mzIdentML 1.3.0 - Essential progress on the support of crosslinking and
other identifications based on multiple spectra
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.