Export mzIdentML

A data analysis pipeline for shotgun mass-spectrometry proteomics.

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#35 Export mzIdentML

Milestone: Oxford

Status: accepted

Owner: Phil Charles

Labels: Feature Request (11) Export (3) Bug (24)

Updated: 2014-10-23

Created: 2014-01-16

Creator: David Trudgian

Private: No

CPFP should be able to export at least rudimentary mzIdenML that can be imported into downstream analysis packages. Should be able to include SINQ output that's not in the pepXML/protXML that can be downloaded. This could also allow pepXML and protXML intermediate files to be dumped when a submission is archived.

Some relevant examples at: http://www.psidev.info/mzidentml

Discussion

David Trudgian - 2014-04-09

Hacked together some code to get mzIdentML from searches (not MSS yet) that will import into Scaffold perSPECtives. Will push when tidied up - embarrassingly ugly and some failure cases at the moment.

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David Trudgian - 2014-08-14

Good enough for UTSW purposes as of [d825cf]

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Commit: [d825cf]

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David Trudgian - 2014-08-14

status: accepted --> closed
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Phil Charles - 2014-10-23

labels: Feature Request, Export --> Feature Request, Export, Bug

status: closed --> accepted

assigned_to: David Trudgian --> Phil Charles

Milestone: UTSW --> Oxford
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Phil Charles - 2014-10-23

Some issues remain for generating strictly valid markup (a problem for PRIDE submissions since they won't accept it if it doesn't pass the validator without any errors).

Partially addressed by [6b0666] but still some issues remaining. N-terminal modifications not handled properly, and there are a couple of missing CV elements. 1.1.0 spec documentation is a bit unclear, waiting for feedback from PRIDE support.

Related

Commit: [6b0666]

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