Menu
▾
▴
psidev-pi-dev
|
From: <cod...@go...> - 2008-11-20 12:21:44
|
Issue 44: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Comment #1 by andrewrobertjones: I don't think we have examples of immonium or other internal ions using the fragmentation ion structure, where the indexes are pairs representing start and end points of ions rather than integer indexes. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-28 15:02:20
|
Comment #2 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 (I've put this response to: http://code.google.com/p/psi-pi/issues/detail?id=42#c44 into issue 44 because it's more of an instance doc issue.) Looking at the instance doc: http://code.google.com/p/psi-pi/source/browse/trunk/examples/MPC_example.axml It's not really clear what : <SourceFile id="SF1" location="proteinscape://.... is pointing to because there is no <pf:fileFormat>. I presume that this is some sort of relational database? Maybe you do want to add a description for the format under PI:00040 ! source file format I guess that we used the term SourceFile because in most cases the "thing" that is used to create the analysisXML instance document will be another file. Maybe SourceData would be a more generic name. <SpectraData id="LCMALDI_spectra" location="proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X"/> What does this point to? From the example under svn, looks as though this in an mgf file (even though that may be stored in a RDB). -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-12-01 17:58:23
|
Comment #3 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Move rank from being a CV item to an attribute Remove: id: PI:00327 name: peptide rank id: PI:00216 name: sequest:PeptideRank -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-05 11:02:18
|
Comment #4 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Need to show how chemical and post translational modifications are handled with the 15N example. (DC) -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-05 11:10:25
|
Comment #5 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Report the type of the decoy: reverse, shuffled, concatenated … Add this to the instance examples. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-05 11:14:26
|
Comment #6 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 No examples of how mzIdentML is tied with mzML. DC to provide one. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-05 11:18:23
|
Comment #7 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Add an example of <pf:components> is used -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-05 11:22:23
|
Comment #8 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Add an example of Element<Modification>, Substitution modification. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-05 11:26:27
|
Comment #9 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Element <DatabaseFilters> Include an example of an exclude value. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-20 11:02:59
|
Comment #10 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding Comment #9: The Mascot_N15_example.mzid search was against all "Arabidopsis" excluding "Arabidopsis neglecta": <DatabaseFilters> <Filter> <FilterType> <pf:cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS" /> </FilterType> <Include> <pf:cvParam accession="NCBI:3701" name="Arabidopsis" cvRef="NCBI-TAXONOMY" /> </Include> <Exclude> <pf:cvParam accession="NCBI:45251" name="Arabidopsis neglecta" cvRef="NCBI-TAXONOMY" /> </Exclude> </Filter> </DatabaseFilters> -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-20 14:46:22
|
Comment #11 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment #6. An example is now provided here: http://code.google.com/p/psi-pi/source/browse/trunk/examples/Mascot_mzml_example.mzid This is a search of small.pwiz.1.1.mzML which is referenced from here: http://psidev.info/index.php?q=node/257 The example shows how the results can be tracked back to the raw data using the nativeID. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-05-20 15:01:26
|
Comment #12 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment#8. Example now included in Mascot N15 example Doesn't use the residues attribute. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-10 15:23:43
|
Comment #13 on issue 44 by andrewrobertjones: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Re-opening this issue: We don't currently have an example for MS:1001089 and MS:1001090 and they are not well defined. [Term] id: MS:1001089 name: protein taxonomy def: "The taxonomy of the resultant protein from the search." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001085 ! protein result details [Term] id: MS:1001090 name: taxonomy nomenclature def: "The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI] is_a: MS:1001089 ! protein taxonomy This seems a little unwieldy to me. How about just having different CV for each type of ID. For example <DBSequence id="x" length="449" SearchDatabase_ref="y" accession="z" > <seq>MGKEKFHINIVVIGHVDSGKSTTTGHLIY...</seq> <pf:cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS" value="Elongation factor..." /> <pf:cvParam accession="MS:xxxxxx1" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="9606" /> <pf:cvParam accession="MS:xxxxxx2" name="taxonomy: common name" cvRef="PSI-MS" value="human" /> <pf:cvParam accession="MS:xxxxxx3" name="taxonomy: scientific name" cvRef="PSI-MS" value="Homo sapiens" /> <pf:cvParam accession="MS:xxxxxx4" name="taxonomy: Swiss-Prot ID" cvRef="PSI-MS" value="HUMAN" /> </DBSequence> -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-12 17:05:38
|
Comment #14 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment #13 - the Mascot examples now include taxonomy information for protein sequences -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 10:23:42
|
Comment #16 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 None of the examples seem to include missedCleavages in <PeptideEvidence>. Added to Mascot examples. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 10:24:37
|
Comment #15 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment #7: Add an example of how <components> are used. Fixed in Mascot_N15_example.mzid -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-24 17:45:28
|
Comment #17 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 None of the examples include a BibliographicReference - added to the PMF_example.mzid -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-26 14:31:47
|
Updates: Labels: Milestone-Release1.0 Comment #18 on issue 44 by eisenachM: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Just to check for correct use: The MPC example uses a decoy DB derived from a IPI_human DB. As DatabaseName the cvParam "IPI_human" (without "_decoy" as part of the name) and as further CVParams the decoy type and generation details are described. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-30 14:50:07
|
Comment #19 on issue 44 by patri...@matrixscience.com: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Could we have an example with a modification with a neutral loss defined? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-07-08 16:57:06
|
Comment #20 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 The Mascot_MSMS_example.mzid file now has an example of manual validation: <ProteinDetectionHypothesis id="PDH_HSP71_RAT" DBSequence_ref="DBSeq_HSP71_RAT" passThreshold="false"> <PeptideHypothesis PeptideEvidence_Ref="PE_2_1_HSP71_RAT" /> <cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS" value="40.95" /> <cvParam accession="MS:1001093" name="sequence coverage" cvRef="PSI-MS" value="2" /> <cvParam accession="MS:1001097" name="distinct peptide sequences" cvRef="PSI-MS" value="1" /> <cvParam accession="MS:1001125" name="manual validation" cvRef="PSI-MS" value="Manually rejected this protein for no particular reason. (Example of manual validation for mzIdentML)" /> </ProteinDetectionHypothesis> -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-07-09 08:24:08
|
Comment #21 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment 19: Could we have an example with a modification with a neutral loss defined? The Mascot 15N example specifies Oxidation, and this can have a neutral loss of: <umod:NeutralLoss avge_mass="64.1069" composition="H(4) C O S" flag="false" mono_mass="63.998285"> Unfortunately, this seems to get lost in the conversion of the unimod.xml to unimod.obo file, so this needs to be fixed. (Please, Martin!) We should probably also specify, for each peptide match, which neutral loss, if any, was 'dominant' and/or used for scoring. Two pieces of information are required: The position and the loss, and there can of course be multiple neutral losses. For an example sequence of ALNVMESK, we'd want to specify that it is residue 5, and the loss is 63.998285 There are 3 possible places for CV terms for this: 1. <Peptide id="peptide_21_1"> <peptideSequence>ALNVMESK</peptideSequence> <Modification location="5" residues="M" monoisotopicMassDelta="15.994919"> <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" /> ---> <cpParam accession="MS:1001xxx" name="neutral loss" cvRef="PSI-MS" value="63.998285" /> </Modification> </Peptide> 2. Or, it could be with other cv terms directly under: <SpectrumIdentificationItem id="SII_21_1" But to cope with multiple pairs of values, this would require a structure similar to the one under <Peptide> and therefore a change to the schema 3. In the fragment arrays (remember it's the 5th residue that is methionine): <SpectrumIdentificationItem id="SII_21_1" <Fragmentation> <IonType index="1 2 3 4 5" charge="1"> <cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b ion"/> <FragmentArray values="72.09201 185.11602 299.24156 398.31937 481.32147 " Measure_ref="m_mz"/> <FragmentArray values="1.217 0.5765 0.9995 0.3048 0.6491" Measure_ref="m_intensity"/> <FragmentArray values="0.0476 -0.0124 0.0702 0.0796 0.0446" Measure_ref="m_error"/> ---> <FragmentArray values="0, 0, 0, 0, 63.998285" Measure_ref="m_neutral_loss"/> </IonType> And we'd also need to define m_neutral_loss: <AnalysisData> <SpectrumIdentificationList id="SIL_1" numSequencesSearched="4944"> <FragmentationTable> <Measure id="m_m_neutral_loss"> ---> <cvParam cvRef="PSI-MS" accession="MS:100xxxx" name="product ion neutral loss"/> </Measure> I propose #3 - anyone disagree? Perhaps we can discuss at the telecon. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-07-09 08:51:23
|
Comment #22 on issue 44 by andrewrobertjones: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 My preference would be to treat a neutral loss as any other modification and go with option 1. Is there some information that would be lost by encoding it in this way? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-07-09 11:32:18
|
Comment #23 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 No, I don't think anything is lost. It's more that the <Peptide> is just about the peptide sequence and any modified residues rather than about how it fragmented. However, it's obviously simpler to use option #1. Both options just require one new CV term. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-07-09 11:36:32
|
Comment #24 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Need to change: <cv id="UNIMOD" URI="http://www.unimod.org/xml/unimod.xml"> to <cv id="UNIMOD" URI="http://www.unimod.org/obo/unimod.obo"> (Done for all Mascot examples) -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-07-09 18:11:15
|
Comment #25 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment 21. We agreed at telecon to keep it simple and go for approach number 1, with the option of *additionally* using approach #3 for more complex cases. Changes made to Mascot examples which use MS:1000336" name="neutral loss" -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
×
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