From: Harald B. <Har...@ui...> - 2016-04-20 16:59:49
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Hi all, Some additional comments after checking the PeptideShaker mzid 1.2 example file with the current validator: 1) At the meeting we agreed to remove the value requirement from the following MS:1001221 (fragmentation information) child terms: - MS:1001226 (product ion intensity) - MS:1002225 (average product ion intensity) - MS:1002226 (product ion intensity standard deviation) - MS:1000904 (product ion m/z delta) The reason being that these terms are used as to describe the data type in mzid files as part of the FragmentationTable element and can thus have no value in this setup. 2) MS:1002404 (count of identified proteins) is _not_ a child of MS:1001184 (search statistics)? Should it not be? 3) MS:1002567 (phosphoRS score threshold) and MS:1002557 (D-Score threshold) ought to be anticipated terms under Threshold under SpectrumIdentificationProtocol? 4) MS:1002497 (group PSMs by sequence with modifications) (and the other new related terms) ought to be anticipated terms under AdditionalSearchParams? 5) MS:1000894 (retention time) ought to be anticipated terms under SpectrumIdentificationResult? 6) MS:1002471, MS:1002470 and MS:1002542 ought to be anticipated terms under ProteinAmbiguityGroup? 7) What is the intended use of MS:1001239 (frag: immonium ion)? How can this be used to annotate immonium ions on specific amino acids? Here's what we currently do using the outdated PRIDE CV terms: <IonType charge="1" index="4 5"> <FragmentArray measure_ref="Measure_MZ" values="120.0808411"/> <FragmentArray measure_ref="Measure_Int" values="14483.125"/> <FragmentArray measure_ref="Measure_Error" values="6.53397579810644E-5"/> <cvParam cvRef="PRIDE" accession="PRIDE:0000244" name="immonium F"/> </IonType> How would the same be done with MS:1001239 (frag: immonium ion)? 8) Why is the following not allowed? "MS:1001969" name="phosphoRS score" value="1:1.0468246849444967E-8:4:false" Is scientific annotation not supported? Full error: "The regular expression in SpectrumIdentificationItem (id='SII_4070_1') element at /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem/cvParam ('phosphoRS score') is not valid." 9) It seems to be mandatory to add MS:1002507 (modification rescoring:false localization rate) (or any of its child terms, of which there are none btw) when including MS:1002491 (modification localization scoring) in the AdditionalSearchParams list. This means that terms such as MS:1001969 (phosphoRS score), MS:1002536 (D-Score), MS:1002550 (peptide:phosphoRS score and MS:1002553 (peptide:D-Score) (and others) cannot be used for the PTM rescoring. I think that either these terms have to be children of MS:1002507 (modification rescoring:false localization rate) or the mandatory term when using modification rescoring ought to be MS:1002505 (regular expression for modification localization scoring) or one of its children? Best regards, Harald Den 2016-04-20 13:46, skrev Jones, Andy: > Hi all, > > Various items from the sessions this morning in Gent: > > 1. mzid 1.2 validator not easy to locate on GitHub - Gerhard, are you > able to make this prominently available as a build under a "Downloads" > webpage on Githut. Apparently, it is fairly easy to build end user > web-pages on GitHub - Tobias has experience of this. > > 2. There are various bugs in the validator - if you have identified > one, please make sure to email it to Gerhard to fix > > 3. Eric has taken an action item to do some CV tidying, particularly > around scores for PSMs, PTM, peptides, proteins and protein groups > > 4. We need ~11 new CV terms, as detailed in Table 2 of the spec doc > (just pushed to GitHub) for combined spectra as input to searches > > 5. Term MS:102499 peptide level score should be deprecated as this > was never intended to go in the CV - Gerhard, can you do this please > > 6. Terms starting "group PSMs by..." are under the wrong parent. They > should be under a new parent term called "identification parameters", > and a new link added to the mapping file for > "AdditionalSearchParameters" allowing the child terms of this term to > be used i.e. these terms are intended to be used in this part of the > Protocol. > > 7. These terms: de novo, proteogenomics spectral need an extra parent > term: special processing (MS:1002489), so they trigger special > behaviour of the validator. > > Please add to this list with things I missed, > best wishes > Andy > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly > and > reduces your MTTR. 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