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From: Mathias W. <not...@gi...> - 2016-04-28 12:33:46
|
@wbittremieux I will merge now, as restructuring is complete now. Old stuff is in legacy folder. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/20#issuecomment-215409477 |
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From: Mathias W. <not...@gi...> - 2016-04-28 12:30:03
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based on M. Eisenacher's table from PSI-Meeting. collect metrics, describe them You can view, comment on, or merge this pull request online at: https://github.com/HUPO-PSI/qcML-development/pull/21 -- Commit Summary -- * restructuring: moved old parts of development to legacy folder, created specification_document folder and version specific folders in schema, moved those schema files there with examples and images * added schema with changes reflecting the discussions at PSI spring meeting Ghent 2016 with generated example instance * added README.md and a qc-metric-collection * Update README.md * replaced special characters < > -- File Changes -- A cv/README.md (21) A cv/qc-metric-collection.md (65) R legacy/pipelines/KNIME Metanodes/Metanode id_ratio.zip (0) R legacy/pipelines/KNIME Metanodes/Metanode mass_accuracy.zip (0) R legacy/pipelines/KNIME Metanodes/Metanode peptide_featurespace.zip (0) R legacy/pipelines/KNIME Metanodes/Metanode tic_plot.zip (0) R legacy/pipelines/detailed QC workflow.zip (0) R legacy/pipelines/simple QC workflow.zip (0) R legacy/qcdb/converters/qcml2qcdb.py (0) R legacy/qcdb/schema/MzQuality_Object_model.png (0) R legacy/qcdb/schema/le_er_model_sqlite.sql (0) R legacy/qcdb/schema/qcDB_er_model.png (0) R legacy/website-images/Alternate qcml implementation zoo.png (0) R legacy/website-images/check_file_inputs.jpg (0) R legacy/website-images/detailed_workflow_extractATgkn.png (0) R legacy/website-images/detailed_workflow_extractATopenms.png (0) R legacy/website-images/detailed_workflow_extractQPxml.png (0) R legacy/website-images/detailed_workflow_fractionalmasses.png (0) R legacy/website-images/detailed_workflow_idratio.png (0) R legacy/website-images/detailed_workflow_massaccuracy.png (0) R legacy/website-images/detailed_workflow_openreport.png (0) R legacy/website-images/detailed_workflow_overview.png (0) R legacy/website-images/detailed_workflow_preprocessing.png (0) R legacy/website-images/detailed_workflow_pt1.png (0) R legacy/website-images/detailed_workflow_pt2.png (0) R legacy/website-images/detailed_workflow_pt3.png (0) R legacy/website-images/detailed_workflow_pt4.png (0) R legacy/website-images/detailed_workflow_pt5.png (0) R legacy/website-images/detailed_workflow_tic.png (0) R legacy/website-images/import_knime_workflow.jpg (0) R legacy/website-images/import_knime_workflow_2.jpg (0) R legacy/website-images/knimeinstallmenu1.png (0) R legacy/website-images/knimeinstallmenu2.png (0) R legacy/website-images/primexs.png (0) R legacy/website-images/qc_workflow_knime.png (0) R legacy/website-images/qc_workflow_knime_pt1.png (0) R legacy/website-images/qc_workflow_knime_pt2.png (0) R legacy/website-images/qc_workflow_knime_pt3.png (0) R legacy/website-images/qc_workflow_knime_pt4.png (0) R legacy/website-images/qc_workflow_knime_pt5.png (0) R legacy/website-images/qc_workflow_knime_pt6.png (0) R legacy/website-images/qc_workflow_knime_pt7.png (0) R legacy/website-images/qcml_illusrt.png (0) R schema/old/example/input/additional_tabular_data.csv (0) R schema/old/example/input/additional_tabular_mapping.csv (0) R schema/old/example/input/ecoli.fasta (0) R schema/old/example/input/theoretical_masses.txt (0) R schema/old/example/plots/accuracy.png (0) R schema/old/example/plots/spec.png (0) R schema/old/example/plots/theoretical_masses_vs_features.png (0) R schema/old/example/plots/tic.png (0) R schema/old/example/qcML_examlple.xml (0) R schema/old/example/qcML_manual_examlple.xml (0) R schema/old/example/report.pdf (0) R schema/old/example/tables/20100219_SvNa_SA_Ecoli_QCCalculator.tsv_id.tsv (0) R schema/v0_0_5/mzQCML_0.0.5.png (0) R schema/v0_0_5/mzQCML_0_0_5.xsd (0) R schema/v0_0_6/examples/samplefile_0_0_6.qcML (0) R schema/v0_0_6/mzQCML_0.0.6.png (0) R schema/v0_0_6/mzQCML_0_0_6.xsd (0) R schema/v0_0_7/examples/samplefile_0_0_7.qcML (0) R schema/v0_0_7/qcML_0.0.7.xsd (0) R schema/v0_0_8/examples/samplefile_0_0_8.qcML (0) R schema/v0_0_8/images/qcml_at.png (0) R schema/v0_0_8/images/qcml_cvlist.png (0) R schema/v0_0_8/images/qcml_qp.png (0) R schema/v0_0_8/images/qcml_root.png (0) R schema/v0_0_8/qcML_0.0.8.xsd (0) A schema/v0_0_9/examples/qcML_0_0_9_instance1.xml (33) A schema/v0_0_9/qcML_0_0_9.xsd (288) -- Patch Links -- https://github.com/HUPO-PSI/qcML-development/pull/21.patch https://github.com/HUPO-PSI/qcML-development/pull/21.diff --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/21 |
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From: andrewrobertjones <not...@gi...> - 2016-04-28 11:39:30
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@smdb21 In this case, you can still represent the final results in a single file, you just have to combine the results into a single SIList -where each SIResult is unique. This makes it easier to work out what is being claimed to have been identified. If the lists are kept separate (in one file with 2 lists) or 2 files (with one list), a reader might double count the number of spectra queried (and possibly over count PSMs), or would need its own logic for combining the same spectrum in different list - which would probably not exist. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/5#issuecomment-215397897 |
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From: Juan A. V. <not...@gi...> - 2016-04-28 09:53:57
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We can then change the specification document to version 1.0.1 (I guess is this needed) to change the phrasing of that paragraph that you mention. Also the change should be highlighted somewhere else in the specification document in a section called "Changes from version 1.0" or similar. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzTab/issues/20#issuecomment-215372537 |
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From: Yasset Perez-R. <not...@gi...> - 2016-04-28 08:30:15
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@jgriss @javizca We should leave it at it is now. The only problem is that schema should respond to this or at least reflect that. I agree that we MUST report only the interesting proteins in mztab and leave in mzidentml the rest. However, I guess the part I highlighted in the specification MUST be changed to reflect that. For example, I have this Mascot mztab file prototype which is completely mztab compliant: https://github.com/PRIDE-Toolsuite/inspector-example-files/tree/master/mztab They produce a valid file but not the one RECOMMENDED one. It is difficult to implement a parser or reader that can realize about this change. Then, my suggestion is that we change in the specification (which looks like a simple change but will make more consistent the file format): Current version: Page 14 > It is RECOMMENDED that “subset proteins” that are unlikely to have been identified SHOULD NOT be reported here. Change to: > The “subset proteins” that are unlikely to have been identified MUST NOT be reported here as individual protein rows. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzTab/issues/20#issuecomment-215351431 |
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From: Johannes G. <not...@gi...> - 2016-04-28 07:56:12
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I second @javizca suggestion. Keep it simple as it is and add a proper section ones it's needed. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzTab/issues/20#issuecomment-215340007 |
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From: Mathias W. <not...@gi...> - 2016-04-27 19:28:24
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You can view, comment on, or merge this pull request online at: https://github.com/HUPO-PSI/qcML-development/pull/20 -- Commit Summary -- * restructuring: moved old parts of development to legacy folder, created specification_document folder and version specific folders in schema, moved those schema files there with examples and images * added schema with changes reflecting the discussions at PSI spring meeting Ghent 2016 with generated example instance -- File Changes -- R legacy/pipelines/KNIME Metanodes/Metanode id_ratio.zip (0) R legacy/pipelines/KNIME Metanodes/Metanode mass_accuracy.zip (0) R legacy/pipelines/KNIME Metanodes/Metanode peptide_featurespace.zip (0) R legacy/pipelines/KNIME Metanodes/Metanode tic_plot.zip (0) R legacy/pipelines/detailed QC workflow.zip (0) R legacy/pipelines/simple QC workflow.zip (0) R legacy/qcdb/converters/qcml2qcdb.py (0) R legacy/qcdb/schema/MzQuality_Object_model.png (0) R legacy/qcdb/schema/le_er_model_sqlite.sql (0) R legacy/qcdb/schema/qcDB_er_model.png (0) R legacy/website-images/Alternate qcml implementation zoo.png (0) R legacy/website-images/check_file_inputs.jpg (0) R legacy/website-images/detailed_workflow_extractATgkn.png (0) R legacy/website-images/detailed_workflow_extractATopenms.png (0) R legacy/website-images/detailed_workflow_extractQPxml.png (0) R legacy/website-images/detailed_workflow_fractionalmasses.png (0) R legacy/website-images/detailed_workflow_idratio.png (0) R legacy/website-images/detailed_workflow_massaccuracy.png (0) R legacy/website-images/detailed_workflow_openreport.png (0) R legacy/website-images/detailed_workflow_overview.png (0) R legacy/website-images/detailed_workflow_preprocessing.png (0) R legacy/website-images/detailed_workflow_pt1.png (0) R legacy/website-images/detailed_workflow_pt2.png (0) R legacy/website-images/detailed_workflow_pt3.png (0) R legacy/website-images/detailed_workflow_pt4.png (0) R legacy/website-images/detailed_workflow_pt5.png (0) R legacy/website-images/detailed_workflow_tic.png (0) R legacy/website-images/import_knime_workflow.jpg (0) R legacy/website-images/import_knime_workflow_2.jpg (0) R legacy/website-images/knimeinstallmenu1.png (0) R legacy/website-images/knimeinstallmenu2.png (0) R legacy/website-images/primexs.png (0) R legacy/website-images/qc_workflow_knime.png (0) R legacy/website-images/qc_workflow_knime_pt1.png (0) R legacy/website-images/qc_workflow_knime_pt2.png (0) R legacy/website-images/qc_workflow_knime_pt3.png (0) R legacy/website-images/qc_workflow_knime_pt4.png (0) R legacy/website-images/qc_workflow_knime_pt5.png (0) R legacy/website-images/qc_workflow_knime_pt6.png (0) R legacy/website-images/qc_workflow_knime_pt7.png (0) R legacy/website-images/qcml_illusrt.png (0) R schema/old/example/input/additional_tabular_data.csv (0) R schema/old/example/input/additional_tabular_mapping.csv (0) R schema/old/example/input/ecoli.fasta (0) R schema/old/example/input/theoretical_masses.txt (0) R schema/old/example/plots/accuracy.png (0) R schema/old/example/plots/spec.png (0) R schema/old/example/plots/theoretical_masses_vs_features.png (0) R schema/old/example/plots/tic.png (0) R schema/old/example/qcML_examlple.xml (0) R schema/old/example/qcML_manual_examlple.xml (0) R schema/old/example/report.pdf (0) R schema/old/example/tables/20100219_SvNa_SA_Ecoli_QCCalculator.tsv_id.tsv (0) R schema/v0_0_5/mzQCML_0.0.5.png (0) R schema/v0_0_5/mzQCML_0_0_5.xsd (0) R schema/v0_0_6/examples/samplefile_0_0_6.qcML (0) R schema/v0_0_6/mzQCML_0.0.6.png (0) R schema/v0_0_6/mzQCML_0_0_6.xsd (0) R schema/v0_0_7/examples/samplefile_0_0_7.qcML (0) R schema/v0_0_7/qcML_0.0.7.xsd (0) R schema/v0_0_8/examples/samplefile_0_0_8.qcML (0) R schema/v0_0_8/images/qcml_at.png (0) R schema/v0_0_8/images/qcml_cvlist.png (0) R schema/v0_0_8/images/qcml_qp.png (0) R schema/v0_0_8/images/qcml_root.png (0) R schema/v0_0_8/qcML_0.0.8.xsd (0) A schema/v0_0_9/examples/qcML_0_0_9_instance1.xml (33) A schema/v0_0_9/qcML_0_0_9.xsd (288) -- Patch Links -- https://github.com/HUPO-PSI/qcML-development/pull/20.patch https://github.com/HUPO-PSI/qcML-development/pull/20.diff --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/20 |
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From: Salvador M. de B. <not...@gi...> - 2016-04-27 17:31:31
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I am not sure about this change. I think is quite common to have more than one search over the same dataset (same spectra), using different parameters (such as HEAVY fixed masses, or PTM search) and then to apply an statistical validation over all of them, resulting in a single protein and peptide list, which means a single resulting file. In this case there is not final PSM list, all of them are final. The final protein list will contain PSMs from all of these searches. So I don't see the reason in this case to have to split into several mzIdentML files. What do you think? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/5#issuecomment-215161856 |
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From: Lutz F. <not...@gi...> - 2016-04-27 17:14:28
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Some points for thought about Cross-linking site localisation * Is a psm/peptide-level site localisation enough * the actual residue pair (as in residue 255 of protein a is linked to residue 136 of protein2) might have different site-localisation probability then the links on each supporting psm. * e.g. applying occams razor and ignoring site localisation on PSM level beyond the simple "it could be this or that"). if we want to store both level of information we could duplicate the peptide-level scores for a protein level score on each PSM, or store these as a list of cvParams on each protein. We could also require, that only one of these cases are permitted to be stored and then we could just go with what we have - at least i think it would do. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/2#issuecomment-215153744 |
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From: Mathias W. <not...@gi...> - 2016-04-27 17:13:34
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Merged #19. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/19#event-643201438 |
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From: Mathias W. <not...@gi...> - 2016-04-27 17:12:34
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Merged #15. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/15#event-643200204 |
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From: Lutz F. <not...@gi...> - 2016-04-27 16:07:10
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I uploaded a initial list of cross-linker. Several points I would make: * Having a all site specificities as a list in on field seems to me the more future proof then having one filed per site and then adding new fields if somebody wants to express something else then dimeric cross-linker * having a field that denotes just the number of reactive sites on a cross-linker * less discussion about how we call what. * how do we treat ms-cleavable cross-linker (e.g. DSSO) * do we store the cross-link product or the identified modifications? * possibly both and link them up? * We have separate entries for the cross-linker and cross-linker with one site e.g. hydrolized * do we somehow flag these up as belonging together? * We have a field "Reference" currently mostly with thermo links * I would prefer something less specific to a company e.g. a publication describing/using the cross-linker * who looks up the paper? * what is the minimum requirement we want for adding something to the list? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/2#issuecomment-215132904 |
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From: Mathias W. <not...@gi...> - 2016-04-27 15:48:40
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## Legacy release 0.0.8 This is the release previous to PSI-QC working group restructurings. Summary: * Status after google code migration * Includes obo schema, examples and schema * Workflows are for KNIME <= 2.x , OpenMS >= 2.0 * old gcode website images --- You are receiving this because you are subscribed to this thread. View it on GitHub: https://github.com/HUPO-PSI/qcML-development/releases/tag/v.0.0.8 |
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From: Gerhard M. <not...@gi...> - 2016-04-27 15:04:53
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Resolved --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/10#issuecomment-215112872 |
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From: Gerhard M. <not...@gi...> - 2016-04-27 15:04:52
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Closed #10. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/10#event-643026520 |
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From: Gerhard M. <not...@gi...> - 2016-04-27 14:32:46
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Should be fixed now. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/6#issuecomment-215102581 |
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From: Gerhard M. <not...@gi...> - 2016-04-27 14:32:46
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Closed #6. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/6#event-642979642 |
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From: Gerhard M. <not...@gi...> - 2016-04-27 14:31:58
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Should be fixed now. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/6#issuecomment-215102334 |
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From: Eric D. <ede...@sy...> - 2016-04-27 14:27:22
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Thanks, Gerhard!
Although I didn’t make it explicit in my earlier message, I think these two
terms need the same units as 1226:
[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified
spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity
[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity
*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Wednesday, April 27, 2016 4:50 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] Version 3.86.1 of psi-ms.obo
Dear proteomics community,
attached there's the new version 3.86.1 of the psi-ms.obo file.
Changed CV terms in version 3.86.1 of psi-ms.obo:
=================================================
************ Added units again to the terms MS:10000904 and MS:1001226
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000040 ! m/z
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector 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
************ Added value type to all child terms of MS:1002646 ! native
spectrum identifier format, combined spectra
to allow specification of the comma separated list of spectra
************ Changed regular expression of term MS:1002505
************ to allow scientific notation of the modification localization
score
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def:
"([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]+:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})"
[PSI:PI]
is_a: MS:1002479 ! regular expression
Best Regards,
Gerhard
--
*--*
*Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER*
*PhD student*
*Medizinisches Proteom-Center*
*DEPARTMENT Medical Bioinformatics*
*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
*E-mail *ger...@ru...
www.medizinisches-proteom-center.de
|
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From: mayerg97 <ger...@ru...> - 2016-04-27 11:49:54
|
Dear proteomics community,
attached there's the new version 3.86.1 of the psi-ms.obo file.
Changed CV terms in version 3.86.1 of psi-ms.obo:
=================================================
************ Added units again to the terms MS:10000904 and MS:1001226
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000040 ! m/z
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector 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
************ Added value type to all child terms of MS:1002646 ! native
spectrum identifier format, combined spectra
to allow specification of the comma separated list of spectra
************ Changed regular expression of term MS:1002505
************ to allow scientific notation of the modification
localization score
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def:
"([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]+:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})"
[PSI:PI]
is_a: MS:1002479 ! regular expression
Best Regards,
Gerhard
--
*--*
*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
*PhD student*
*Medizinisches Proteom-Center*
*DEPARTMENT Medical Bioinformatics*
*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
*E-mail***ger...@ru... <mailto:ger...@ru...>
www.medizinisches-proteom-center.de
<http://www.medizinisches-proteom-center.de/>
|
|
From: Juri R. <jur...@ed...> - 2016-04-27 09:36:14
|
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
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From: Jones, A. <And...@li...> - 2016-04-27 09:22:35
|
Hi all, This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1 The main topic for discussion will be encoding cross-linking in mzIdentML 1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here: https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open issues around cross-linking by tomorrow. The current version of the specifications are here (rather long I’m afraid) along with a powerpoint explaining the encodings for new features: https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2 If Lutz is able to create a CV file for reagents before the call, we will also post that online for discussions. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 19 April 2016 15:56 To: tobias <to...@eb...> Cc: eug...@tu...; le...@im...; sul...@ug...; ju...@ed...; eli...@ug...; Lutz Fischer <lfi...@st...>; Robert Chalkley <cha...@cg...>; Juan Antonio Vizcaino <ju...@eb...>; Yasset Perez-Riverol <yp...@eb...>; psi...@li... Subject: Cross-linking discussions at PSI meeting Hi all, This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list. The major outcomes from today are as follows: 1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info. 2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format) 3. Some additions to mzid 1.2 to cover: - cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism) - Adding protein-level interaction evidence - Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity 4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2 5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship 6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper. I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look. ACTION items: - We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec - Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub) - Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered - Andy to continue cleaning and updating specification document I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it. best wishes Andy |
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From: Juan A. V. <not...@gi...> - 2016-04-27 08:50:14
|
Do we need to consider at all that a zero-based coordinate system in used in Bed and BAM files, but not in GFF3/GTF files? I guess it is good to assume that we will use a zero-based coordinate system by default. This should be written in the specification document. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-215014952 |
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From: Juan A. V. <not...@gi...> - 2016-04-27 08:40:05
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About the concatenated searches, this is not a unique case for proteogenomics. People can make the same (e.g. organisms that don't have a complete genome sequences, and sequences are merged together from different sources). I don't know if this case was explained before in detail in the specification document, but whatever is decided for proteogenomics should be applicable to these cases as well. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-215012253 |
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From: Juan A. V. <not...@gi...> - 2016-04-27 08:33:44
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Maybe it is worth checking the PSI-MS CV first, to see if these scores are already there. I know that at least some work has already been done in this context there. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/2#issuecomment-215010953 |
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