
+ MS:1000??? chromatogram peak
+ MS:100??? chromatogram peak intensity (has units, etc.)
+ MS:100???? chromatogram peak height (has units, etc.)
+ MS:100???? chromatogram peak area
[Term]
id: MS:100????
name: chromatogram peak
def: "A localized region of relatively large ion signal in a chromatogram."
[PSI:MS]
relationship: part_of MS:1000625 ! chromatogram
[Term]
id: MS:100????
name: chromatogram peak intensity
def: "Intensity of ions as measured by the height or area of a peak in a
chromatogram." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
relationship: part_of MS:1000231 ! chromatogram peak
[Term]
id: MS:100????
name: chromatogram peak height
def: "Intensity of ions as measured by the height of a peak in a
chromatogram." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:100???? ! chromatogram peak intensity
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
[Term]
id: MS:100????
name: chromatogram peak area
def: "Intensity of ions as measured by the area of a peak in a
chromatogram." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:100???? ! chromatogram peak intensity
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
+ Andy will check with Martin on what to do with these. Tidy them up a
little at least:
“peak area” x2
“peak intensity”
Eric had suggested:
MS:1001843 MS1 feature height quantification (no units or value) (concept
of performing quant via this method)
MS:1001844 MS1 feature area quantification (no units or value) (concept of
performing quant via this method)
Next meeting:
- Nov 22nd 8am Seattle Time?
+ yes
|
|
From: Eric D. <Eri...@sy...> - 2012-02-28 16:40:05
|
Notes from the MSS WG call 2012-02-28 + Present: Florian, Eric, Matt, Pierre-Alain Agenda: 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 - Evaluate MIAPE – Quant for SRM specifically - Evaluate mzQuantML for SRM specifically and generate examples - Assemble guideline recommendations for the HPP + We will work together with Christoph’s track on this - TraML implementations - Other 2) mzML status - No critical issues + Need to add an ion mobility array? + It would be good to discuss at the SD meeting how to encode ion mobility data in mzML (Wed?) + There seem to be several possible ways to do it. Can we settle on one? 3) TraML status - No critical issues - Propose TraML examples for encode small molecules using BRENDA or SMILES or other? 4) Discuss controlled vocabulary items - Only currently open issues appear to be PI/MSI related - Any additional terms needed to support metabolomics - CV Terms from Gerhard: [Term] id: MS:1001966 name: product ion mobility def: "The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry." [PSI:MS] is_a: MS:1001221 ! fragmentation information [Term] id: MS:1001967 name: product ion drift time def: "The ion drift time of an MS2 product ion." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." relationship: has_units UO:0000028 ! millisecond is_a: ??????? + Maybe not necessary??? [Term] id: MS:1001968 name: PTM scoring algorithm name def: "Name of the algorithm used for post-translational modification scoring." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details + Instead of a free text string, this should be a parent term with enumerated children. [Term] id: MS:1001969 name: PTM scoring algorithm version def: "Version of the post-translational modification scoring algorithm." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details [Term] id: MS:1001970 name: PTM scoring value def: "Score value for post-translational modification." [PSI:MS] xref: value-type:xsd\:float "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 + This needs a lot more discussion 5) MIAPE – MS - Trying to collect some final example files from Matt and Salva + We now have all the example documents for MIAPE – MS + MIAPE – MSI is now nearly ready + MIAPE – MS is ready. Will be submitted by the end of the week. 6) MIAPE – Quant - In doc process - Needs review with SRM in mind - Needs an SRM example document + Work on this in San Diego Next meeting: in person in San Diego March 12th *From:* Eric Deutsch [mailto:Eri...@sy...] *Sent:* Monday, February 27, 2012 11:47 PM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI MSS WG call reminder Hi everyone, this is a reminder about the PSI MSS WG teleconference call tomorrow, Tuesday, at the usual time. 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + Finland: 080011569 + UK: 08081095644 + USA: 1-866-832-8490 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 2) mzML status 3) TraML status 4) Discuss controlled vocabulary items 5) MIAPE – MS 6) MIAPE – Quant Next meeting: - in San Diego March 12 |
|
From: Henk v. d. T. <h.w...@uu...> - 2012-03-02 10:56:32
|
Dear workgroup, I missed Gerhard's proposal, or else I would have tried to join the WG call. I'm happy to see the quick response! I fully agree we should have an enumeration for the PTM-score name. On the other hand, if I look at the PSM scores, I see a flat list (e.g. Mascot:score). Would this be the naming convention of choice (like ProteomeDiscoverer:pRS site probability) or would the enumeration be a better way? Moreover, different scores exist (at least in Proteome Discoverer) for different things: pRS score pRS probability pRS sequence probability Site probability pRS score and pRS probability are the same thing, but site probability is specific to a modification. Can this be captured in the proposed scheme? Could this be applied to proteins as well? Thanks, Henk On 2/28/2012 5:39 PM, Eric Deutsch wrote: > > Notes from the MSS WG call 2012-02-28 > > + Present: Florian, Eric, Matt, Pierre-Alain > > Agenda: > > 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 > > - Evaluate MIAPE -- Quant for SRM specifically > > - Evaluate mzQuantML for SRM specifically and generate examples > > - Assemble guideline recommendations for the HPP > > + We will work together with Christoph's track on this > > - TraML implementations > > - Other > > 2) mzML status > > - No critical issues > + Need to add an ion mobility array? > > + It would be good to discuss at the SD meeting how to encode ion > mobility data in mzML (Wed?) > > + There seem to be several possible ways to do it. Can we settle on one? > > 3) TraML status > > - No critical issues > > - Propose TraML examples for encode small molecules using BRENDA or > SMILES or other? > > 4) Discuss controlled vocabulary items > > - Only currently open issues appear to be PI/MSI related > > - Any additional terms needed to support metabolomics > > - CV Terms from Gerhard: > > [Term] > > id: MS:1001966 > > name: product ion mobility > > def: "The mobility of an MS2 product ion, as measured by ion mobility > > mass spectrometry." [PSI:MS] > > is_a: MS:1001221 ! fragmentation information > > [Term] > > id: MS:1001967 > > name: product ion drift time > > def: "The ion drift time of an MS2 product ion." [PSI:MS] > > xref: value-type:xsd\:float "The allowed value-type for this CV term." > > relationship: has_units UO:0000028 ! millisecond > > is_a: ??????? > > + Maybe not necessary??? > > [Term] > > id: MS:1001968 > > name: PTM scoring algorithm name > > def: "Name of the algorithm used for post-translational modification > > scoring." [PSI:MS] > > xref: value-type:xsd\:string "The allowed value-type for this CV term." > > is_a: MS:1001471 ! peptide modification details > > + Instead of a free text string, this should be a parent term with > enumerated children. > > [Term] > > id: MS:1001969 > > name: PTM scoring algorithm version > > def: "Version of the post-translational modification scoring algorithm." > > [PSI:MS] > > xref: value-type:xsd\:string "The allowed value-type for this CV term." > > is_a: MS:1001471 ! peptide modification details > > [Term] > > id: MS:1001970 > > name: PTM scoring value > > def: "Score value for post-translational modification." [PSI:MS] > > xref: value-type:xsd\:float "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 > > + This needs a lot more discussion > > 5) MIAPE -- MS > > - Trying to collect some final example files from Matt and Salva > > + We now have all the example documents for MIAPE -- MS > > + MIAPE -- MSI is now nearly ready > > + MIAPE -- MS is ready. Will be submitted by the end of the week. > > 6) MIAPE -- Quant > > - In doc process > > - Needs review with SRM in mind > > - Needs an SRM example document > > + Work on this in San Diego > > Next meeting: in person in San Diego March 12^th > > *From:*Eric Deutsch [mailto:Eri...@sy... > <mailto:Eri...@sy...>] > *Sent:* Monday, February 27, 2012 11:47 PM > *To:* Mass spectrometry standard development > *Cc:* Eric Deutsch > *Subject:* PSI MSS WG call reminder > > Hi everyone, this is a reminder about the PSI MSS WG teleconference > call tomorrow, Tuesday, at the usual time. > > 08:00 San Francisco > > 11:00 New York > > 16:00 London > > 17:00 Geneva > > + Germany: 08001012079 > > + Switzerland: 0800000860 > > + Finland: 080011569 > > + UK: 08081095644 > > + USA:1-866-832-8490 > > Generic international: +44 2083222500 (UK number) > > access code: 297427 # > > Agenda: > > 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 > > 2) mzML status > > 3) TraML status > > 4) Discuss controlled vocabulary items > > 5) MIAPE -- MS > > 6) MIAPE -- Quant > > Next meeting: > > - in San Diego March 12 > -- ------------------------------------------------------------------------------------------------------- *Henk van den Toorn, bioinformatician* Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu... Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X