The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

Molecular & Cellular Proteomics : MCP
Juan Antonio VizcaínoAndrew R Jones

Abstract

The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012-capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well-supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (1) scores associated with localization of modifications on peptides; (2) statistics performed at the level of peptides; (3) identification of cross-linked peptides; and (4) support for proteogenomics approaches. In addition, there is now improved support for the encoding of de novo sequencing of peptides, spectral library searches, and protein inference. As a key point, the underlying XML schema has only undergone very minor modifications to simplify as much as possible the transition from version 1.1 to version 1.2 for implementers, but there have been several notable updates to the format specification, implementation guidelines, controlled vocabularies and validation software. mzIdentML 1...Continue Reading

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

Scaffold
AnalysisSoftwareList
PIA ( Protein Inference Algorithms )
PeptideShaker
AdditionalSearchParams
jPOST
mzid Library
ProteinPilot
mzML
ProteomeDiscoverer

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