{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/172","repository_url":"https://api.github.com/repos/compomics/peptide-shaker","labels_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/172/labels{/name}","comments_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/172/comments","events_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/172/events","html_url":"https://github.com/compomics/peptide-shaker/issues/172","id":155957988,"number":172,"title":"mzIdentML Peptide element missing","user":{"login":"jj-umn","id":2116803,"avatar_url":"https://avatars.githubusercontent.com/u/2116803?v=3","gravatar_id":"","url":"https://api.github.com/users/jj-umn","html_url":"https://github.com/jj-umn","followers_url":"https://api.github.com/users/jj-umn/followers","following_url":"https://api.github.com/users/jj-umn/following{/other_user}","gists_url":"https://api.github.com/users/jj-umn/gists{/gist_id}","starred_url":"https://api.github.com/users/jj-umn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jj-umn/subscriptions","organizations_url":"https://api.github.com/users/jj-umn/orgs","repos_url":"https://api.github.com/users/jj-umn/repos","events_url":"https://api.github.com/users/jj-umn/events{/privacy}","received_events_url":"https://api.github.com/users/jj-umn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-05-20T13:01:31Z","updated_at":"2016-05-20T13:04:36Z","closed_at":null,"body":"I can attempt to either find the problem or I provide the data to reproduce the issue, but here's the quick synopsis:\r\n\r\nI ran across this issue reading the PeptideShaker (v1.10.2) mzIdentML with uk.ac.ebi.JmzIdentMLParser:\r\n\r\n2016-05-17 16:22:38,890 ERROR RawXMLListener - Error trying to instantiate\r\nreference resolver:\r\nuk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefResolver\r\njava.lang.IllegalStateException: Could not unmarshall refId:\r\nIMGIPEDEQMGIIR_15.99491461956-ATAA-2 for element type: class\r\nuk.ac.ebi.jmzidml.model.mzidml.Peptide\r\nat\r\nuk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractReferenceResolver.unmarshal(AbstractReferenceResolver.java:106)\r\n\r\n\r\nA quick check of the file mzid file indicates that there isn't a Peptide element for the single modification: \r\n\"IMGIPEDEQMGIIR_15.99491461956-ATAA-2\"  \r\n\r\ngrep -n 'IMGIPEDEQMGIIR' peptideAhaker.mzid\r\n835287:         <Peptide id=\"IMGIPEDEQMGIIR_15.99491461956\">\r\n1283658:                <Peptide id=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\">\r\n1606322:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_199554\" />\r\n1608661:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_201893\" />\r\n1613393:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_206625\" />\r\n1616829:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_210061\" />\r\n1625048:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_218280\" />\r\n5753689:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" calculatedMassToCharge=\"889.450872015192\" experimentalMassToCharge=\"889.452576\" chargeState=\"2\" id=\"SII_60397_1\">\r\n5798433:                                        <SpectrumIdentificationItem passThreshold=\"false\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956\" calculatedMassToCharge=\"587.9713686258787\" experimentalMassToCharge=\"587.97229\" chargeState=\"3\" id=\"SII_61181_1\">\r\n5895010:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" calculatedMassToCharge=\"889.450872015192\" experimentalMassToCharge=\"889.45282\" chargeState=\"2\" id=\"SII_62886_1\">\r\n5958747:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" calculatedMassToCharge=\"593.3030068323986\" experimentalMassToCharge=\"593.303955\" chargeState=\"3\" id=\"SII_64014_1\">\r\n6112333:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-2\" calculatedMassToCharge=\"881.453414705412\" experimentalMassToCharge=\"881.4552\" chargeState=\"2\" id=\"SII_66756_1\">\r\n"},"comment":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/comments/220599911","html_url":"https://github.com/compomics/peptide-shaker/issues/172#issuecomment-220599911","issue_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/172","id":220599911,"user":{"login":"jj-umn","id":2116803,"avatar_url":"https://avatars.githubusercontent.com/u/2116803?v=3","gravatar_id":"","url":"https://api.github.com/users/jj-umn","html_url":"https://github.com/jj-umn","followers_url":"https://api.github.com/users/jj-umn/followers","following_url":"https://api.github.com/users/jj-umn/following{/other_user}","gists_url":"https://api.github.com/users/jj-umn/gists{/gist_id}","starred_url":"https://api.github.com/users/jj-umn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jj-umn/subscriptions","organizations_url":"https://api.github.com/users/jj-umn/orgs","repos_url":"https://api.github.com/users/jj-umn/repos","events_url":"https://api.github.com/users/jj-umn/events{/privacy}","received_events_url":"https://api.github.com/users/jj-umn/received_events","type":"User","site_admin":false},"created_at":"2016-05-20T13:04:36Z","updated_at":"2016-05-20T13:04:36Z","body":"`835287:         <Peptide id=\"IMGIPEDEQMGIIR_15.99491461956\">\r\n1283658:                <Peptide id=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\">\r\n1606322:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_199554\" />\r\n1608661:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_201893\" />\r\n1613393:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_206625\" />\r\n1616829:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_210061\" />\r\n1625048:                <PeptideEvidence isDecoy=\"false\" pre=\"R\" post=\"V\" start=\"328\" end=\"341\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-2\" dBSequence_ref=\"Q8VDD5\" id=\"PepEv_218280\" />\r\n5753689:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" calculatedMassToCharge=\"889.450872015192\" experimentalMassToCharge=\"889.452576\" chargeState=\"2\" id=\"SII_60397_1\">\r\n5798433:                                        <SpectrumIdentificationItem passThreshold=\"false\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956\" calculatedMassToCharge=\"587.9713686258787\" experimentalMassToCharge=\"587.97229\" chargeState=\"3\" id=\"SII_61181_1\">\r\n5895010:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" calculatedMassToCharge=\"889.450872015192\" experimentalMassToCharge=\"889.45282\" chargeState=\"2\" id=\"SII_62886_1\">\r\n5958747:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-10_15.99491461956-ATAA-2\" calculatedMassToCharge=\"593.3030068323986\" experimentalMassToCharge=\"593.303955\" chargeState=\"3\" id=\"SII_64014_1\">\r\n6112333:                                        <SpectrumIdentificationItem passThreshold=\"true\" rank=\"1\" peptide_ref=\"IMGIPEDEQMGIIR_15.99491461956-ATAA-2\" calculatedMassToCharge=\"881.453414705412\" experimentalMassToCharge=\"881.4552\" chargeState=\"2\" id=\"SII_66756_1\">\r\n`"}}
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