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mzIdentML 1.3.0 - Essential progress on the support of crosslinking and other identifications based on multiple spectra
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  • Colin William Combe,
  • Lars Kolbowski,
  • Lutz Fischer,
  • Ville Koskinen,
  • Joshua Klein,
  • Alexander Leitner,
  • Andy Jones,
  • Juan Antonio Vizcaino,
  • Juri Rappsilber
Colin William Combe
University of Edinburgh
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Lars Kolbowski
Technische Universit├Ąt Berlin
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Lutz Fischer
Technische Universit├Ąt Berlin
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Ville Koskinen
Matrix Science Ltd
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Joshua Klein
Boston University
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Alexander Leitner
ETH Zurich
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Andy Jones
University of Liverpool
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Juan Antonio Vizcaino
EMBL-EBI
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Juri Rappsilber
University of Edinburgh

Corresponding Author:[email protected]

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Abstract

The mzIdentML file format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0, which introduces new functionality and support for additional use cases. First of all, a new mechanism for encoding identifications based on multiple spectra. Furthermore, the main mzIdentML specification document can now be supplemented by extension documents which provide further guidance for encoding specific use cases for different proteomics subfields. One extension document has been added, covering additional use cases for the encoding of crosslinked peptide identifications. The ability to add extension documents facilitates keeping the mzIdentML standard up to date with advances in the proteomics field, without having to change the main specification document. The crosslinking extension document provides further explanation of the crosslinking use cases already supported in mzIdentML version 1.2.0, and provides support for encoding additional scenarios that are critical to reflect developments in the crosslinking field and facilitate its integration in structural biology. These are: (i) support for cleavable crosslinkers, (ii) support for internally linked peptides, (iii) support for noncovalently associated peptides, and (iv) improved support for encoding scores and the corresponding thresholds.
04 Oct 2023Submitted to PROTEOMICS
09 Oct 2023Assigned to Editor
09 Oct 2023Submission Checks Completed
09 Oct 2023Review(s) Completed, Editorial Evaluation Pending
09 Oct 2023Reviewer(s) Assigned