  Mass spectrometry has experienced a rapid development since its first
application for protein analysis in the 1980s. While the most common use of
mass spectrometry for protein analysis is identification and quantification
workflows on peptides (digested from their parent protein), there is also a
rapidly growing use of mass spectrometry for structural proteomics. One example
is the analysis of cross-linked proteins that can give valuable structural
information, complementing the information gained by classical protein
structure determination methods, useful for integrated methods of structure
determination and modeling. For a broad and reproducible application of
cross-linking mass spectrometry a standardized representation of cross-linking
experimental results is necessary. This paper describes the developing and
release of the xlmod ontology from the HUPO-PSI. xlmod contains terms for the
description of reagents used in cross-linking experiments and of cross-linker
related chemical modifications together with their main properties relevant for
planning and performing cross-linking experiments. We also describe how xlmod
is used within the new release of HUPO-PSI-s mzIdentML data standard, for
reporting the used cross-linking reagents and results in a consistent manner.
In addition xlmod contains terms for GC-MS and LC-MS derivatization reagents
for specifying them in the upcoming mzTab-M and mzTab-L formats.
